Biological Sciencess

Most Important Components of Protein Synthesis ! Biological Sciencess !!

2018-10-26T09:11:00.000+05:30

PROTEIN SYNTHESIS

I. Overview of Translation

A. Translation is the process by which a polypeptide chain is synthesized by ribosomes using the sequence of codons in an mRNA to direct the sequence of amino acids.

B. Translation is the ultimate step in gene expression.

C. The energy cost for protein synthesis is very high.
1. Only a small fraction of the energy input of translation is needed to form the peptide bond.
2. The majority of energy is invested to assure that the sequence of the polypeptide
is correct.
3. If incorrect polypeptides (e.g. enzymes) are made by the cell, it could have
devastating effects on cell function.

D. The mRNA is always read from 5' to 3'.

E. The polypeptide is always synthesized in the direction of amino-terminus to carboxyl-terminus.

II. Components of Translation

A. mRNA

The mRNA serves at the template that will determine the sequence of amino acids in the new polypeptide.

1. Structure of mRNA
(a) 5' untranslated region (5' UTR).
(i) This is the sequence of the mRNA extending from the 5' end of the mRNA
to the initiation codon.
(ii) It is not translated into polypeptide sequence.
(iii) It has a function analogous to the function of a promoter on a gene. It will
direct the binding of the ribosome to the initiation codon.

(b) Initiation codon
(i) This is the triplet codon at which polypeptide synthesis begins.
(ii) It is always AUG and codes for a methionine.
(iii) As a result, all polypeptides are synthsized with an amino-terminal
methionine.

(c) Coding region
(i) This is the sequence of mRNA that contains the consecutive triplet codons
that direct polypeptide synthesis.
(ii) This region spans from the start codon to the stop codon.
(iii) The coding region is often referred to as the open reading frame or ORF.

(d) Stop codon
(i) This is the triplet codon that signals the termination of translation.
(ii) There are three possible stop codon sequences: UAA, UAG, UGA.
(iii) Stop codons have no corresponding tRNA or amino acid.

(e) 3' untranslated region (3' UTR)
(i) This is the nucleotide sequence downstream from the stop codon.
(ii) It extends from the stop codon to the 3' end of the mRNA
(iii) It does not code for amino acid sequence.
(iv) It may function in stabilizing the mRNA.

B. tRNA

1. The function of tRNA is deliver the correct amino acid to the ribosome as directed by the codon on the mRNA for incorporation into the polypeptide.

2. The tRNA has two important functional features

(a) A tRNA is covalently bound to an amino acid at its 3' end.
(i) This form of tRNA is called an amino acyl tRNA.
(ii) Each tRNA will be bound to only one of the twenty possible amino acids.
However, there can be multiple tRNAs for each amino acid.

(b) The tRNA contains a triplet sequence of nucleotides that are complementary to the triplet codons of the mRNA. This sequence is called the anti-codon.

(i) The covalently bound amino acid and the anti-codon strictly correspond to
one another.
(ii) As a result, the pairing of codon of the mRNA and the anti-codon of the
amino acyl-tRNA during translation will deliver the correct amino acid to
the growing polypeptide chain.

3. Structure of tRNA

(a) Cloverleaf structure
(i) 73-93 bases in length
(ii) Many unusual bases (Psuedo Uracil, Thymine, Dihdroxy Uracil etc.)
(iii) The nucleotides form many intra-chain base pairs, resulting in a secondary structure that resembles a cloverleaf.

(b) Acceptor Stem
(i) This is a region of the tRNA that is the site of attachment for the appropriate
amino acid.
(ii) It is formed by seven regular Watson & Crick base pairs between the 5' and 3' ends of the tRNA.
(iii) The 3' terminal end of all tRNAs is always CCA-OH.
(a) It is not base paired and is the site of attachment of the amino acid.
(b) The amino acid is covalently bound through an ester linkage between the carboxyl group of the amino acid and the 3' hydroxyl group of the ribose of the tRNA.

(c) Anticodon Loop
(i) The anti-codon loop contains the three nucleotide sequence that is the reverse
complement of the codon of mRNA to which it corresponds.
(ii) It consists of a total of seven unpaired bases; three of which are the anti-
codon

Wobble Hypothesis

(a) Four common bases in mRNA can be arranged in 43 or 64 different combinations

(b) How does this relate to the 20 aa’s available for translation?
(i) Genetic code is redundant
(a) 3 codons used as stops UAA, UAG, UGA.
(b) 61 available as codons

(c) 1965, Francis Crick proposed the Wobble Hypothesis to account for this
inconsistency
(i) Codons in mRNA and anti-codons interact in an anti-parallel manner at the
ribosome so that positions 1 and 2 of the codon form normal Watson-Crick base pairs.
(ii) The third position allows non-standard base pairing or wobble.

(d) Consequences: Different anti-codons can pair with one codon.

Ribosome

1. Performs 3 essential functions

(a) Selection of mRNA initiation site.
(b) Ensures correct pairing of codons and anticodons.
(c) Catalyzes formation of peptide bonds.

2. Ribosomes are large protein-RNA complexes that are divided into a large and small subunit.

(a) Large subunit.
(i) In prokaryotes this subunit is called the 50S subunit.
(ii) In eukaryotes this subunit is called the 60S subunit.
(iii) It contains the active site for catalyzing polypeptide bond formation. This enzyme within the ribosome is called the peptidyl transferase.

(b) Small subunit
(i) In prokaryotes this subunit is called the 30S subunit.
(ii) In eukaryotes this subunit is called the 40S subunit.
(iii) It is primarily responsible for positioning the ribosome at the intitiation
codon and pairing codon and anti-codon during synthesis.

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TRANSPORT ACROSS Plasma MEMBRANES ! Biological Sciencess !!

2018-10-25T15:52:00.002+05:30

TRANSPORT ACROSS MEMBRANES

1. Movement of Small Molecules Across Membranes can involve simple diffusion or protein-mediated transport. Cell membranes are selectively permeable.

(a) Passive Diffusion. Lipophilic solutes cross the membrane freely by dissolving
in the lipid bilayer. This is passive diffusion. Examples: ethanol (alcohol,contains both polar and non-polar regions); also fatty acids, glycerol, steroids,etc. Also nonpolar gases like O=O (O2)

(b) Selective transport by protein carriers = “permeases”. Polar or ionic small solutes may be transported across membranes if specific protein carriers are in the membrane. Examples: sugars, amino acids, ions.

(c) Many substances cannot cross the membrane. Examples: large molecules
such as proteins, nucleic acids. Also small polar molecules or ions for which
there is no protein carrier.

2. Some protein transporters require energy; others do not. There are 2 possible situations:

(a) facilitated diffusion. Membrane has specific protein carrier, will bind to
molecule and bring it across cell membrane. No energy required. No preferential direction. If molecule is more concentrated outside than inside cell, net movement will be out of cell. Examples include-
• Glucose transporters- 5 different GLUT proteins and 2 types that cotransport
Na and glucose (these are used for secondary active transport)
• Water channels- 8 different types of aquaporins

(b) Active transport. Membrane has specific protein carrier, also a requirement
for energy (ATP or other form of energy). Will move solute against a concentration
gradient, so can concentrate material even if diffusion would favor opposite direction of flow.

Example: Na+- K+ ATPase in nerve cells. Pumps Na+ to outside, K+ in, maintains electrical potential against diffusion. When nerve cell “fires”,momentary gates open to let diffusion occur. Then pumps are turned back on to restore potential.

3. Active transport can involve ATP pumps, symport, or antiport

(a) ATP pumps.

• ATP-powered pumps (ATPases) couple the splitting, or hydrolysis, of ATP
with the movement of ions across a membrane against a concentration
gradient.
• ATP is hydrolyzed directly to ADP and inorganic phosphate, and the energy
released is used to move one or more ions across the cell membrane.
• As much as 25% of a cell’s ATP reserves may be spent in such ion transport.

• Examples include:
1. The Na+-K+ ATPase pumps Na+ out of the cell while it pumps K+ in Because the pump moves three Na+ to the outside for every two K+ that are moved to the inside, it creates an overall charge separation known as polarization. This electrical potential is required for nervous system activity, and supplies energy needed for other types of transport such as symport and antiport.

2. Ca++ ATPases are responsible for keeping intracellular Ca++ at low levels, a necessary precondition for muscle contraction.

(b) Symport

• To transport some substances against a concentration gradient, cells use energy already stored in ion gradients, such as proton (H+) or sodium (Na+) gradients, to power membrane proteins called transporters.
• When the transported molecule and the co-transported ion move in the same direction, the process is known as symport.

• Example: transport of amino acids across the intestinal lining in the human gut.

(c) Antiport

Cell uses movement of an ion across a membrane and down its concentration
gradient to power the transport of a second substance “uphill” against its gradient.
• In this process, the two substances move across the membrane in opposite
directions.
• Example: transport of Ca2+ ions out of cardiac muscle cells. Muscle cells are triggered to contract by a rise in intracellular Ca2+ concentration, so it
is imperative that Ca2+ be removed from the cytoplasm so that the muscle can relax before contracting again. This antiport system is so effective that it can maintain the cellular concentration of Ca2+ at levels 10,000 times lower than the external concentration.

4. Cells Regulate Permeability by Adding & Removing Membrane Transport Proteins

(a) Insulin is transported by transporter GLUT4. Insulin causes glucose transport
molecules to be inserted into muscle and adipose tissue cells. Glucose is then
taken up into those tissues, lowering the blood concentration.

(b) Antidiuretic Hormone (ADH) is transported via aquaporin. ADH causes aquaporin 2 proteins to be added to the kidney collecting duct membranes. The result is water conservation.

(c) Aldosterone is transported by Na Pump. Aldosterone causes cells in the distal
tubules and collecting duct of the kidney to make more Na pump molecules. The final result is that the body retains more Na and secretes more K into the urine.

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54 EXTRA CONCEPTS: Cell Reproduction or Cell Division ! Biological Sciencess !!

2018-10-25T10:55:00.000+05:30

EXTRA CONCEPTS: Cell Reproduction or Cell Division

1. Cell Division was first studied by Strasburger (1875) in plants, W. Flemming (1882) in animal cells and Prevost and Dumas (1824) in frog egg.

2. Any agent that stimulates cell division is called mitogen. Temperature, cytokinin,
auxin, gibberllin, insulin, steroids and mitogens.

3. The continuation of species from one generation to next is governed by two processes; syngamy (union of gametes) and division of cells (meiosis and mitosis).

4. A cell divides to have high surface area per unit of volume and high nucleocytoplasmic ratio. The smaller the size of cell, more the surface area and nucleo-cytoplasmic ratio it has.

5. Genetic continuity is due to duplication of DNA in cell division that occurs in S-phase.

6. Mitotic poisons are inhibitors of cell divisions. Azides and cyanides inhibit prophase; colchicines checks spindle formation; chalones inhibit cell division in vivo and in vitro both; ribonuclease blocks prophase; heat shocks prevent cell division and Mustard gas agglutinate all chromosomes.

7. Animal cytokinesis is centripetal and plant cytokinesis is centrifugal.

8. In fungi, spindle is formed inside nucleus (intranuclear division); nuclear membrane
remains intact; nucleus divides by furrow (karyochoriosis).

9. Endomitosis is duplication of chromosomes without division of nucleus.

10. Non-disjunction is failure of migration of chromatids at anaphase; discovered by
Bridges (1961).

11. Brachymeiosis: It is believed by some mycologists that in some ascomycetes,
fertilization takes place in single celled stage resulting in a diploid nucleus which
then undergoes free nuclear divisions followed by pairing (dikaryon formation). These dikaryons then fuse and thus become a tetraploid nucleus. This is ascus mother cell. If it has to form haploid ascospores it must now undergo two reductional & one
equational division. This is knows as brachymeiosis.

12. Acetocarmine is made by dissolving carmine dye (obtained from cochineal Coccus insect) in acetic acid. It gives purple red colour to chromosomes.

13. C-mitosis is colchicines induced mitosis. Colchicine is an alkaloid, obtained from
underground corms of autumn crocus – Colchicum autumnale. It was discovered by
Dustin (1934) and used by Blakeslee (1937) to induce polyploidy. Granosan is similar
to colchicines in action. Both inhibit spindle formation.

14. In Cyperus, one meiosis produces one pollen grain instead of four.

15. Cell doubles in size and then stops growing in G1 phase. G1 is longest, most variable phase in which maximum growth occurs. Circumstances which induce a cell to divide arise in G1 under the influence of some cytoplasmic clock. Decision for cell division also occurs here.

16. Size of nucleus increases in interphase; size of nucleolus increases in first four
substages of Prophase-I of meiosis.

17. Aristolochia (duck weed) has all types of tetrads.

18. Protein (histone) for DNA synthesis is formed in S-phase while tubulin protein requiredfor spindle is synthesized in G2.

19. All organelles (organoids) including centrioles are doubled in G2.

20. Amount of DNA doubles in S-phase.

21. Interphase is most active phase followed by prophase. This interphase takes 70-95%
of total time of cell cycle. M-phase takes very less time.

22. Amitosis is called direct or incipient cell division and is found in yeasts, protozoans,
monerans (prokaryotes), cartilage and degenerated/old tissues.

23. Mitosis forms 2 daughter cells that are morphologically and genetically similar. It
distributes chromosomes equally both quantitatively and qualitatively. Term mitosis was given by W. Flemming (1870). Meristems, cells of bone marrow, base of nails and skin are used to study mitosis.

24. Spindle is astral (amphiastral) and arises from centriole in animal cell and in plantbcell; it is anastral and arise from cytoplasmic proteins by gelation. It consists of microtubules made up of sulphur rich tubulin protein (95-97%), RNA (3-5%) and
ATPase. Spindle is seen with polarizing microscope only.

25. Prophase is of longest duration.

26. Metaphasic chromosomes are least coiled. The structure of chromosomes is best studied at metaphase while shape of chromosomes is best studied at
anaphase.

27. Anaphase is of shortest duration; centromere divides and disjunction occurs here. About 30 molecules of ATP are needed to move one chromosome from equator to
pole.

28. Telophase is reverse of prophase. Nuclear membrane reappears from ER and remnants of original nuclear membrane.

29. Meiosis was first discovered by Boveri (1892), studied by Strasburger (1883) and
Winiwarter (1990); term by Farmer and Moore (1905). It is double division in which nucleus divides twice but chromosomes only once. It is antithesis of fertilization
and havles the number of chromosomes. It maintains number of chromosomes
constant through successive generations.

30. Meiosis occurs in diploid reproductive cells (meiocytes) at the time of reproduction.

31. Anthers of unopened young flowers and testes of grasshopper are widely used to
study meiosis.

32. Zygotene is zipping or synapsis or pairing of homologous chromosomes.
33. Tetrad formation occurs at pachytene stage.

34. Diplotene is of longest duration and involves chiasmata formation very distinctly. Crossing over begins at pachytene but chiasmata becomes distinct at diplotene, hence we can say crossing over occurs at diplotene.

35. Transportation is exchange and rejoining of chromatids parts during crossing over.

36. In metaphase-I, migrating chromosomes are dyad, i.e., each chromosome has 2
chromatids.

37. Reduction in number of chromosomes occur in anaphase-I but haploidy (reduction) in terms of DNA occur during anaphase-II.

38. In Trillium, anaphase-I directly enters into metaphase-II.

39. Tetrad is a group of 4 haploid cells formed during meiosis. It can be tetrahedral,isobilateral, linear, decussate or T-shaped but tetrahedral tetrad is most common in plants.

40. Kinetochore is a proteinaceous region of the centromere in chromosome to which
spindle fibres attach.

41. Nucleoprotein complex present between synapsed chromosomes is called synaptinemal complex.

42. Karyokinesis is division of nucleus. It was first studied by Schleiden.

43. Chromatids move towards the pole at a speed of 1 µm per minute.

44. Chiasmata are the result of crossing over and first observed by Janseens (1909).

45. He La cells are human cancer cells of a patient Henrietta Lack; maintained in
tissue culture since 1953. They divide and double their number in every 24 hrs &
widely used in research.

46. During G2, a cell contains double the amount of DNA (4n) as compared to original diploid cell (2n).

47. Repair of damaged DNA also takes place in the interphase.

48. In plants, mitosis occur in meristematic tissues (shoot & root tips). Root tip is the
most preferred regions to observe mitosis.

49. Anaphase is a rapid phase lasting only 2-3 minutes. It starts abruptly. The
centromere splits into two; each chromatid is pulled slowly towards a spindle pole
(each chromatid with own centromere now becomes a separate single stranded (1
DNA) chromosome. The chromatids are moved (towards the pole they face) at a
speed of 1µm/minute. The separation of the chromatids starts at the centromeres
while the arms trail behind it. As a result, the chromosomes are pulled into V, J and
T shapes.

50. The telophase lasts for an hour or so.

51. Stimulation of mitosis: Kinetin (6-furturyl amino purine) increases the mitotic rate in meristems of Allium. At low concentration, it reduces the duration of interphase and increases the mitotic rate.

52. In human males, meiosis starts after puberty.

53. In human females, meiosis starts at the end of 3rd month of prenatal life. In the fifth month of prenatal life, the oocytes reach the diplotene stage and remain arrested at this stage for many (About 12) years, when ovulation occurs.

54. Number of meiosis required to form n number of seeds/grains = n + n/4 (for all cases except cyperus); in cyperus, it is = n + n.

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Gametogenesis And Oogenesis ! Process, Mechanism, Stages !! Biological Sciencess !!!

2018-10-24T13:05:00.000+05:30

GAMETOGENESIS

The process of formation off gametes in the gonads is called gametogenesis. Gametes are produced by way of meiotic division resulting in the reduction of number of chromosomes to one half. The production of sperms in the seminiferous tubules of testis is called spermatogenesis and production of ova in ovaries is called oogenesis.

1. Spermatogenesis

Spermatogenesis is the process of formation of haploid functional spermatozoa from diploid germinal cells of seminiferous tubules. Lining layer of seminiferous tubules possesses primary germ cells and indifferent cells that mature into nurse cells or Sertoli cells.

(i) Multiplication Phase

Diploid primary germ cells undergo repeated mitosis to form a number of diploid spermatogonia.

(ii) Spermatocytogenesis

Each spermatogonia divided mitotically to from two interconnected primary spermatocyte

(iii) Growth Phase

Primary spermatocytes grow in size.

(iv) Maturation Phase

Each diploid primary spermatocyte undergoes meiosis I to form two haploid secondary spermatocytes. All the secondary spermatocytes derived from a single spermatogonium remain attached to one another. Secondary spermatocytes- divides by meiosis II, each giving rise to two haploid spermatids. The spermatids become partially embedded in Sertoli cells for nourishment and support.

(v) Spermiogenesis

Spermiogenesis is differentiation of a spermatozoon from a spermatid. Golgi apparatus forms acrosome. Centriole divides into two. Distal centriole forms axial filament. Mitochondria collect around upper part of axial filament. Nucleus undergoes condensation. A spermatozoon now separates while the unused cytoplasm degenerates. Heads of spermatozoa remain embedded for some time in Sertoli cells but ultimately the spermatozoa are released into lumen of seminiferous tubule for onward passage.

Sperm

Human sperm is dart-like flagellate structure of 60 µm length. It has four parts—
(i) Head. Knob-like terminal part has two components, acrosome and nucleus. Acrosome contains sperm lysins. Nucleus is compact mass of DNA having some protamines. On the outside is present a double membrane head cap.

(ii) Neck. It is short narrow part between head and middle piece, which contains two
centrioles, unconnected proximal centriole and distal centriole attached to axial
filament (that passes into middle piece).

(iii) Middle Piece. It is cylindrical part. It has axial filament surrounded by 10-14 spiral turns of mitochondria and bearing towards the end a ring centriole or annulus.
Mitochondria provide energy for swimming but food is limited.

(iv) Tail. It is narrow vibratile long part, with two regions, main and end piece. Main
piece of tail is 0.5 mm in diameter near the beginning but gradually narrows behind.
It has an axial filament, small amount of cytoplasm and plasma membrane. In the
end piece, cytoplasm and membrane are absent.

2. Oogenesis

It is the process of formation, development and maturation of haploid ova from diploid germinal cells of ovary. Oogenesis occurs in three phases

(i) Multiplication Phase

Diploid primary germ cells from germinal epithelium of ovary multiply mitotically and form oogonia. The latter produce ovigerous cords or egg tubes of Pfluger in mammals.

(ii) Growth Phase

It is prolonged and slow. Oogonia form rounded masses or egg nests at the tips of egg tubes of Pfluger. An egg nest forms ovarian follicle. One central oogonium grows and functions as primary oocyte. The others form the covering follicular cells. The latter provide nourishment to primary oocyte. Some nourishment also comes from outside. Enlarged primary oocyte secretes mucoprotein membrane or zona pellucida outside its own plasma membrane or vitelline membrane. There is increase in reserve food, size of nucleus, number of mitochondria, functioning of Golgi apparatus and complexity of endoplasmic reticulum.

(iii) Maturation Phase

Meiosis occurs. Nucleus shifts towards animal pole and undergoes meiosis I. A daughter nucleus alongwith small quantity of cytoplasm is extruded as primary polar body or polocyte below zona pellucida. Simultaneously primary oocyte is changed into haploid secondary oocyte. Ovum is generally shed in secondary oocyte stage. Meiosis II is completed in fallopian tube at the time of fertilization. It then produces a small secondary polar body and a large ovum. The primary polar body may also divide.

Ovum

Human egg or ovum is noncleidoic and alecithal (nearly microlecithal), rounded female gamete having a diameter of about 100 mm. The ovum possesses three coverings – inner thickened plasma membrane or vitelline membrane, middle mucoprotein zona pellucida and outer cellular corona radiata with radially elongated scattered cells held in mucopolysaccharide (hyaluronic acid). In between plasma membrane ( = vitelline membrane) and zona pellucida is peri-vitelline space in which are present 1- 3 polar bodies towards animal pole. The opposite end is vegetal pole. Cytoplasm of ovum is called ooplasm. It has a large nucleus or germinal vesicle. Ectoplasm
possesses

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Asexual Reproduction ! Types, Definitions !! Biological Sciencess !!!

2018-10-23T14:26:00.000+05:30

REPRODUCTION

Reproduction is the formation of new similar young living organisms by the grown up individuals of a species or race. It is meant for perpetuation of the race /species because individuals are bound to die after a life span. Reproduction provides group immortality. Four processes are
basic to reproduction – DNA replication, cell division, formation of reproductive units and development of a new individual.

Animal reproduction is of two types, asexual and sexual.

Asexual Reproduction

It is a mode of reproduction or formation of new young individuals from a specialized or unspecialized part of single parent without the formation and fusion of gametes. Besides being uniparental and absence of gametes, asexual reproduction is characterized by divisions through mitosis only, genetic similarity between parent and young ones, rapidity and absence of haploid-diploid alteration. Asexual reproductive propagule is called blastos. It contains totipotent cells like archaeocytes (sponges), interstitial cells (cnidaria), parenchyma (platyhelminthes) and neoblasts (annelids), etc. An individual produced through asexual reproduction is ramet. Clone is group of all genetically similar individuals formed through asexual reproduction.

1. Fission

It is a type of asexual reproduction in which the body of an individual undergoes division to produce two or more equal sized daughters.

(i) Binary Fission.

The mature individual divides into two equal sized daughter individuals. Binary fission is irregular (can occur in any plane) in Amoeba, longitudinal in Euglena, oblique in dinoflagellates and transverse in Paramecium and Planaria. In unicellular forms, binary fission is accomplished through mitotic nuclear division followed by cytokinesis. In multicellular individuals like Planaria the posterior part is fixed firmly to substratum while anterior part extends forward and exerts a pull causing the middle part to break.

(ii) Multiple Fission

It is formation of a number of small daughters by division of a parent. In unicellular forms, the nucleus divides a few times followed by collection of cytoplasm around each daughter nucleus forming a number of daughter cells, e.g., Amoeba, Plasmodium, Monocystis.

(iii) Plasmotomy

Cleavage of plasmodium or multinucleate body into multinucleate parts, e.g., Opalina, Pelomyxa.

(iv) Strobilisation

A modification of multiple fission is strobilisation in multicellular animals (body segmentation for reproduction as forming zooids in coelenterates like Aurelia and proglottides in Tapeworm).

2. Cysts and Spores

They are minute propagules, which function as dissemules as well as perennating structures. Each cyst or spore gives rise to a new individual.

3. Budding

It is a mode of asexual reproduction in which new organisms develop as
outgrowth or buds from a parent.

(i) Exogenous/ External Budding.

The bud develops externally on the parent. In the young condition the two are internally connected to provide nourishment to the bud. Later on, the bud enlarges and becomes nutritionally independent. It then separates as a new individual, e.g., Yeast, Hydra. However, in some cases, the new individual remains joined to the parent to form colony, e.g., Scypha.

(ii) Endogenous/ Internal Budding.

Internal buds or gemmules/ statoblasts occur in sponges/bryozoans to help in dispersal as well as perennation.

4. Fragmentation

It is breaking of an individual into two or more parts due to external (e.g., Star fish) or internal forces (e.g., Tunicates). Each fragment grows into a new individual.

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Physiology Practice Questions Part 2 ! Net CSIR !! Biological Sciencess !!!

2018-10-23T13:45:00.004+05:30

Physiology Practice Questions Part 2

1. After fertilization, the _ develops into a seed and the _ develops into a fruit.

(a) ovule . . . ovary
(b) pollen grain . . . ovule
(c) ovary . . . ovule
(d) egg . . . ovule

2. Plants growing in harsh environments such as deserts, sand dunes, and arctic tundra often reproduce vegetatively. This is because

(a) there are few animals available to pollinate them.
(b) they are members of plant families that only reproduce asexually.
(c) fruits would freeze or dry out in these environments.
(d) vegetative reproduction is not as risky as making seeds.

3. In contrast to animals, plants exhibit __ and _.

(a) determinate growth . . . persistent morphogenesis
(b) indeterminate growth . . . are not capable of morphogenesis throughout their
lifespan
(c) indeterminate growth . . . persistent morphogenesis
(d) growth . . . morphogenesis

4. Which of the following seedlings will probably bend toward the light?

(a) tip covered with a cap made of black plastic
(b) tip separated from base by a gelatin block
(c) tip separated from base by aluminum foil
(d) tip cut off and place a block of agar over half of the cut portion; the side with the
agar block will bend towards the light

5. In shoots, branching is inhibited by _ from the tip of a growing shoot, but this effect is countered by _ from the roots.

(a) cytokinins . . . auxins
(b) gibberellins . . . ethylene
(c) auxins . . . cytokinins
(d) gibberellins . . . abscisic acid

6. As leaf lettuce matures, the basal edible leaves suddenly send up a tall flowering shoot. After the plant bolts like this, it no longer produces broad, tasty leaves. Suppose you wanted to prevent bolting so that you could harvest lettuce longer. You might look for some way to interfere with the effects of

(a) abscisic acid. (b) gibberellins.
(c) cytokinins. (d) ethylene.

7. Seeds of many desert plants will not germinate until a heavy rain washes away their

(a) phytochrome. (b) abscisic acid.
(c) gibberellins. (d) auxins.

8. The abscission layer

(a) causes a shoot to bend toward light.
(b) secretes cytokinin.
(c) is the location of the biological clock in a plant.
(d) is where a leaf separates from a stem.

9. When a plant structure such as a leaf is injured, it produces ______, which may cause the part to age and drop off.

(a) cytokinins (b) ethylene
(c) auxins (d) abscisic acid

10. Once a flower is pollinated, changes occur that make it less attractive to insects. Its petals, for example, shrivel and fall off. Pollination must

(a) increase the output of cytokinins in the flower.
(b) block the flow of auxins from the roots.(c) trigger the release of ethylene in the flower.
(d) increase the formation of phytochrome, which sets the biological clock.

11. In the autumn, the amount of increases and the amount of decreases in fruit and leaf stalks, causing a plant to drop fruit and leaves.

(a) ethylene . . . auxin
(b) gibberellin . . . abscisic acid
(c) cytokinin . . . abscisic acid
(d) auxin . . . ethylene

12. Plant hormones act by affecting the activities of

(a) genes. (b) genes and enzymes.
(c) enzymes. (d) genes, membranes, and enzymes.

13. _______ appear to be responsible for gravitropism.

(a) Statoliths (b) phytochromes
(c) Gibberellins (d) Cytokinins

14. A rapid loss of water in specialized cells in the sensitive plant Mimosa pudica causes

(a) the plant to bend toward light.
(b) stomatal opening so photosynthesis can begin.
(c) stress that results in the production of PR proteins.
(d) leaves to droop.

15. A biological cycle with a period of about 24 hours is called

(a) thigmotropism. (b) a circadian rhythm.
(c) photoperiod. (d) abscission.

16. An Rajasthani hunter was worried about being attacked by grizzly tigers, so he left the lights in his cabin on all the time. Plants near the cabin flowered a month early. Which of the following best explains this?

(a) They must have been long-night plants.
(b) The lights must have emitted far-red light.
(c) They must have been long-day plants.
(d) They must have been short-day plants.

17. Most plants flower when

(a) the soil reaches a certain temperature.
(b) the days are of right length.
(c) a certain number of days have passed since they last flowered.
(d) the nights are of right length.

18. A certain short-day plant flowers when days are less than 12 hours long. Which of the following would cause it to flower?

(a) a 9-hour night and 15-hour day with 1 minute of darkness after 7 hour.
(b) an 8-hr day and 16-hour night with a flash of white light after 8 hr.
(c) a 13-hour night and 11-hour day with 1 minute of darkness after 6 hr.
(d) a 12-hour day and 12-hour night with a flash of red light after 6 hr.

19. A chemical change in a substance called phytochrome

(a) causes a plant to bend toward light.
(b) triggers fruit drop.
(c) enables a plant to respond to the presence of light.
(d) is responsible for gravitropism.

20. Which of the following tissues produces voluntary body movements?

(a) smooth muscle (b) simple cuboidal epithelium
(c) cardiac muscle (d) skeletal muscle

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Physiology based Practice Questions Part 1 Net CSIR !! Biological Sciencess !!!

2018-10-23T13:26:00.001+05:30

Physiology based Practice Questions Part 1

1. Mineral nutrients

(a) are not essential to plant growth, since all a plant needs is water and CO2.
(b) contribute little to the weight of a plant.
(c) enter plants via the stomata.
(d) are organic nutrients.

2. Professor Arun claims to have discovered a new macronutrient required for plantgrowth. Most of Professor Arun’s colleagues are skeptical of this claim. Why might they consider it unlikely?

(a) All the nutrients required for plant growth have already been found.
(b) It is very difficult to prove that a plant needs a certain nutrient.
(c) Plants need thousands of nutrients; a new one is not significant.
(d) Any nutrient needed in large amounts has probably been found already.

3. Soil could be deficient in any of the following nutrients. If you had to supply one of them, which would be needed in the smallest amount?

(a) iron (b) phosphorus
(c) nitrogen (d) potassium

4. Which of the following is a symptom of magnesium deficiency?

(a) yellowing of younger leaves’ prior to yellowing of older leaves.
(b) enhanced plant growth, since magnesium is toxic to plants.
(c) chlorosis
(d) decreased transpiration

5. Topsoil

(a) is the relatively inert upper layer of soil.
(b) does not retain water.
(c) is a mixture of rock fragments, living organisms, and humus.
(d) is uniform in texture.

6. The roots of many aquatic plants have special structures that project above the surface of the water. For example, cypress trees (which grow in swamps) have knees that extend upward above water level. Which of the following is the most logical function of these structures?

(a) obtaining carbon dioxide for photosynthesis
(b) nitrogen fixation
(c) obtaining oxygen for the roots
(d) transpiration

7. The clay particles in soil are important because they

(a) are composed of nitrogen needed by plants.
(b) eliminate spaces for air and facilitate drainage.(c) fill spaces and keep oxygen out of the soil.
(d) are charged and hold ions needed by plants.

8. Soil can easily become deficient in _____, because these ions are negatively charged and do not stick to negatively charged clay particles.

(a) potassium. (b) calcium.
(c) magnesium. (d) nitrate.

9. Fertilizers are usually enriched in

(a) iron, manganese, and zinc.
(b) calcium, boron, and carbon.
(c) nitrogen, phosphorus, and potassium.
(d) molybdenum, copper, and magnesium.

10. Nitrogen-fixing bacteria in the soil

(a) convert nitrates to N2.
(b) convert ammonia into ammonium.
(c) convert atmospheric nitrogen into ammonia.
(d) use nitrates to make amino acids that plants can use.

11. Nitrogen fixation is

(a) using nitrogen to build molecules such as proteins and nucleic acids.
(b) converting nitrogen in the air into a form usable by plants.
(c) recycling nitrogen from organic matter in the soil.
(d) absorbing N2 from the soil.

12. The enzyme that catalyzes the conversion of atmospheric nitrogen into ammonia is

(a) catalase. (b) nitrogenase.
(c) reductase. (d) rubisco.

13. The relationship between legumes and Rhizobium is

(a) mutualistic. (b) parasitic.
(c) competitive. (d) commensalism

14. Mycorrhizae are

(a) nutrients required by plants in relatively small amounts.
(b) plants such as mistletoe that parasitize other plants.
(c) cells that control evaporation of water from leaves.
(d) associations of roots with beneficial fungi.

15. The term alternation of generations refers to a plant’s life cycle alternating between

(a) the production of haploid gametes by meiosis with the production of diploid spores by mitosis.
(b) a haploid gametophyte generation and a haploid sporophyte generation.
(c) a haploid gametophyte generation and a diploid sporophyte generation.
(d) a flower producing generation and a leaf-producing generation.

16. Self-incompatibility

(a) works the same way in all plants.
(b) are all based on the same mechanism of transplant rejection seen in animals.
(c) maintains variation.
(d) is the rejection of a graft by a plant.

17. In angiosperms, each pollen grain produces two sperm. What do these sperm do?

(a) Each one fertilizes a separate egg cell.
(b) One fertilizes an egg and the other fertilizes the fruit.
(c) One fertilizes an egg and the other is kept in reserve.
(d) One fertilizes an egg and the other fertilizes a cell that develops into stored food.

18. What is endosperm?

(a) male reproductive cells in plants
(b) stored food in a seed
(c) cells that make up the bulk of a pollen grain
(d) the fleshy part of a fruit such as an apple or strawberry

19. The correct arrangement of the meristematic tissue of an embryo is

(a) a ring of lateral meristem surrounding apical meristem.
(b) a ring of procambium surrounding a ring of meristem surrounding a ring of
protoderm.
(c) a ring of hypocotyl surrounding a ring of radicle surrounding a ring of epicotyl.
(d) a ring of protoderm surrounding a ring of ground meristem surrounding
procambium.

20. The scutellum

(a) is a specialized cotyledon found in certain monocots.
(b) develops into the seed coat.
(c) presents a barrier to self-fertilization.
(d) is a specialized cotyledon found in dicots.

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What is Protein Structure And Functions ! Biological Sciencess !!

2018-10-23T10:52:00.000+05:30

PROTEIN STRUCTURE

I. Peptide bond – amide bond between alpha-amino and alpha-carboxyl groups of 2 amino acids

A. Chemical properties

1. Peptide bond is polar and planar
(a) electron resonance structure
(b) has partial (40%) double bond character
(c) amide group is planar, usually trans
2. Synthesis
(a) condensation produces water
(b) energy required (ATP hydrolysis)
3. Peptide bond is hydrolyzable
(a) acid hydrolysis generates free amino acids
(i) 6N Hydrochloric acid heated at 110°C for 24 hr in a vacuum
(b) base hydrolysis generates free amino acids
(i) 4N Sodium hydroxide heated at 100°C for 4 hr
(c) cyanogen bromide cleaves at the COOH-terminal side of Met
(d) enzymatic hydrolysis of peptide bonds by proteases
(i) peptidases are specific for certain amino acids
4. Polypeptides are polyampholytes
(a) ampholyte has both acidic and basic pKa values

(b) isoelectric point

pH at which the net charge is zero
For example: H3N+–Ala–Lys–Ala–Ala–COO–
pKa of the Alpha-carboxyl group = 3.6 pKa of the Alpha-amino group = 8.0 pKa of the delta-amino of the Lysine = 10.6 at pH = 1 the net charge is +2 at pH = 6 the net charge is +1 at pH = 14 the net charge is –1
the isoelectric point pI = (pKa2 + pKa3)/2 = (8 +10.6)/2 = 9.3

B. Nomenclature

1. Size
(a) dipeptide (2 aminoacids & 1 peptide bond), tripeptide (3 aminoacids & 2 peptide
bonds)
(b) oligopeptide – several amino acids (up to 20)
(c) polypeptides (more than 20 amino acids). All proteins are polypeptides

II. Physical Forces Governing Protein Conformation

A. Physical forces govern 3-D structure of proteins (Pauling and Corey)

1. bond lengths and angles should be distorted as little as possible
2. structures must follow Van der Waal’s rules for atomic radii
3. peptide bond is planar and trans
4. noncovalent bonding stabilizes structure
5. conformation can change without breaking bonds (flexibility)

B. Types of non-covalent forces important to protein conformation

1. Hydrophobic forces
(a) hydrophobic residues orient to inside
(b) hydrophilic residues orient out
2. Van der Waal’s potential:
includes electron shell repulsion, dispersion forces, and electrostatic interactions
3. Salt bridges, electrostatic forces
4. Hydrogen bonds

C. Angles of rotation of the polypeptide chain determine structure

1. angles of rotation around alpha-carbon are [y (psi) and j (phi)]
(a) y (psi) is the angle of the alpha-carbon bond to the carbonyl-carbon
(b) j (phi) is the angle of the alpha-carbon bond to the amide-nitrogen
2. primary sequence and angles of rotation for each alpha-carbon completely define
protein conformation
3. only a small number of psi and phi angles are allowed
4. statistical analysis of all proteins yields groups of prefered angles
(a) areas of repeating (psi) and (phi) angles are secondary structures

III. Levels of Protein Structure

A. Primary Structure – amino acid sequence of a polypeptide

1. primary structure determines 3-dimensional structure (Anfinsen)
2. always represented N H 2-terminus to COOH-terminus

B. Secondary structure – regular local conformation of linear segments of the polypeptide chain

1. Secondary structure are stabilized by hydrogen bonds between amide and carbonyl
groups
2. Several types of secondary structure

(a) alpha-helix

1. right handed helix
2. 3.6 amino acids per turn, rise per helix 5.4 Å, rise per aminoacid 1.5 Å
3. carbonyl oxygen hydrogen bonded to 4th amide hydrogen (nÆn+4)
4. amino acid R-groups orient out
5. proline breaks the helix

(b) beta-pleated sheet

(i) polypeptide chains side by side
(ii) polypeptide chains can be parallel or antiparallel
(iii) carbonyl oxygen hydrogen bonded to amide hydrogen
(iv) beta-strand is a single pass of the polypeptide

(c) reverse turn, beta-bend

(i) allows a sharp turn in polypeptide chain
(ii) carbonyl oxygen hydrogen bonded to 3rd amide hydrogen (nÆn+3)
(iii) Glycine is required

3. Fibrous proteins demonstrate secondary structure
(a) Fibroin
(i) silk is fibroin
(ii) antiparallel-beta-pleated sheet
(b) alpha-Keratin and tropomyosin
(i) alpha-keratins in wool and hair and epidermal layer
(ii) tropomyosin is a thin filament in muscle
(iii) alpha-helix allows elasticity
(iv) alpha-keratin converts to beta-pleated sheet with heat or stretching- disulfides are important to maintenance of keratin secondary structure- alpha-keratins are beta-pleated sheets; feathers and claws

(c) Collagen
(i) structural protein; skin, bones
(ii) triple helix (not alpha-helix)
(iii) sequence (Gly-Xaa-Pro) ‘ x or (Gly-Xaa-HyPro) x
(iv) glycine required for triple helix to form, contains many modified amino acids
(v) hydroxyproline stabilizes the structure, vitamin C required for hydroxylation;
scurvy

C. Tertiary structure – overall folded conformation of the polypeptide

1. Physical forces affect tertiary structure
(a) Hydrophobic forces - hydrophobic residues orient to inside & hydrophilic orient out
(b) salt bridges, electrostatic forces
(c) Van der Waals radii
(d) Hydrogen bonds
(e) Disulfide bridges

D. Quaternary structure – subunit structure

1. aggregation of 2 or more subunits
(a) hetero- or homo- polymers
2. same forces drive tertiary and quaternary structure
E. Structural elements
1. Sequence motif – small functional linear polypeptide sequence (may not be 3-D)
(a) signal peptide
(b) ER-retention signal
(c) mitochondrial and nuclear targeting signals
(d) RGD cell adhesion motif
2. Supersecondary structure (structural motif)
(a) smallest conformational unit (may be functional)
(b) exam p les àà (helix-loop-helix), hairpin, beta-barrels
- Rossman fold, a nucleotide binding site
- leucine zipper mediates transcription factor dimerization
- zinc finger is a DNA binding motif
3. Domain
(a) the part of a polypeptide chain that can independently fold into a tertiary structure
(b) often domains have units of function
(c) proteins may contain one or many domains

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Amino Acids ! Types, Definitions, Properties !! Biological Sciencess !!!

2018-10-23T09:53:00.000+05:30

AMINO ACIDS

I. Function of amino acids

A. Building blocks of polypeptides

1. polymerized to form polypeptides
(a) linked by a peptide bond
(b) synthesized during translation of messenger RNA
2. primary structure of a protein is the sequence of amino acids
3. both peptides and polypeptides can be functional
Structure –OOC–CH2–CH2–NH3+ GABA
Structure +H3N–CH2–CH2–SO3–TAURINE

B. Amino acids may be functional

1. neurotransmitters- glutamate and aspartate (excitory)
- glycine, taurine, and aminobutyric acid (GABA) (inhibitory)

C. Precursors to other molecules

1. metabolic intermediates citrulline and ornithine in urea cycle can be metabolized to form glucose or acetyl CoA
2. neurotransmitters – serotonin, dopamine, epinephrine, etc.
3. tyrosine (thyroid hormone)
4. porphyrins
5. creatine (energy storage)
6.histamine (mediator of immune response)
7. nucleotide synthesis – S-adenosylmethionine

II. Structure of amino acids

A. 20 standard alpha-amino acids

1. Structure.
- alpha-carbon
- alpha-amino group
- alpha-carboxyl group
- side chain (R group)
2. “Standard” amino acids are encoded by messenger RNA
3. Amino acids are abbreviated by a 3-letter and 1-letter code

B. Some amino acids are not incorporated into proteins during translation

1. Modified amino acids

(a) Hydroxyproline and hydroxylysine
(i) hydroxylated enzymatically after translation
(ii) important in collagen structure (Structures of phosphoserine, 4-OH-
proline, 5-OH-lysine)
(b) phosphoamino acids
(i) Tyr, Ser, Thr hydroxyl groups can be phosphorylated
(ii) important in activation and inhibition of enzymatic or signalling activity

2. Other important amino acids
(a) Urea cycle intermediates – ornithine, citrulline, arginosuccinate
(b) Thyroid hormone (tyrosine Æ thyroxine)

III. Chemical Properties of Amino Acids

A. Physical characteristics

1. Charge
(a) Amino acids are dipolar ions (zwitterions) at neutral pH
(i) zwitterion is a dipolar molecule with pos. and neg. charges spatially separated
(ii) definition of zwitterion in book is incorrect
(b) Ionic states of amino acids depend on pH
(i) amino acids have two or three dissociable protons
(ii) pKa of the dissociable proton and the pH determine its degree of dissociation
H–H equation: pH = pKa + log{[A–]/[HA]}

2. Titration curve of an amino acid
(a) calculated using the H-H equation
(b) Isoelectric point (pI) – pH at which the molecule has a net charge = 0 (average of
the two appropriate pKa values)

3. Polarity
(a) nine nonpolar amino acids
(i) tend to orient to the inside of proteins
(ii) Gly, Ala, Val, Leu, Ile, Met, Pro, Phe, Trp
(b) eleven polar amino acids
(i) tend to orient to the outside of proteins
(ii) Ser, Thr, Tyr, Asp, Glu, Asn, Gln, Cys, Arg, Lys, His

4. Hydropathicity – index of solubility characteristics in H2O
(a) combines hydrophobic and hydrophilic tendencies
(b) can be used to predict protein structure
Hydrophobic Ile>Val>Leu>Phe>Met (listed from most hydrophobic)
Less Hydrophobic Ala>Gly>Cys>Trp>Tyr>Pro>Thr>Ser
Hydrophilic His>Glu>Asn>Gln>Asp>Lys>Arg (arg is most hydrophilic)
5. UV absorbance
(a) aromatic a.a.s (Trp, Tyr, Phe) absorb UV light
(b) absorbs UV light between 260-280 nm

B. Stereochemistry

1. Most amino acids have optical activity
(a) chiral centers are asymmetric centers (usually carbons)
(b) a-carbon of amino acids is chiral
(c) chirality yields stereospecificity
(d) Gly is not chiral (has no a-carbon)
2. L and D enantiomers (stereoisomers)
(a) enantiomers are nonsuperimposable mirror images of the same molecule
(i) L is levorotatory, D is dextrarotatory
(b) L and D nomenclature from L and D-glyceraldehyde (Fisher convention)
(i) not equivalent to R and S
(ii) most natural a.a.s are L
(iii) some a.a.s are R, some are S
(c) L and D forms are chemically and physically distinguishable
(i) different activity, melting points, and spectra

C. Cysteine can form disulfide bonds

1. cysteine is the reduced form (sulfhydryl)
2. cystine is the oxidized form (disulfide)
3. disulfide bridges formed between cysteines are important in protein structure

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Mechanism Of FERTILIZATION IN HUMANS ! Biological Sciencess !!

2018-10-22T11:05:00.002+05:30

FERTILIZATION IN HUMANS

Only a single ovum is released in human females from one of the two ovaries towards the middle of ovarian/menstrual cycle. It passes into fallopian tube and rests inside ampulla for some time. Human male produces 300 - 400 million sperms per ejaculation. They are deposited in vagina during coitus. The process of deposition of sperms in the female genital tract is called
insemination. A number of them are demobilised or eaten.

Fertilization involves the following steps

(i) Approximation of Sperm and Ovum.

Sperms can remain motile for 24-48 hours.
They swim at the rate of 1. 5 - 3.0 mm/min. They are able to reach the ampulla part
of female genital tract partly by their own swimming and partly by contraction of
uterus and fallopian tubes. One sperm comes to lie against the ovum and undergo
fertilizin (from ovum) and antifertilizin (from sperm) compatibility reaction (Lillie,
1919) in the region of animal pole.
(ii) Acrosome Reaction. It prepares the sperm to fertilize ovum. The phenomenon is called capacitation. In contact with corona radiata, the acrosome covering lyses to release acrosome. With the help of sperm lysins (chiefly hyaluronidase), acrosome
dissolves corona radiata and zona pellucida in front of it.

(iii) Egg Reaction.

A small protuberance or fertilization cone (cone of reception), develops from the surface of ovum in the region of animal pole.

(iv) Penetration of Sperm.

Sperm head establishes contact with lateral surface of fertilization cone. Plasma membranes of the two dissolve. Contents of head (nucleus), neck and middle piece of sperm enter ooplasm. Tail is left outside. Fertilization cone subsides. Depolarisation of egg membrane kills other sperms. Plasma membrane of the egg is now modilled with the help of mucopolysaccharide cortical granules into
fertilization membrane. A perivitelline space is created between it and zona pellucida.

(v) Activation of Ovum.

Ovum (previously in secondary oocyte stage) undergoes meiosis II and extrudes a secondary polar body. It is now the actual ovum or female gamete.

(vi) Fusion of Sperm and Egg Nuclei.

The envelopes of the sperm and egg nuclei
degenerate and their chromosomes intermingle to form ‘synkaryon’. The act is called karyogamy or syngamy. The proximal centriole brought by sperm help~ form the spindle for the division of synkaryon (cleavage nucleus). Fertilized egg is also called zygote

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Exocytosis & Endocytosis ! Types, Definitions, Mechanism !! Biological Sciencess !!!

2018-10-22T10:49:00.002+05:30

Movement of Large Molecules: Exocytosis & Endocytosis

(a) Large molecules (proteins, nucleic acids, polypeptides larger than a few amino acids, polysaccharides larger than a few sugars) are not carried by transport proteins.

(b) There are mechanisms for moving larger molecules, but they don’t enter into
cytoplasm.

(i) Exocytosis

Membrane vesicle fuses with cell membrane, releases enclosed material to extracellular space. Ex: release of digestive enzymes from pancreatic cells; mucus, milk, hormones, etc.

(ii) Endocytosis

Cell membrane invaginates, pinches in, creates vesicle enclosing contents.

Three common situations

1. Phagocytosis

Typically works on debris, bacteria, other particulate matter. Contents of the “phagosome” are usually fused with lysosome to create “phagolysosome”, where material is broken down. Especially common in white blood cells such as macrophages and other leukocytes.

2. Pinocytosis

Similar to phagocytosis, but ingests fluid rather than particulate matter. “Cell drinking”. Ex. cells lining blood capillaries
take fluid from blood (but not red cells), move fluid across their cytoplasm, release into extracellular space surrounding cells outside the capillary.

3. Carrier-mediated endocytosis (CME)/ receptor-mediated endocytosis:

Very specialized system. Certain important molecules or ions are not brought into cell by transport processes, but by CME. The body uses hormones to regulate membrane transport in this way Eg. 1. iron is carried through blood tightly bound to transferrin protein carrier. To get iron into cells, cell membrane contains special receptor
proteins that bind transferrin, move towards special regions of membrane under which lie clathrin proteins.

Endocytosis occurs inside clathrin “cage”, moves inside cell. Cage eventually recycles back to cell surface, returning transferrin proteins to cell exterior. However, iron is released inside cell, exits from vesicles, becomes bound to ferritin.

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How Plants Response to Stress ! Biological Sciencess !!

2018-10-22T10:31:00.000+05:30

RESPONSE TO STRESS

Stress

Stress can be defined as any environmental factor that can have an adverse effect on a
Plant’s growth, reproduction, and survival. Plants can respond to stress in several ways they can escape the effects of stress by completing their growth during less stressful periods or they may suffer injury if the stress is present and they cannot cope. Plants can cope with environmental stress through a combination of development and physiological responses.

Response to water stress

On bright, warm, dry day, a plant may be stressed by a water deficiency because it is losing water by transpiration faster than the water can be restored by uptake from the soil. This continuous drought can stress plants for weeks or month. Severe water defict, may kill a plant.

But plants have control systems that enable them to cope with less extreme water deficts. Many of a plants responses to water defict help the plant conserve water by reducing the rate of transpiration. Water defict can stimulates increased synthesis and release of abscisic acid from mesophyll cells in the leaf, and this hormone helps keep stomata closed by acting on guard cell membranes and causes guard cell to loose turgor.

Leaves respond to water defict in
several other ways, because cell expansion is a turgor- dependent process, a water defict will inhibit the growth (expansion) of yong leaves. This response minimizes the transcriptional loss of water by slowing the increase in leaf surface.

When the leaves of many grasses and other
plants wilt from a water defict, they roll into a shape that reduces transcription by exposing less leaf surface to the sun. While all of these responses of leaves help the plant conserve water, they also reduces photosynthesis. This is one reason a drought diminished crop yield

Response To Oxygen Stress

An overwatered house plant may suffocate because the soil lacks the air spaces that provide oxygen for cellular respiration in the roots. Some plants are structurally adapted to very wet habitats. For example, the submerged roots of trees called mangroves, which inhabit coastal marshes, are continuous with aerial roots that provide access to oxygen. Experimentally it was shown that oxygen deprivation stimulates the production of hormone ethylene, which causes some of the cells in the roots cortex to age and die.

Enzymatic destruction of the cell walls
creates air tubes that function as ‘snorkes’ providing oxygen to the submerged roots.
Response To Salt Stress An excess of sodium chloride or other salts in the soil threatens plants for two reasons.

First, by lowering the water potential of the soil solution, salt can cause a water defict in plants even though the soil has plenty of water. This is because in an environment with a water potential more negative than that of the root tissue, roots will lose water rather than absorb it. The second problem with saline soil is that sodium and certain other ions are toxic to plants when their concentration is relatively high.

The selectively permeable membranes of root cells impede the uptake of most harmful ions, but this only aggravates the problem of acquiring water from soil that is rich in solutes. Many plants can respond to moderate soil salanity by producing
compatible solutes, organic compounds that keeps the water potential of cells more negative than that of the soil solution without admitting toxic quantities of salt.

However, most plants cannot survive salt stress for very long. The exception are halophytes, salt tolerant plants with
special adaptations such as salt glands, which pump salts out of the plant across the leaf epidermis.

Response to Heat Stress

Exccesive heat can harm and eventually kill a plant by denaturing its enzymes and damaging its metabolism in other ways. One function of transpiration is evaporative cooling. On a warm day, for example, the temperature of a leaf is below air temperature which favours transpiration
and causes water deficiency in many plants; the closing of stomata in response to this stress conserves water but sacrifices evaporative cooling. This dilemma is one of the reasons that very hot, dry days take such a toll on most plants. Many plants response to this stress by synthesizing relatively large quantities of special proteins called heat shock proteins. Some
heat shock proteins are identical to chaperon proteins, which function in unstressed cells as temporary scaffolds that other proteins fold into their functional conformations.

Response to Cold Stress

One problem plants face when the temperature of the environment falls is a change in the fluidity of cell membranes. When a membrane cools below a critical point, it loses its fluidity as the lipids become locked into crystalline structures. This alters solute transport across the
membrane and also adversely affects the functions of membrane proteins. Plants respond to cold stress by altering the lipid composition of their membranes.

For example, membrane lipids increase in their proportion of unsaturated fatty acids, which have shapes that help keep
membranes fluid at lower temperature by impeding crystal formation. Freezing is a more severe version of cold stress. At freezing temperatures, ice crystals begin to form in most plants. If ice crystals are confined to cell walls and Intercellular spaces, the plant will probably survive.

However, if ice crystals begin to form within protoplasts, the sharp crystal perforate membranes and organelles, killing the cells. However, plants like oaks, maple, rhododendrons native to regions where winters are cold have special adaptations that enable to cope with
freezing stress. For example, changes in the solute composition of live cells allow the cytosol to cool below 0 degree Celsius without crystal formation Although ice crystals may form in the cell walls.

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Lipids ! Definition, Types !! Biological Sciencess !!!

2018-10-22T09:41:00.001+05:30

Lipids

Lipids are esters of fatty acids and polyhydric alcohol. The term ‘lipid’ was first used by Bloor (1943). These are the compounds of C, H, O but the ratio of H and O is more than 2:1 (i.e., the ratio of oxygen is lesses as compared to carbohydrates). These are water-insoluble organic substances which can be extracted from the cells by organic solvents such as ether, chloroform and benzene. Their general form ula is C nH2nO2. Some lipids
have P, N and S also.

1. Simple lipids

Esters of fatty acids with alcohol. Simplest alcohol in fats is glycerol( a trihydric alcohol) e.g., fats, oils and waxes. Triglycerides are common in nature.

2. Compound lipids

These lipids contain an additional group alongwith fatty acids and alcohols, e.g., phospholipids, glycolipids and lipoprotein.

3. Derived lipids

These are isoprenoid structures e.g., steroids, terpenes, carotenoids.
• Fatty acids are carboxylic acid with a chain of more than four carbon atoms ending with COOH group. Plants can synthesize all fatty acids. Animals can not synthesize linoleic, linolenic and arachidonic acid. These are called essential fatty acids. Their deficiency causes sterility, kidney failure and stunted growth.

• Saturated fatty acids have no double bond. Their melting point is high. Palmitic acid,
stearic acid are saturated fatty acids.

• Unsaturated fatty acids are commonly present in vegetable oils, cod/shark oil. Their melting points are low. Oleic acid has one double bond, linoleic acid has two, linolenic acid has three and arachiodonic acid has 4 double bonds. Fatty acids with more than one double bond are called polyunsaturated fatty acid (PUFA).

• Drying oils are unsaturated fatty acids which can be converted in hard fats on
being exposed.

• Edible oils can be converted into hard fats through hydrogenation.

• Waxes are esters of long chain monohydric alcohols like cetyl, ceryl or mericyl.

• Lanolin forms a protective, water insoluble coating on animal fur.

• Bees wax secreted from abdominal glands of honey bees has palmitic acid
and mericyl alcohol.

• Paraffin wax is a petroleum product.

• Cutin is formed by cross esterification and polymerization of hydroxyl fatty
acids and other fatty acids without esterification by alcohols other than glycerol. Cuticle has 50-90% cutin.

• Suberin is condensation product of glycerol and phellonic acid. It makes the
cell wall impermeable to water.

• Phospholipids are triglycerides in which one fatty acid is replaced by phosphoric
acid which is often linked to additional nitrogenous groups like choline (in lecithin), ethanolamine (in cepalin), serine or inositol. These are amphipathic i.e. have
both polar and non polar groups. These form cell membranes along with proteins.

• Sphingolipids have amino alcohol sphingosine. Sphingomyelins are present in
myelin sheath of nerves. They have additional phosphate attached to choline, are present in nerve membrane. Cerebrosides are present in nerve membrane and have galactose.

• Gangliosides – have glucose, galactose, sialic acid and acetyl glucosamine, present in grey matter, receptors of viral particles, excess causes Tay-Sachs disease.

• Sterols or steroids contain 4 fused hydrocarbon rings called cyclopentane perhydrophenanthrene and a long side chain e.g. cholesterol, stigmasterol, campesterol, sitosterol, ergasterol.

• Cholesterol helps in absorption of fatty acids, sex hormones, vitamin D and bile
salts. Potato is rich in cholesterol. Excess of cholesterol causes atheroscherosis.

• Prostagladins are hormone modulators.

• Terpenes are lipid like carbohydrates formed of isoprene units e.g., menthol, camphor, carotenoids.

• Major function of lipids is to act as energy stores.

• Plants usually store oil than fats. Seeds, fruits and choloroplasts are often rich
in oils.

• Glycolipids are important components of cell membranes, chloroplast
membranes.

• Fatty substance in the cell wall (Wax, cutin, suberin) helps reduce transpiration
and provide mechanical protection from injury and parasites.

• Diosgenin is a steroid obtained from the plant called Dioscorea. It is used for
manufacturing antifertility pills.

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How Enzymes Action Can Be Inhibited ? Inhibition Types !! Biological Sciencess !!!

2018-10-21T09:45:00.001+05:30

Enzyme action Inhibition

(a) denaturation of enzymes
(b) competitive inhibition
(c) non competitive inhibition
(d) allosteric modification of feedback inhibition

(a) Denaturation

Change in the spatial arrangement of polypeptide chain within the protein molecule so that its unique structure is changed. As a result, the physical or biological properties are changed.

(b) Reversible Inhibition

1. Competitive inhibition

A substance which closely resembles actual
substrate structure competes with the substrate for the active site. There is a decline in the number of actual substrate molecule binding the site, as many of these are occupied by closely resembling substance. As a result, enzyme action is inhibited. Can be reversed by increasing the substrate concentration. Vmax unaffected & Apparent Km increased by factor (1 + [I]) /KI).

Examples:
• Inhibition of activity of succinate dehydrogenase by malonate & oxaloacetate.
• Sulpha drugs e.g. sulphanilamide inhibit the synthesis of folic acid in bacteria by competing with p-amino benzoic acid (PABA).
• AZT and AIDS
• Methotrexate and dihydrofolate reductase

2. Non competitive inhibition

The inhibitor has no structural similarity
to the substrate and forms an enzyme-inhibitor complex at a point other
than its active site so that the globular structure of the enzyme is changed.
As a result, even if the substrate is able to bind with the enzyme, catalysis cannot take place. It is characteristic of allosteric and multisubstrate enzymes. Km unaffected in simplest case. Vmax decreased by factor (1
+ [I])/KI) Cyanide inhibits the activity of cytochrome oxidase. Di isopropyl
fluorophosphates (nerve gas) effects nerve impulse transfer by combining
irreversibly with amino acid serine of acetylcholine esterase. It also poisons a number of other enzymes with trypsin, chymotrypsin, phsphoglucomutase,
elastase etc. Iodo acetamide inhibits enzymes having sulphahydrol or
imidazole group.

3. Uncompetitive

(I binds to ES complex). Km, Vmax both decrease.

Characteristic of multisubstrate enzymes

(c) Irreversible inhibitors

Generally achieved by Covalent modification. Similar to non-competitive kinetics (Vmax lowered, Km unaffected) Examples:
(i) PCMB and GAPDH
(ii) DFP and Serine hydrolases (trypsin, chymotrypsin, acetyl choline esterase,
etc)
(iii) Suicide substrates: generation of reactive intermediate by enzyme

(d) Feedback inhibition

The product of an enzyme catalysed reaction/chain of reactions accumulates and acts as inhibitor of the reaction. e.g. Inhibition of threonine deaminase by isoleucine. Proteases are added in detergents and amylase is used for dish washing.

• Trypsin is added to partially predigested food. Immobilisation of enzymes is done by attaching or trapping enzymes in inert supporting materials for better efficiency and recovering them after the reaction.

• Alloenzymes are enzymes which are produced by different genes.

• Constitutive enzymes are always present because they are always required for vital process e.g. glycolysis.

• Repressible enzymes – normally remain present but are repressed when a specific chemical or product is present e.g. glucokinase.

• Inducible enzymes – are formed in response to presence of its substrate
e.g. lactose.

• ELISA – It is an enzyme linked immunosorbentassay when a protein,
antibody or antigen is detected by means of a specific enzyme e.g. AIDS.

• Restiction endonuclease – These are enzymes which are used to break DNA at a specific site producing sticky ends. The enzymes are highly important for genetic engineering. Arber, Nathans and Smith were awarded Nobel Prize in 1978 for their discovery.

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Humoral And Cell Mediated Immune response ! Biological Sciencess !!

2018-10-21T07:41:00.001+05:30

IMMUNE RESPONSE

1. Immunity means protection from disease and especially infectious disease. Cells and molecules involved in such protection constitute theimmune system and the response to introduction of a foreign agent is known as the immune response.

2. Not all immune responses protect from disease; some foreign agents, such as the
allergens found in house dust mite, cat dander or rye grass pollen, cause disease as
a consequence of inducing an immune response.

3. Likewise some individuals mount immune responses to their own tissues as if they were foreign agents. Thus, the immune response can cause the autoimmune diseases common to man such as multiple sclerosis, diabetes, rheumatoid arthritis or myasthenia gravis.

4. Most individuals do not suffer from autoimmune disease because they have developed tolerance towards their own (self) tissues.

Humoral And Cell Mediated Immune response

1. Humoral immunity produces antibodies in response to toxins (ex bee venom), free
bacteria, and viruses present in the body fluids.

2. "Humor” is medieval term for body fluids. Here it refers to the fluid of the blood and the lymph.

3. Antibodies to these types of antigens are synthesized by B- lymphocytes and then
secreted as soluble proteins which circulate through the body in blood plasma and
lymph.

4. Cell-mediated immunity is the response to intracellular bacteria and viruses, fungi,
protozoans, worms, transplanted tissues, and cancer cells.

5. Depends on the direct action of various types of T-lymphocytes rather than antibodies.

6. T-lymphocytes differentiate into 4 different varieties of T-cells.
• Helper/inducer T-cells (Links Cell meduated and Humoral Immunity)
• Suppressor T cells (Suppresses the immune response when antigens are disposed off)
• Cytotoxic T cells or killer cells (Effector cells of cell mediated immunity)
• Memory T-cells
.
7. “Memory B and T cells” are cells that have been exposed to an antigen and are readily converted to “Effector cells” by a later encounter with the same antigen. Unlike other lymphocytes, they persist in the body for months or even years.

8. The killer T-cells directly attack and destroy antigens. They move to the site of
invasion and produce chemicals that attract phagocytes. Helper T-cells act to stimulate
antibody production by B-cells, while suppressor T-cells suppresses the total immune system from attacking the body’s own cells.

9. Thymus-Independent Antigens: Some bacterial polysaccharides can active B-cells.
Antigens capable of doing so are called thymus independent antigens because these antigens do not require the cooperation of Helper T-cells for activating B-cells.

Thymus dependent antigens; many antigens require the cooperation of T-cells for activating B-cells. The antigens present on organ transplant are thymus dependent
antigens. So a person whose thymus gland is removed is not able to reject organ
transplant.

10. MHC are major histocompatibilty complex (glycoproteins) prensent on cells which present processed intracellular antigen to T-Lymphocytes. They are also called as Human Leucocyte Antigen (HLA) in humans.

11. MHC-I is present on all nucleated cells and are recognized by CD 8+ arms of T-
Cytotoxic cells and present processed antigen to T-cytotoxic cells while MHC-II are present on T & B lymphocytes, dendritic cells and mast cells and recognized via CD
4+ arm present on T-Helper cell.

12. Lymphokines: They are a family of soluble chemical mediator released by helper T-cells. Lymphokines have two broad functions. One group of lymphokines is concerned with growth and differentiation of B and T cells. The other group helps phagocytosis by attracting phagocytic cells when required through chemotaxis and by activating the phagocytic cells.

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What is an antigen? Biological Sciencess !

2018-10-20T21:25:00.000+05:30

What is an antigen?

1. An antigen is defined as “anything that can be bound by an antibody”. This can be an enormous range of substances from simple chemicals, sugars, small peptides to complex protein complexes such as viruses.

2. The small antigens are not, however immunogenic in themselves and need to be
coupled to a carrier to elicit an immune response. Such small antigens are referred
to as haptens.

3. Requirement of Antigen to cause immune response are: Non-self, Complex in structure, should more then 5 KD in size and must have atleast on epitope.

4. In fact antibodies interact specifically with relatively small parts of molecules. These are known as antigenic determinants or epitopes.

5. Sometimes the epitope is composed of a string of amino acids as might be found in a
short peptide, such epitopes are said to be linear. Other epitopes are formed by more
complex 3-dimensional structures present only as part of a native protein, such epitopes are called conformational.

Adaptive immunity

1. The second level of defence increases in strength and effectiveness with each
encounter. The foreign agent is recognised in a specific manner and the immune
system acquires memory towards it.

2. The first encounter with an antigen is known as the primary response. Re-encounter with the same antigen causes a secondary response that is more rapid and powerful.

3. Acquired immunity is a useful evolutionary adaptation because it improves the efficacy of the innate immune response by focusing the response to the site of invasion/infection as well as providing additional effector mechanisms that are unique to lymphocytes.

4. The difference between innate and acquired immunity lies in the antigen specificity of lymphocytes. This property is conferred upon lymphocytes by the expression of cell surface receptors that recognise discrete parts of the antigen known as antigenic epitopes.

5. The cell surface receptor of B lymphocytes, (derived and mature in Bone marrow in mammals or the Bursa of fabricius in chickens) is an immunoglobulin molecule which, when secreted by the B cell, is known as an antibody.

6. Immunity provided by Immunoglobulins (antibodies) is termed as humoral immunity(Humor=fluid/blood)

Antibodies work in three ways

1. Agglutination: Antibodies bind to antigens to produce large insoluble complexes, which render them harmless and facilitate their destruction by other cells of the immune system.

2. Opsoniation: IgG molecules coat the surface of antigens and this stimulates their
recognition and digestion by phagocytes.

3. Complement mediated cell lysis: Complement system is a group of enzymes.
They are triggered by IgM - IgG bound to the surface of foreign cells. The activity of
some of these enzymes leads to the formation of pores on the plasma membrane ofbthe invading cell causing them to lyse.

Structure of Antibody: Antibodies have two ends. One end interacts with the antigen (the variable part) leaving the other (constant ) end free to interact with the
immunoglobulin receptors on these cells. During an immune response, a complex lattice of interlinked antigens and antibodies, known as an immune complex, will present an array of constant regions which can activate the various cells mentioned above through ligation of their immunoglobulin receptors.

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Top 9 characteristics of Oncogenes and tumour suppressor genes ! Biological Sciencess !!

2018-10-20T21:16:00.000+05:30

The characteristics of Oncogenes and tumour suppressor genes

1. Dominant gain-of-function mutations in proto-oncogenes and recessive loss-of-function mutations in tumor-suppressor genes are oncogenic.

2. Among the proteins encoded by proto-oncogenes are positive-acting growth factors and their receptors, signal-transduction proteins, transcription factors, and cell-cycle control proteins.

3. An activating mutation of one of the two alleles of a proto-oncogene converts it to an
oncogene, which can induce transformation in cultured cells or cancer in animals.

4. Activation of a proto-oncogene into an oncogene can occur by point mutation, gene amplification, and gene translocation.

5. The first recognized oncogene, v-src, was identified in Rous sarcoma virus, a cancer-
causing retrovirus. Retroviral oncogenes arose by transduction of cellular proto-
oncogenes into the viral genome and subsequent mutation.

6. The first human oncogene to be identified encodes a constitutively active form of Ras, a signal-transduction protein. This oncogene was isolated from a human bladder carcinoma.

7. Slow-acting retroviruses can cause cancer by integrating near a proto-oncogene in such a way that gene transcription is activated continuously and inappropriately.

8. Tumor-suppressor genes encode proteins cell cycle if DNA is damaged or chromosomes are abnormal, receptors for secreted hormones that function to inhibit cell proliferation, proteins that promote apoptosis, and DNA repair enzymes.

9. Inherited mutations causing retinoblastoma led to the identification of RB, the first tumor-suppressor gene to be recognized.

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Proto-Oncogenes and Tumor-Suppressor Genes ! Biological Sciencess !!

2018-10-20T21:10:00.002+05:30

Proto-Oncogenes and Tumor-Suppressor Genes

1. Two broad classes of genes

proto-oncogenes (e.g., ras) and tumor-suppressor genes (e.g., APC) play a key role in cancer induction. These genes encode many kinds of proteins that help control cell growth and proliferation; mutations in these genes can contribute to the development of cancer.

2. Most cancers have inactivating mutations in one or more proteins that normally
function to restrict progression through the G1 stage of the cell cycle (e.g., Rb and
p16). Virtually all human tumors have inactivating mutations in proteins such as p53 that normally function at crucial cell-cycle checkpoints, stopping the cycle if a previous step has occurred incorrectly or if DNA has been damaged. Likewise, a constitutively active Ras is found in several human tumors of different origin. Thus normal growth control and malignancy are two faces of the same coin.

3. An oncogene is any gene that encodes a protein able to transform cells in culture or
to induce cancer in animals.

4. Of the many known oncogenes, all but a few are derived from normal cellular genes
(i.e., proto-oncogenes) whose products participate in cellular growth-controlling
pathways. For example, the ras gene is a proto-oncogene that encodes an intracellular signal-transduction protein;

5. Conversion, or activation, of a proto-oncogene into an oncogene generally involves a gain-of-function mutation.

6. Tumor-suppressor genes generally encode proteins that in one way or another inhibit cell proliferation. Loss of one or more of these “brakes” contributes to the development of many cancers.

7. Five broad classes of proteins are generally recognized as being encoded by tumor-suppressor genes:

• Intracellular proteins, such as the p16 cyclin-kinase inhibitor, that regulate or
inhibit progression through a specific stage of the cell cycle
• Receptors for secreted hormones (e.g., tumor derived growth factor ?) that function to inhibit cell proliferation
• Checkpoint-control proteins that arrest the cell cycle if DNA is damaged or
chromosomes are abnormal
• Proteins that promote apoptosis and Enzymes that participate in DNA repair

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Characteristics of Cancer Cells ! Biological Sciencess !!

2018-10-20T08:53:00.004+05:30

Characteristics of Cancer Cells

1. They are usually less well differentiated than normal cells or benign tumor cells. The presence of invading cells is the most diagnostic indication of a malignancy.

2. Cancer cells can multiply in the absence of growth-promoting factors required for
proliferation of normal cells and are resistant to signals that normally program cell death (apoptosis).

3. Cancer cells also invade surrounding tissues, often breaking through the basal laminas that define the boundaries of tissues and spreading through the body to establish secondary areas of grow th, a process called metastasis

4. Both primary and secondary tumors require angiogenesis, the recruitment of new blood vessels, in order to grow to a large mass.

5. Cancer cells, which are closer in their properties to stem cells than to more mature differentiated cell types, usually arise from stem cells and other proliferating cells

Cancer Cells Have Escaped Cell Cycle Controls

• Cancer cells do not exhibit density dependent inhibition.
• Cancer cells do not stop growing when growth factor is depleted.
• Cancer cells stop at random points in cell cycle (not checkpoints).
• Some cancer cell lines are immortal and can divide indefinitely given the right
ingredients.e.g. HeLa cells.
• p53 gene mutations in tumor suppressor genes (e.g. p53) result in cancer functional
p53 aids cell in checkpoint control at G1 and G2

He La cells are human cancer cells of a patient Henrietta Lack; maintained in
tissue culture since 1953. They divide and double their number in every 24 hrs &
widely used in research.

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Prokaryotic Cell Division ! Binary Fission !! Biological Sciencess !!!

2018-10-20T08:46:00.000+05:30

Prokaryotes divide by fission

1. Prokaryotic cells grow in size, replicate DNA, and divide into two new cells. This
process is called fission.

2. Escherichia coli (a bacterium) simply divides as quickly as resources permit. At 37oC, this is about once every 40 minutes. When resources are abundant, E. coli can divide every 20 minutes.

3. Prokaryotes generally have just one circular chromosome.
• The E. coli chromosome is 1.6 mm in diameter, making the unfolded circle 100
times greater than the size of the cell. The molecule is packaged by folding in on
itself with the aid of basic proteins that associate with the acidic DNA.
• Circular chromosomes appear to be characteristic of all prokaryotes.

4. The prokaryotes have a site called ori, where DNA replication begins, and a site ter, where it ends.
• Ori is short for origin of replication.
• Ter is short for terminus of replication.

5. As DNA replicates, each of the two resulting DNA molecules attaches to the plasma membrane. As the bacterium grows, new plasma membrane is added between the attachment points, and the DNA molecules are moved apart.

6. Cytokinesis, which is cell partitioning, begins around 20 minutes after chromosome duplication is completed. A pinching of the plasma membrane to form a constricting ring separates the one cell into two, each with a complete chromosome.
• A tubulin-like fiber is involved in the purse-string constriction.

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Regulation of the Cell Cycle ! Biological Sciencess !!

2018-10-20T08:38:00.003+05:30

Regulation of the Cell Cycle

1. Cell cycle is driven by specific chemical signals in the cytoplasm.

2. M phase cells that are fused with any other phase cell, the latter cell will enter
mitosis.

3. Cell cycle control system triggers and coordinates key events in the cell cycle.

4. Cell cycle checkpoints act as stop and go signals. Three major checkpoints found in
G1
, G2
, and M phases.

(a) G1 is critical checkpoint. If cells make it past G1, the entire cell cycle is completed.
(b) Non-dividing cells are in G0 state.

5. Fluctuations in cell cycle control molecules abundance and activity control cell cycle.

• Protein kinases are activated by cyclin proteins.
• Activity of protein kinase is correlated with concentration of specific cyclin (cyclin
dependent kinase or “Cdk”).
6. MPF (maturation promoting factor) was first Cdk described.
• Cyclin level rises during interphase.
• At G2, enough active MPF (cyclin + Cdk) is present to promote mitosis.
• Numerous phosphorylation events that cause nuclear envelope to fragment
and activate other enzymes.
• Cyclin is broken down by proteolytic cleavage (MPF inactive) and Cdk is recycled.
• Proteolysis also drives M-phase past anaphase by breaking down proteins that
hold sister chromatids together.

7. Internal and External Cues Regulate Cell Cycle Internal signal delays start of
anaphase (separation of chromosomes) until all kinetochores are attached to spindle
fibers.

• Anaphase promoting complex (APC) is kept in inactive state by proteins associated
with kinetochores.
• Signal ceases when all kinetochores are attached.

8. Growth factors are external signals that stimulate cells to divide.

• Platelet derived growth factor (PDGF) is required for division of fibroblasts.
• PDGF binds to tyrosine kinase receptors on surface of cells and triggers signal
transduction pathway.

9. Density dependent inhibition describes phenomenon whereby cells stop growing
after reaching a certain density. Growth is limited by availability of growth factor.

10. Cancer Cells Have Escaped Cell Cycle Controls

• Cancer cells do not exhibit density dependent inhibition.
• Cancer cells do not stop growing when growth factor is depleted.
• Cancer cells stop at random points in cell cycle (not checkpoints).
• Some cancer cell lines are immortal and can divide indefinitely given the right
ingredients.e.g. HeLa cells.
• p53 gene mutations in tumor suppressor genes (e.g. p53) result in cancer functional
p53 aids cell in checkpoint control at G1 and G2

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Cyclins and other proteins signal events in the cell cycle ! Biological Sciencess !!

2018-10-20T08:26:00.001+05:30

Cyclins and other proteins signal events in the cell cycle

1. Transitions from G1 to S and G2 to M depend on activation of a protein called cyclin-dependent kinase, or Cdk.

2. A kinase is an enzyme that transfers a phosphate from ATP to different protein(s).
This is called phosphorylation.

3. Activated Cdk transfers phosphates from ATP to certain amino acids of proteins that
then move the cell in the direction of cycling.

4. The Cdk effect on the cell cycle is a common mechanism in eukaryotic cells.
• Studies in sea urchin eggs uncovered a protein called the maturation promoting
factor.

• A mutant yeast that lacked Cdk was found, which stalled at the G1–S boundary.

• These two proteins, one from sea urchins and the other from yeast, were similar
in structure and function. Other Cdks have been found in other organisms, including humans.

5. Cyclin is a protein that interacts with Cdk. Cyclin binding of Cdk exposes the active
site of the kinase.

6. The cyclin-Cdk complex acts as a protein kinase that triggers transition from G1 to S.
The cyclin then breaks down and the Cdk becomes inactive. Several different cyclins
exist, which, when bound to Cdk, phosphorylate different target proteins.

• Cyclin D-Cdk4 acts during the middle of G1. This is the restriction point in G1,
beyond which the rest of the cell cycle is inevitable.

• Cyclin E-Cdk2 acts at the boundary of G1 to S to initiate DNA replication.

• Cyclin A-Cdk2 acts during S and also stimulates DNA replication.

• Cyclin B-Cdk1 acts at the G2-to-M boundary, initiating mitosis.

7. Cyclin-Cdk complexes act as checkpoints. When functioning properly, they allow or prevent the passage to the next cell cycle stage, depending on the extra- and intracellular conditions.

• An example is the effect of p21 on the G1-to-S phase transition.
• If DNA is damaged by UV radiation, p21 is synthesized (a protein of 21,000
daltons).

• It binds to the two different types of G1 Cdk molecules, preventing their activation
until damaged DNA is repaired. The p21 is then degraded, allowing the cell
cycle to proceed.

8. Some targets for cyclin-Cdk complexes include proteins that condense chromosomes and others that cause fragmentation of the nuclear envelope.

9. Cyclin-Cdk defects have been found in some cancer cells.
• A breast cancer with too much cyclin D has been found.
• The protein p53, which inhibits activation of Cdk, is found defective in half of all
human cancers.

Growth factors can stimulate cells to divide

1. Cyclin-Cdk complexes provide internal control for cell cycle decisions.

2. Cells in multicellular organisms must divide only when appropriate. They must
respond to external signals, controls called growth factors.

3. Some cells respond to growth factors provided by other cells.

• Platelets release platelet-derived growth factor, which diffuses to the surface of
cells to stimulate wound healing.
• Interleukins are released from one type of blood cell to stimulate division of
another type resulting in body immune system defenses.
• The cells of the kidney make erythropoietin, which stimulates bone marrow cells to divide and differentiate into red blood cells.

4. Cancer cells cycle inappropriately because they either make their own growth factors or no longer require them to start cycling.

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Cytoskeletal Structures of the Cells! Biological Sciencess !!

2018-10-20T08:17:00.000+05:30

Cytoskeltal structures

These are fibrous or fine tubular structures which form the supportive structures of the cell. These are of three types
microtubules,
microfilaments
Intermediate filaments

(a) Microtubules

discovered by Robertis and Franchi, (1953) term coined by Slautterback (1963), are unbranched hollow non contractile tubules of indefinite length, 25 nm in thickness with 15 nm core and formed of 13 helically arranged protofilaments of a and b-tubilin protein. Microtubules grow from nucleating
centres. Microtubules are basic structures of spindle apparatus, centrioles, basal
bodies, cilia and flagella and are responsible for cell motility and maintenance of shape.

Their tips can grow and shorten quickly. GTP, Ca2+, Mg2+ and a calmodulin bound protein are required for assembly. Colchicine prevents it.
Microtubules are basic structures of spindle apparatus, centrioles, basal bodies, cilia and flagella. They are also present in other cellular structures like sensory hair, nerve processes, sperm tail, etc. Microtubules present in cytoplasm provide shape and polarity to cells. Microtubules are absent in procaryotes (except Anabaena),Amoeba and Slime Moulds.

(b) Microfilaments

They are cylindrical solid, contractile rods or filaments of actin and myosin protein with a diameter of 6 to 10 nm. Microfilaments can form hexagonal
bundles, take part in cytoplasmic streaming, membrane undulations, cleavage, contraction of muscles, movement of microvilli to absorb food and endocytosis.

(c) Intermediate Filaments

They are intermediate in size having diameter around 10-15 nm and are composed of non-contractile proteins. Intermediate fibres (IF) are of four types–keratin filaments, neurofibrils, glial filaments and heterogeneous filaments (viz., desmin filaments, vimentin filaments, synemin filaments).They privide rigidity to cell and maintains the cell structure

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Types of Microbodies Present in The Cells ! Biological Sciencess !!

2018-10-19T09:30:00.000+05:30

Microbodies

These are (lysosomes, sphaerosomes, glyoxysomes and peroxisomes)

They are smallest single membrane bounded organelle. Lysosomes (suicidal bags, disposal units, scavenger of cell) are microbodies of 0.2-0.8 µ size filled with 40 types of acid hydrolases to digest (autolysis) almost every type of organic matter except
cellulose.

They are common in WBC, liver, spleen etc. They work at pH-5 and cause lysis of foreign body; discovered accidently by Christian de Duve (1955) from rat liver. Novikoff (1956) observed them under TEM. They show pleomorphism (polymorphism).

They are of four types

(i) Primary lysosomes (Storage granules) have inactive enzymes; (ii) Secondary lysosomes (Heterophagosomes or Digestive vacuoles or Phagolysosomes) cause digestion (Heterophagy); (iii) Tertiary lysosomes (Residual bodies or Telolysosomes) removes wastes by ephagy from cell by acting as scavenger or disposal unit; (iv) Autophagic vacuoles (Cytolysosome orAutophagosomes) are complex lysosomes and digest old / injured / dead cells and tissues to keep cell healthy (autolysis or autodigestion).

Scavenging, disappearance of tail, softening of gums, acrosomal activity of sperm are few other examples. Autophagy is digestion of stored food (glycogens, fat and proteins) during starvation to provide energy. Thus autophagy has no role in scavenging. If lysosomes burst and release their enzymes, the entire cell is digested and liquefied. It is called autolysis.

Osteoclasts (which digest bones) are rich in lysosomes; Plant cells lack lysosomes
except Neurospora, root tip of maize, yeast and seeds of pea and cotton.

Lack of Lysosome cause Pombe’s Disease. They are also involved with diseases such
as Tay-Sachs Syndrome and Rheumatic Arthritis (An Autoimmune disease).

Types of Microbodies

(a) Sogaerisines (Plant lysosomes) are micro bodies filled with hydrolytic enzymes for fat synthesis. They are highly refractile and rich in fat (98%) and take black stain with Sudan iii / Osmium tetraoxide. These are abundant in endosperm of oily seeds.

(b) Transosomes are triple layer bounded organelle in ovary follicle cells of birds
to help in yolk formation.

(c) Lomasomes are boder bodies between cell wall and cell membrane, common in
fungi, discovered by Moore and Mc Allister (1961) and help in cell proliferation and elongation for diffusion of substances required in cell wall formation.

(d) Peroxisomes (uricosomes) are microbodies containing enzymes for peroxide formation. Catalase and peroxidase are largest and smallest enzymes found in peroxisomes. In plants they do photo-respiration in C3 plants (Tolbert,1972). In animals they take part in lipid synthesis (b-oxidation of fatty acids).

(e) Glyoxysomes- Largest microbody of size upto 10 µ and similar to peroxisomes
as these contain catalase and other enzymes for glyoxylate cycle (a modified
Krebs’ cycle in which fats are converted into carbohydrates). These are common
in germinating oil seeds of castor, groundnut and cucumbers and disappear after germination.

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Fluid Mosaic Model of Plasma Membrane ! Biological Sciencess !!

2018-10-19T09:15:00.003+05:30

Fluid mosaic model of plasma membrane

Singer and Nicolson (1972) put forward the “fluid mosaic model” of membrane structure. It is the latest and most widely accepted model. According to this model,
the cell membrane consists of a highly viscous fluid matrix of two layers of phospholipids molecules.

These serve as a relatively impermeable barrier to the passage of most
water soluble molecules.

Protein molecules on their complexes occur in the membrane, but not in continuous layer; instead, these occur as separate particles asymmetrically arranged in a mosaic pattern.

Some of these (peripheral or extrinsic proteins) are loosely bound at the polar surfaces of lipid layers. Others (called integral or intrinsic proteins), penetrate deeply into the lipid layer. Some of the integral proteins penetrate through the phospholipids layers and project on both the surfaces.These are called Trans membranes or tunnel proteins.

The plasma membrane contains lipids (32%), proteins (42%), carbohydrates (6%) and water (20%) although variations are always there.

The carbohydrates occur only at the outer surface of the membrane. Their molecules
are covalently linked to (i) the polar heads of some lipid molecules (forming glycolipids) and (ii) most of the proteins exposed at outer surface (forming
glycoproteins). The carbohydrates so bound to membrane components constitute
the glycocalyx of cell surface.

The sugar portions of glycolipids and glycoproteins are involved in recognition mechanisms:-
(a) Sugar recognition sites of two neighbouring cells may bind each other causing cell-to-cell adhesion. This enables cells to orient themselves and to form tissues.

(b) Through glycoproteins, bacteria recognise each other (female bacteria are
recognized by male bacteria; Paramoecia of different mating types recognize each other).

(c) These provide the basic of immune response and various control systems, where glycoproteins act as antigens.

Lipids and integral proteins are amphipathic in nature (i.e. have both hydrophobic and hydrophilic groups). The hydrophobic ends are situated inside the bilayer while the hydrophilic groups are directed outwards. Thus, the membrane is held together primarily by hydrophobic attraction.

However, the lipids have links in their fatty acid tails. These links prevent close packing of molecules and make the membrane structure more fluid. The fluidity increases with decreasing length of fatty acid tails.

Thousand of different types of proteins can occur in cell membranes. These may be
purely structural (provide elasticity and mechanical support) or have additional
functions as :
(a) Carriers, for transporting specific molecules into or out of the cell.
(b) Receptors, for immediate flow of information into the cells.
Gases like O2 and CO2 diffuse rapidly in solution through membranes.

Biological Sciencess

Most Important Components of Protein Synthesis ! Biological Sciencess !!

PROTEIN SYNTHESIS

I. Overview of Translation

II. Components of Translation

A. mRNA

B. tRNA

Wobble Hypothesis

Ribosome

1. Performs 3 essential functions

2. Ribosomes are large protein-RNA complexes that are divided into a large and small subunit.

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TRANSPORT ACROSS Plasma MEMBRANES ! Biological Sciencess !!

TRANSPORT ACROSS MEMBRANES

1. Movement of Small Molecules Across Membranes can involve simple diffusion or protein-mediated transport. Cell membranes are selectively permeable.

2. Some protein transporters require energy; others do not. There are 2 possible situations:

3. Active transport can involve ATP pumps, symport, or antiport

(a) ATP pumps.

(b) Symport

(c) Antiport

4. Cells Regulate Permeability by Adding & Removing Membrane Transport Proteins

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54 EXTRA CONCEPTS: Cell Reproduction or Cell Division ! Biological Sciencess !!

EXTRA CONCEPTS: Cell Reproduction or Cell Division

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Gametogenesis And Oogenesis ! Process, Mechanism, Stages !! Biological Sciencess !!!

GAMETOGENESIS

1. Spermatogenesis

(i) Multiplication Phase

(ii) Spermatocytogenesis

(iii) Growth Phase

(iv) Maturation Phase

(v) Spermiogenesis

Sperm

2. Oogenesis

(i) Multiplication Phase

(ii) Growth Phase

(iii) Maturation Phase

Ovum

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Asexual Reproduction ! Types, Definitions !! Biological Sciencess !!!

REPRODUCTION

Asexual Reproduction

1. Fission

(i) Binary Fission.

(ii) Multiple Fission

(iii) Plasmotomy

(iv) Strobilisation

2. Cysts and Spores

3. Budding

(i) Exogenous/ External Budding.

(ii) Endogenous/ Internal Budding.

4. Fragmentation

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Physiology Practice Questions Part 2 ! Net CSIR !! Biological Sciencess !!!

Physiology Practice Questions Part 2

1. After fertilization, the _____ develops into a seed and the _____ develops into a fruit.

2. Plants growing in harsh environments such as deserts, sand dunes, and arctic tundra often reproduce vegetatively. This is because

3. In contrast to animals, plants exhibit ______ and _____.

4. Which of the following seedlings will probably bend toward the light?

5. In shoots, branching is inhibited by _____ from the tip of a growing shoot, but this effect is countered by _____ from the roots.

7. Seeds of many desert plants will not germinate until a heavy rain washes away their

8. The abscission layer

9. When a plant structure such as a leaf is injured, it produces ______, which may cause the part to age and drop off.

10. Once a flower is pollinated, changes occur that make it less attractive to insects. Its petals, for example, shrivel and fall off. Pollination must

11. In the autumn, the amount of ____ increases and the amount of ____ decreases in fruit and leaf stalks, causing a plant to drop fruit and leaves.

12. Plant hormones act by affecting the activities of

13. _______ appear to be responsible for gravitropism.

14. A rapid loss of water in specialized cells in the sensitive plant Mimosa pudica causes

15. A biological cycle with a period of about 24 hours is called

16. An Rajasthani hunter was worried about being attacked by grizzly tigers, so he left the lights in his cabin on all the time. Plants near the cabin flowered a month early. Which of the following best explains this?

17. Most plants flower when

18. A certain short-day plant flowers when days are less than 12 hours long. Which of the following would cause it to flower?

19. A chemical change in a substance called phytochrome

20. Which of the following tissues produces voluntary body movements?

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Physiology based Practice Questions Part 1 Net CSIR !! Biological Sciencess !!!

Physiology based Practice Questions Part 1

1. Mineral nutrients

2. Professor Arun claims to have discovered a new macronutrient required for plantgrowth. Most of Professor Arun’s colleagues are skeptical of this claim. Why might they consider it unlikely?

1. After fertilization, the _ develops into a seed and the _ develops into a fruit.

3. In contrast to animals, plants exhibit __ and _.

5. In shoots, branching is inhibited by _ from the tip of a growing shoot, but this effect is countered by _ from the roots.

11. In the autumn, the amount of increases and the amount of decreases in fruit and leaf stalks, causing a plant to drop fruit and leaves.