Model AnswerFor Science

B Sc (Zoology Hon’s) Second Semester-2014

Zoology II paper

LZC 202: Biochemistry

SECTION A

1. Multiple choice type questions (Select the appropriate answer) 1 x 10 = 10

1). The protein present in hair is

(a) Elastin (b) Threonine

(c) Keratin (d) Gliadin

2) Neutral amino acid is

(a) Leucine (b) Lysin

(c) Aspartic acid (d) Histidine 3). Cholesterol is transported from liver to extrahepatic tissues by

(a) Chylomicrons (b) VLDL

(c) HDL (d) LDL

4). The major storage form of lipids is

(a) Esterified cholesterol (b) Glycerophospholipids

(c) Triglycerides (d) Sphingolipids

5) Isoelectric pH is that at which protein is electrically

(a) Neutral (b) Anionic

(c) Cationic (d) None of these

6). A Holoenzyme is

(a) Functional unit (b) Apoenzyme

(c) Coenzyme (d) All of these

7). The number of ATP molecules generted for each turn of the citric acid cycles is

(a) 8 (b) 12

(c) 24 (d) 38

8). Oxidation of one molecule of glucose yields

(a) 12 ATP (b) 24 ATP

(c) 36 ATP (d) 38 ATP

9). GAG triplet codon and is a

(a) Glycoseminoglycans (b) Monosaccharide

(c) Proteins (d) Fats

10). During the process of replication Direction of polymerization is

(a) 3′-5′ (b) 4′-5′

(c) 5′-3′ (d) 3′-4′

SECTION B

QII: Descriptive Type question.

Note: Attempt any four questions from this section 20 mark

1). “Water is best biological solvent” Justify the statement. (5)

Ans 2 Water as Biological Solvent

• A water molecule (H2O), is made up of three atoms --- one oxygen and two hydrogen.

• Water is Polar therefore- In each water molecule, the oxygen atom attracts more than its "fair share" of

electrons

• The oxygen end “acts” negative

• The hydrogen end “acts” positive

• Causes the water to be POLAR

• However, Water is neutral (equal number of e- and p+) --- Zer

Hydrogen Bonds Exist Between Water Molecules

Interaction Between Water Molecules- Negative Oxygen end of one water molecule is attracted to the Positive

Hydrogen end of another water molecule to form a HYDROGEN BOND

• At sea level, pure water boils at 100 °C and freezes at 0 °C.

• Other Properties, Cohesion, Adhesion, High Specific Heat, High Heat of Vaporization, Less Dense as a

Solid

• High Heat of Vaporization- Water's heat of vaporization is 540 cal/g.

• Water is Less Dense as a Solid

• One of the most valuable properties of water is its ability to dissolve.

• An individual water molecule has a bent shape with a H-O-H bond angle of approximately 105 degrees.

• Water is polar thus having positive & negative partial charges on its ends.

• The positive ends of a water molecule are attracted to negative cations and the negative ends are

attracted to positive cations in an ionic compound – this is called hydration.

• The ions become hydrated& move around independently.

Covalent Compounds in Water-

• Water also dissolves many nonionic substances such as ethanol (C2H5OH).

2). Derive relation between Km and Vmax by using MichaelisMeten concept. Give its limitations (5)

Ans 4: Different classes of enzymes and mechanism of action

OXIDOREDUCTASES:

To this class belong all enzymes catalysingoxidoreduction reactions. The substrate that is

oxidized is regarded as hydrogen donor. The systematic name is based

on donor:acceptoroxidoreductase. The common name will be dehydrogenase, wherever this is

possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the

acceptor.

TRANSFERASES:

Transferases are enzymes transferring a group, e.g. a methyl group or a glycosyl group, from one

compound (generally regarded as donor) to another compound (generally regarded as acceptor).

The systematic names are formed according to the scheme donor:acceptorgrouptransferase. The

common names are normally formed according to acceptor grouptransferase or donor

grouptransferase. In many cases, the donor is a cofactor (coenzyme) charged with the group to

be transferred. A special case is that of the transaminases

HYDROLASE:

These enzymes catalyse the hydrolytic cleavage of C-O, C-N, C-C and some other bonds,

including phosphoric anhydride bonds. Although the systematic name always

includes hydrolase, the common name is, in many cases, formed by the name of the substrate

with the suffix -ase. It is understood that the name of the substrate with this suffix means a

hydrolytic enzyme.

LYASES:

Lyases are enzymes cleaving C-C, C-O, C-N, and other bonds by elimination, leaving double

bonds or rings, or conversely adding groups to double bonds. The systematic name is formed

according to the pattern substrate group-lyase. The hyphen is an important part of the name, and

to avoid confusion should not be omitted, e.g. hydro-lyase not 'hydrolyase'. In the common

names, expressions likedecarboxylase, aldolase, dehydratase (in case of elimination of CO2,

aldehyde, or water) are used. In cases where the reverse reaction is much more important, or the

only one demonstrated, synthase (not synthetase) may be used in the name. Various subclasses of

the lyases include pyridoxal-phosphate enzymes that catalyse the elimination of a β- or γ-

substituent from an α-amino acid followed by a replacement of this substituent by some other

group.

ISOMERASES:

These enzymes catalyse geometric or structural changes within one molecule. According to the

type of isomerism, they may be called racemases, epimerases, cis-trans-isomerases, isomerases,

tautomerases, mutases or cycloisomerases.

LIGASES:

Ligases are enzymes catalysing the joining together of two molecules coupled with the

hydrolysis of a diphosphate bond in ATP or a similar triphosphate. The systematic names are

formed on the system X:Y ligase (ADP-forming). In earlier editions of the list the

term synthetase has been used for the common names. Many authors have been confused by the

use of the terms synthetase (used only for Group 6) and synthase (used throughout the list when

it is desired to emphasis the synthetic nature of the reaction). Consequently NC-IUB decided in

1983 to abandon the use of synthetase for common names, and to replace them with names of the

type X-Y ligase. In a few cases in Group 6, where the reaction is more complex or there is a

common name for the product, a synthase name is used (e.g. EC 6.3.2.11 and EC 6.3.5.1).

Mechanism of enzyme action.

The biological processes that occur within all living organisms are chemical reactions,

and most are regulated by enzymes. Without enzymes, many of these reactions would not take

place at a perceptible rate. Enzymes catalyze all aspects of cell metabolism. This includes the

digestion of food, in which large nutrient molecules (such as proteins, carbohydrates, and fats)

are broken down into smaller molecules; the conservation and transformation of chemical

energy; and the construction of cellular macromolecules from smaller precursors. Many inherited

human diseases, such as albinism, result from a deficiency of a particular enzyme. There are

several theories has been put forwarded by different biochemists to explain the mechanism of the

enzyme action.

(i) Lock and key thoery:

According to Emil Fisher only a specific substrate can combine with the active site of a

particular enzyme as a specific key fits to open a specific lock. In this enzyme molecule posses

an active site to fit correctly with the substrate forming ES complex. When reaction completed

ES complex breaks into products and enzymes. Enzymes remain intact.

(II) Inducted fit Theory:

According to Koshland, when a suitable substrate approaches the active site of an enzyme, the

substrate inducts some conformational changes in the enzyme as a result the attractive groups

and buttressing groups form a complementary structure so that the catalytic group of the active

site is in proximity of the bonds to be broken.

After the suitable enzyme substrate complex has been formed, the subtract molecule is held by

hydrogen bonds while a strain nucleophilic attack of the charged catalytic groups of the active

site. The strain weaker the bond which is ultimately broken and the products are formed.

4). Discuss stepwise Embden-Meyerhof pathway showing degradation of glucose to pyruvic

acid.

Answer 5: Glycolysis : Glycolysis (from glycose, an older term for glucose + -lysisdegradation) is

the metabolic pathway that converts glucoseC6H12O6, into pyruvate, The free energyreleased in this

process is used to form the high-energy compounds ATP (adenosine triphosphate) and

NADH (reduced nicotinamide adenine dinucleotide). Glycolysis is a determined sequence of

ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis. For

example, most monosaccharides, such as fructose andgalactose, can be converted to one of these

intermediates. The intermediates may also be directly useful. For example, the

intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with

fatty acids to form fats.

Glycolysis occurs, with variations, in nearly all organisms, bothaerobic and anaerobic.

The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic

pathways It occurs in the cytosol of the cell.

5). Answer 6: Triglycerides and functional significance

A. Simple lipids or Homolipids. These are esters of- fatty acid with farious alcohols.

1. Fats and oils (triglycerides, triacylglycerols).

These are esters of fatty acids with a trihydroxy alcohol, glycerol. A fat is solid at ordinary room

temperature wheras an oil is liquid.

2. Waxes. These are esters of fatty acids with high molecular weight monohydroxy alcohols.

B. Compound lipids or Heterolipids. These are - esters of fatty acids with alcohol and possess

additional group(s) also.

1. Phospholipids (phosphatids), These are compounds containing, in addition to fatty acids and

glycerol, a phosphoric acid, nitrogen bases and other Substituents.

2. Glycolipids (cerebrosides). These are the compounds of fatty acids with carbohydrates and

contain

nitrogen but no phosphoric acid. The glycolipids also include certain structurally-related compounds

comprising the groups, gangliosides, sulfolipids and sulfatids.

C. Derived lipids. These are the substances derived -from simple and compound lipids by hydrolysis.

These include fatty acids, alcohols, mono- and diglycerides, steroids, terpenes and carotenoids.

Glycerides and cholesterol esters, because of their uncharged nature, are also called neutral lipids

Triglycerides (TAG) - Simple lipids/ Homolipids

constitute about 98% of total dietary lipids ; the remaining 2% consists of phospholipids and cholesterol

and its esters. They are the major components of storage or depot fats in plant and animal cells but are

not normally found in membranes. They are nonpolar, hydrophobic molecules since they contain no

electrically charged or highly polar functional groups. In animals, the fat cells or adipocytes contain

very large quantities of triglycerides in the form of fat droplets, which fill almost the entire cell

volume . Adipocytes are abundantly found under the skin, in the abdominal cavity and in the

mammary glands. Triglycerides can be stored in quantities, sufficient to supply the energy needs of the

body for many months, as in the case of obese persons. Triglycerides are much better adapted than

glycogen to serve as storage form of energy. They are not only stored in large amounts but also yield

over twice as much energy as carbohydrates. Since fats tend to remain in the stomach longer than

carbohydrates and are digested more slowly, they also have greater satiety value than carbohydrates.

The arctic and antarctic animals (Fig. 13-2) such as whales, seals, walruses and penguins are amply

padded with triglycerides to serve both as energy storage depots and as an insulation against very low

temperatures. Most fats and oils, upon hydrolysis, yield several fatty acids as well as glycerol.

However, the milk of spiny anteater is an exception in that it comprises almost pure triolein. Human

body contains enough fat to make 7 bars of soap. TAG is found in all organs of the human body,

particularly in adipose tissue, in which droplets of triacylglycerols may represent more than 90% of the

cytoplasm of the cells. Body lipid is a reservoir of potential chemical energy. About 100 times more

energy is stored asmobilizable lipid than as mobilizablecarbohyldrate in the normal human being.

TAG is stored in a relatively water-free state in the tissue, in comparison to carbohydrate, which is

heavily hydrated.Chemically, triglycerides are esters of glycerol with 3 fatty acid molecules.

Optically active forms of triglycerides - When the groups attached to carbon 1 and 3 differ, a centre of

asymmetry is created at C 2. The 2 optical isomers may, thus, be represented- The naturally-occurring

fats are of L-type.

Simple triglycerides- A fat molecule contains 3 moles of fatty acids which may be similar or dissimilar.

Those containinga single kind of fatty acid in all 3 positions (α, β, α′) are called simple (or

symmetrical) triglycerides ;they are named after the fatty acids they contain . Ex. tripalmitin,

tristeariand triolein. They occur in natural fats. Such simple triglycerides have, however, been

synthesized in the laboratory e.g., tristearin and triolein

Mixed triglycerides- Most of the triglycerides of nature are mixed (or asymmetrical) triglycerides, i.e.,

they contain 2 or 3 different fatty acid units in the molecule. Representatives of such mixed

triglycerides are oleodipalmitin and oleopalmitostearin

6). Write an account on Watson – Crick DNA double helix structure with diagrammatic illustration. (5)

7) Answer the following (any two): 2.5 x 2 = 5

Initiation of Replication

For a cell to divide, it must first replicate its DNA. This process is initiated at particular

points in the DNA, known as "origins", which are targeted by initiator proteins.In E. coli this

protein is DnaA; in yeast, this is the origin recognition complex. Sequences used by initiator

proteins tend to be "AT-rich" (rich in adenine and thymine bases), because A-T base pairs have

two hydrogen bonds (rather than the three formed in a C-G pair) which are easier to unzip. Once

the origin has been located, these initiators recruit other proteins and form the pre-replication

complex, which unzips the double-stranded DNA.

2. Prostaglandin

The prostaglandins are a group of lipid compounds that are derived enzymatically from fatty acids and have

important functions in the animal body. Every prostaglandin contains 20 carbon atoms, including a 5-carbon

ring.They are mediators and have a variety of strong physiological effects, such as regulating the contraction and

relaxation of smooth muscle tissue. Prostaglandins are not endocrine hormones, but autocrine or paracrine, which

are locally acting messenger molecules. They differ from hormones in that they are not produced at a discrete site

but in many places throughout the human body. Also, their target cells are present in the immediate vicinity of the

site of their secretion (of which there are many).The prostaglandins, together with

the thromboxanes and prostacyclins, form the prostanoid class of fatty acid derivatives, a subclass of eicosanoids.

The abbreviation for "prostaglandin" is PG; specific prostaglandins are named with a letter (which indicates the type

of ring structure) followed by a number (which indicates the number of double bonds in the hydrocarbon structure).

For example, prostaglandin E1 is abbreviated PGE1 or PGE1, and prostaglandin I2 is abbreviated PGI2 or PGI2. The

number is traditionally subscripted when the context allows, but as with many similar subscript-containing

nomenclatures, the subscript is simply forgone in many database fields that can store only plain text (such

as PubMed bibliographic fields), and readers are used to seeing and writing it without subscript.

Function

There are currently ten known prostaglandin receptors on various cell types. Prostaglandins ligate a sub-

family of cell surface seven-transmembrane receptors, G-protein-coupled receptors. These receptors are

termed DP1-2, EP1-4, FP, IP1-2, and TP, corresponding to the receptor that ligates the corresponding

prostaglandin (e.g., DP1-2 receptors bind to PGD2).

The diversity of receptors means that prostaglandins act on an array of cells and have a wide variety of

effects such as:

cause constriction or dilation in vascular smooth muscle cells

cause aggregation or disaggregation of platelets

sensitize spinal neurons to pain

induce labor

decrease intraocular pressure

regulate inflammatory mediation

regulate calcium movement

control hormone regulation

control cell growth

acts on thermoregulatory center of hypothalamus to produce fever

acts on mesangial cells in the glomerulus of the kidney to increase glomerular filtration rate

acts on parietal cells in the stomach wall to inhibit acid secretion

brain masculinization (in rats)

Prostaglandins are potent but have a short half-life before being inactivated and excreted. Therefore, they

send only paracrine (locally active) or autocrine (acting on the same cell from which it is synthesized)

signals.

3. Enzyme distribution on mitochondrial membrane

4. 30S initiation complex

30S INITIATION COMPLEX

• Formation of Initiation complex involves protein initiation factors

• IF-3 keeps ribosome subunits apart

• IF-2 identifies and binds initiator tRNA. IF-2 must bind GTP to bind tRNA.

• IF-1, IF-2, and IF-3 bind to 30S subunit to form initiation complex

• Once 50S subunit binds initiation complex, GTP is hydrolyzed, initiator tRNA enters P-

site and IFs disassociate