-by Sayed Mohamed-

Carbohydrates
IV. Enumerate (Mention):
1. Two sugar alcohols one from aldoses and one from ketoses
Glycerol
D- Sorbitol & D-Manitol
2. One sugar acid
Glucuronic acid
3. One amino sugar
D- Galactosamine
4. Two trioses and two pentoses
Dihydroxyacetone & D-Glyceraldehyde
D-Ribose & D-Xylose
5. Two aldose- ketose isomers
Fructose & Glucose
Ribose & Ribulose
6. Two reducing disaccharides
Maltose & Isomaltose & Lactose
7. Two disaccharides one of them has fructose as hydrolytic product and one has
galactose as hydrolytic product.
Sucrose > Fructose
Lactose > Galactose
8. A non-reducing disaccharide
Sucrose

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9. A sulfate free GAG
Hyaluronic acid
10. Two Sulfate containing GAGs
Heparan sulfate
Keratan sulfate
11. Two glucans
Starch & Glycogen & Cellulose & dextrin
12. The sugar alcohol from each of the following: glucose, galactose, and fructose.
Glucose > Sorbitol
Galactose > Dulcitol
Fructose > Sorbitol & Mannitol
13. Sugar acid from glucose
Glucuronic acid
14. Two monosaccharide derivatives
Sugar acid – Glucose > Glucuronic acid
Sugar alcohol – Glucose > Sorbitol
15. Glycosidic linkages in: starch, glycogen, maltose, isomaltose.
Starch, glycogen, maltose >  1-4 Glycosidic linkages
Isomaltose >  1-6 Glycosidic linkages

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V. On biochemical basis explain:
1. Sucrose is a non-reducing sugar.
Because it's non-reducing as both anomeric carbons of glucose & fructose
are involved in the linkage so it doesn’t have  or  forms.
2. Polysaccharides are non-reducing.
Polysaccharides are composed of more than 10 monosaccharide units linked by
glycosidic bonds. since the condensation of the monosaccharide units involves the
carbonyl groups of the sugars leaving one free carbonyl group at the end of a big
molecule so polysaccharides are non-reducing
3. Maltose or (lactose) is a reducing sugar.
As both of them have free annomeric carbon
4. Cellulose can prevent constipation.
It can’t be hydrolyzed by amylase enzyme as amylase is specific only for the 
glucosidic bond, and bond in cellulose is 1-4 glucosidic bond .. so it makes a bulk
of food > stimuli intestine > prevent constipation
5. GAGs act as a shock absorbent.
when (GAGs) Solution is compressed, water is squeezed out & GAGS occupy a
smaller volume. When the compression is released, their molecules regain their
original hydrated size. This gives GAGs solutions the shock Absorbing properties
6. Heparin acts as an anticoagulant.
As it binds to factor lX & Xl
And activation of antithrombin III

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7. Glucose and mannose are epimers.
As all the asymmetric carbons are the same only one is different
They are epimers at C2
8. Glucose and galactose are epimers.
As all the asymmetric carbons are the same only one is different
They are epimers at C4

9. GAGs have many important functions.

GAGs are unbranched heteropolysaccharides (amino sugar+uronic acid)

-Component of ECM
-Attract water to ECM, so it act as hydralyated gel makes shock absorption
-Lubricant
-Limit passage of large molecule
-Compressibility of cartilage & resilience of eyeball
-Aggregation, present in cartilage
-keratan sulfate, present in cornea
-Heparan sulfate, present in structure of cell membrane

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 Lipids
III-Enumerate (Mention):
1. Four glycerol -containing phospholipids
Lecithin, Cephalin, inositol, phosphatidyl glycerol, phosphatidyl serine
2. Four functions of cholesterol
A- It is a precursor of all steroid hormones
B- formation of vitamin D3
C. Its converted into bile acid & bile salt in the liver.
D- It moderates fluidity of cell membranes to adapt temperature changes.
3. Four functions of phospholipids
A- Amphipathic molecules
B- Emulsifying factors of fat
C- Hydrotropic substances
D- lung surfactant.
4. Two non-essential fatty acids: one is an 3 and the other is an 6.
> timnodonic acid.
> arachidonic acid.
5. Two saturated fatty acids
Acetic acid (C2)
palmitic acid (C16)
6. Two poly unsaturated fatty acids (PUFA).
α linolenic (3)
linoleic acid (6)

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7. Two essential fatty acids.
α linolenic
linoleic acid
8. Two non-essential fatty acids.
Palmitic acid
Acetic acid
9. Two sphingosine containing lipids (sphingolipids).
Ceramide
sphingomyelin
10. Two choline containing phospholipids.
Plasmalogen
Lecithin (phosphatidyl choline)
Sphingomyelin
11. Two phospholipids containing glycerol
Phosphatidyl glycerol
Lecithin (phosphatidyl choline)
12. Three useful by-products that cholesterol can be converted into within the
body
Bile salts
Vit D3
Steroid hormones

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13. Three examples of eicosanoids and one function of each of them
A- prostacyclin (PGI2), Vasodilation and decrease platelet aggregation
B- Thromboxanes, Vasoconstriction and increase platlet aggregation
C. prostaglandin (PG), Mediators in inflammation
D. Leukotrienes
14. One saturated fatty acid and one unsaturated fatty acid each of them
contains 18 C.
Unsaturated FA, Oleic acid
Saturated FA, Stearic acid
16. Three glycerophospholipids
Lecithin, Cephalin, Phosphatidyl serine
17. One ether phospholipid
plasmalogen
18. Two 3 PUFA (one trienoic & one pentaenoic )
Trienoic > -linolenic acid
Pentanethoid acid > Timnodonic acid
19. Two acyclic eicosanoids.
Leukotrienes, lipoxinen
20. Three cyclic eicosanoids.
Prostaglandins (PG), Prostacyclins (PGI), Thromboxanes
21. Two steroid hormones, one mineralocorticoid and the one is a glucocorticoid.
Mineral> Aldosterone.
Gluco> Cortisone

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IV. On biochemical basis explain:
1. Phospholipids are amphipathic
because they have hydrophobic tails and hydrophilic heads. The tails of the
phospholipid are made of fatty acid chains and the head is made of the phosphate
part.
2. Snake bites may lead to death. (OR are toxic)
Snake venom toxins contains lecithinase enzyme with PLA₂ activities
it converts phospholipids in RBCs membrane into lysophospholipids, resulting in
hemolysis of RBCs.
3. Cholesterol moderates fluidity of cell membranes.
- At warm temp: cholesterol makes the membrane less fluid, by limiting
the movement of fatty acid tails of the Phospholipids.
- At low temp: cholesterol decreases close packing of phospholipids, increasing
fluidity & decreasing gel formation.

4. Phospholipids play an important role in signal transduction.

once specific ligand interacts with receptor, G protein is activated, then
phospholipase C is activated, it converts PIP2 to IP3 then IP3 & DAG act as 2nd
messengers.
-IP3 increase the release of Ca
-DAG & calcium activates protein kinase C
which leads to phosphorylation of various proteins that have specific cellular
response.
5. Deficiency of phospholipids cause respiratory distress syndrome.
because lung surfactant is formed mainly of dipalmitoyl- lecithin, the lack of which
is responsible for (respiratory distress syndrome).

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6. Cholesterol is a very important sterol.
Refer to question No.2
7. Biomedical importance of trans fatty acids.
Increase saturated FA > increase cholesterol > increase coronary heart disease
8. Biomedical importance of PUFA.
They decrease
-Cholesterol, atherosclerosis & coronary heart diseases
-Blood pressure
-Plasma TAG
-Tendency of thrombosis
9. IP3 and DAG play an important role in intracellular signal transduction.
DAG & calcium activates protein kinase C , which leads to phosphorylation of
various proteins that have specific cellular response.
10. a linolenic and linoleic acids must be supplied in diet.
linoleic decreases plasmas cholesterol while  linolenic; reduces cardiovascular
diseases by lowering plasma TAG & lowering pressure & decreases thrombosis.
11. Phospholipids are important constituent of cell membranes.
Phospholipids are amphipathic because they have hydrophobic tails and
hydrophilic heads. The tails of the phospholipid are made of fatty acid chains. This
part of the molecule is hydrophobic and faces inward in the cell membrane to
avoid contact with water whereas the hydrophilic head faces outwards.
12. Lipids are import lipid ore important dietary constituents
because of;
A- Source of high energy
B- lipids are found in plasma, tissue & Biological membranes
C- Formation of Fat-Soluble vitamins & essential F.A.

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13. Phospholipids are important for blood clotting.
phospholipids are essential for blood clotting; they provide Platelet Activating
Factor which is a choline plasminogen.
14. Glycolipids are very important compounds.
Glycolipids are found in brain, myelin sheath & cell membranes
They are also a component of cell membrane receptors for hormone.

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 Protein
III-Enumerate (Mention):
1- Four effects of denaturation on proteins.
A- Loss of secondary, tertiary & quaternary structured of proteins.
B- Increase viscosity, decrease solubility
C- loss of biological activity (inactivation of enzymes or hormones)
D- Loss of antigenic properties
2- Two bonds that maintain the tertiary structure of proteins.
Hydrogen bond
Ionic bonds
Vander waals forces
3- Two essential amino acids: one containing sulfur and one branched.
Methionine > Containing
Valine > Branched
4- Three types of forces that hold the tertiary structure of proteins.
Hydrophobic interaction
Hydrogen bond
Ionic bonds
Vander waals forces
5- Two sulfur containing amino acids: one essential and one non-essential.
Methionine > essential
Cysteine > non-essential
6- Two hydroxyl- containing amino acids.
Serine, Homoserine

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7- Two sulfur containing amino acids.
Methionine & Cysteine
8- Two aromatic amino acids.
Tryptophan & Tyrosine
9- Four essential amino acids.
Valine, leucine, Isoleucine, Lysine
10- A semi-essential amino acid.
Arginine
11-Two pure glucogenic amino acids.
Methionine & Cysteine
12-Two pure ketogenic amino acids.
Leucine & Lysine
13-Two non-polar amino acids.
Glycine & Alanine
14-Two polar amino acids with uncharged groups.
Serine & threonine

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IV-On Biochemical basis explain:
1. Denaturation of proteins is associated with decreased solubility and increased
digestibility.
- Decreased solubility of deuterated protein, due to exposure of non-polar aa.
- Increased digestibility; due to exposure of peptide bond.
2. Proteins are amphoteric.
proteins are amphoteric because amino acid can react with acid & bases
-In acidic Medium they carry +ve charge
-In based Medium they carry -ve charge
3. Denaturation has several effects on proteins.
A - loss of secondary, tertiary & quaternary structure
B - Increased viscosity
C - Decreased solubility
D - Increased digestibility due to exposure of peptide bond
G- loss biological activity (inactivation of enzymes & hormones)
F - loss of antigenic property.
4. Some amino acids are polar although having uncharged (R) groups.
Because they are water soluble. because they form hydrogen bonds with water
5. Arginine is a semi-essential amino acid.
Arginine is formed in the body at a rate enough for an adult but not for growing
animal.

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6. The biological importance of proteins.
- provide the body with essential aa, nitrogen & sulfur
- Enzymes are proteins
- Antibodies are protein.
- Hemoglobin is chromoproteins.
- plasma protein is responsible for osmotic pressure
- plasma protein help the transport of many substances in blood.
- Receptors & transporters are made by proteins.
7. At the isoelectric point (IEP), the amino acid cannot migrate in electric field.
because aa form dipolar ions = zwitterions (carry both +ve & -ve) at pH 6.02, in
this form aa can't migrate in the electric field

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V- Compare between:
1. Essential & non-essential amino acids (definition, example).
Essential non-essential
aa that not formed in the body should aa that can formed in the body for
be supplied in the diet adult & growing
Valine, leucine, isoleucine, threonine, All aa except the essential aa
Methionine, Lysine, Histidine,
Phenylalanine, Tryptophan

2. High & low biological value protein (definition, example).

High biological value protein low biological value protein
Contain all essential aa Deficient of one of 9 essential aa
Easy to be digested Difficult to be digested

3. Primary & Secondary protein structure (definition, bonds stabilizing).

Primary protein structure Secondary protein structure
Def.: Number and Sequence of aa that Def.: Folding of the polypeptide chain
form the backbone of the polypeptide into:
chain. - helix
- pleated sheets
Peptide bond. - helix >
hydrogen bond (intrachain)

- pleated sheets >

hydrogen bond (interchain)

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 Enzyme
III-Enumerate (Mention):
1. Three factors affecting enzyme activity
- Concentration Substrate
- Concentration Enzyme
- Concentration cofactors
- Temperature (optimum temp 37)
- pH, each enzyme has optimum pH between 5-9. Slight changes in pH causes
changes in their activity
2. Two examples of competitive enzyme inhibitors
A- warfarin (Anticoagulant because its similar to vit. K)
B - Statin (competitive to HMG-CoA reductase, therefore, lowering plasma
cholesterol level)
3. Two isoenzymes increased in myocardial infarction
Creatine kinase(CK) > CK2: MB
Lactate dehydrogenase(LDH) > LDH1
4. Two examples of irreversible enzyme inhibitors that exert their effects on
cofactors. or prosthetic groups
-Fluoride; inhibits enzymes that requires Ca & Mg
-Cyanide; inhibits cytochrome oxidase by blocking the iron of heme.

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5. Characters of isoenzymes (Isozymes)
- They catalyze same reactions.
- They have different affinity to substrate.
- They have different polypeptide chains
- They are separated by electrophoresis.
- They are present in the same or different cells
6. Two examples of irreversible enzyme inhibitors that exert their effects on
enzymes.
A - strong acids > dentures enzymes
B - Antienzymes > Antithrombin inhibits blood clotting.

IV-On Biochemical Basis Explain:

1. Enzyme activity stops at 70 °C
due to denaturation of the enzyme protein
2. Cyanides are very toxic compounds
because it inhibits the activity of cytochrome oxidase (an enzyme of respiratory
chain) by blocking iron of heme.
3. Sulfonamide acts as a bacteriostatic agent
sulfanilamide acts as a bacteriostatic agent, because Bacteria synthesize folic acid
from PABA), sulfonamide is a structure analog of PABA, So, it blocks Synthesis of
folic acid by competitive inhibition
4. Dicumarol is an anticoagulant.
Because Dicumarol is similar to vit. K , So it competes with vit. K reductase
enzyme which leads to decrease of active form of vit. K and hence weak
coagulation

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5. Aspirin acts as an anti-inflammatory agent
Aspirin acts as an anti-inflammatory agent because it produces acetylation of the
hydroxyl group of serine at the active site of Cyclooxygenase enzyme (responsible
for prostaglandin synthesis).
6. Allopurinol is used in treatment of gout.
because it is analogue of hypoxanthine, so it blocks the formation of uric acid by
inhibiting xanthine oxidase enzyme by competitive inhibition.

V-Compare between:
1. Competitive and allosteric enzyme inhibitors
Competitive allosteric
-similar to substrate - not similar to substrate
-competes with substrates to bind to - binds to the allosteric site of the
the active site of the enzyme enzyme
-Vmax is not changed - Vmax 
-Km  - Km 

2. Repressor and inhibitor

Repressor inhibitor
 enzyme synthesis  enzyme activity

3. The mechanism of inhibition of enzymes by H₂O₂ and inhibition of xanthine

oxidase by allopurinol.
allopurinol
-Competitive inhibitor
-similar to substrate
-inhibition is reversible.
H₂O₂
- SH group inhibitor
- not similar to substrate
- inhibition is irreversible

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 ECM
II-On biochemical basis explain:
1. Collagen molecules have very firm structure.
high content of glycine the polypeptide chains are very close to each other.
high content of hydroxyproline > Formation of hydrogen bonds.
Each turn contains only 3 aa residues → Tight helix
formation of right-handed superhelix.
Specific arrangement into fibrils and fibers
2. By age, collagen becomes less flexible.
By age, collagen becomes less flexible. Because of weakening of the covalent
cross linkage between & within the triple Helical units by age.
3. Elastin is rubber like.
because 3 allysin & 1 lysine form desmosine cross-link, which gives its rubber
property

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III-Enumerate
1. Three connective tissue proteins.
- structural proteins; collagen & elastin
- Specialized proteins; fibronectin & fibrillin & laminin
- proteoglycans; formed of GAGs
2. Two bone proteins: one collagenous and one non-collagenous.
- Collagenous protein > Collagen type I
- non-Collagenous protein > glycoproteins
3. Two cartilage proteins: one collagenous and one non-collagenous.
- cartilaginous protein > Collagen type II
- non-cartilaginous protein > aggrecans
4. Three structures to which fibronectin can bind.
Heparin, Collagen, integrins

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 Hemoprotein
II-Compare:
1-Hb A and fetal hemoglobin

2- Hemoglobin and myoglobin as regards structure and function.

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3- Hb S and Hb C
Hb S Hb C
Mutation Glutamate(polar) → valine(non polar) Glutamate → valine
at position 6 of  chain position 6 of  chain
Result of Valine→ sticky patch that bind to No conformational
mutation sticky receptor, in deoxy form, Hb changes
polymerizes into long insoluble fibers
manifestation Heterozygous sickle cell anemia: no Mild anemia
manifestation

Homozygous sickle cell anemia:

anoxia, pain, infarction, Hemolytic
anemia.

III. On biochemical basis explain:

1-Apomyoglobin reduces the affinity of heme for carbon monoxide.
Decreases affinity of heme to CO from 25,000 to 200. Still Heme has a higher
affinity to CO than O2.
CO binds to heme at the same binding site of O2→Hemoglobin can't carry O2
There is an angle between the 1st and 2nd oxygen atoms about 121°
The preferred position for CO is Fe, C and O perpendicular to the plane ofthe ring.
When O2 binds to heme the 1st oxygen perpendicular to the plane of thering and
the bond between the 1st and 2nd oxygen is 121°.
Distal histidine in polypeptide chain produces steric hindrance stabilizing O 2
binding and destabilizing CO binding.

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2-The glutamate residue at position six in the ß-globin chain of hemoglobin is
important for its function.
it is important for its function any mutation occurs in the gene that encodes
Glutamate will cause disorders like sickle cell disease (Hb S) or hemolytic disease
such as Hb C.
3-Globin part of hemoglobin is essential for normal function of hemoglobin.
1.makes heme soluble.
2. Prevents diffusion of heme from RBCs to plasma.
3.Keeps iron in the ferrous state (as heme pocket is surrounded by non-polar
amino acids) and Prevents oxidation of heme into hematin and prevent
formation of heme-O-heme complex.
4. Decreases affinity of heme to CO from 25,000 to 200.
Heme has a higher affinity to CO than O2.
CO binds to heme at the same binding site of O2 →Hemoglobin can't carry O2
Distal histidine in polypeptide chain produces steric hindrance stabilizing O2
binding and destabilizing CO binding.
5.sigmoid shape of O2 dissociation curve of hemoglobin.

4-The fetus appears normal at birth in ß-thalassemia major

The fetus body tries to compensate the absence of Hb A by preserving HbA₂ &
Hb F and thus the fetus looks normal at birth

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IV. Enumerate:
1-Three minor forms of normal hemoglobin.
- HbA₂
- Hemoglobin Gower
- Fetal hemoglobin (Hb F)

2-Three causes of methemoglobinemia.

-Free radical e.g., H2O2 (hydrogen peroxide)
- Drugs e.g., sulfonamides
- Reduced activity of NADH-methemoglobin

3- Three hemoglobinopathies.
- Hb S ; Glutamate replaced by valine ( sickle cell disease)
- Hb C ; Glutamate is replaced by lysine (hemolytic anemia)
- HbM, distal histidine is replaced by tyrosine. (Suffering from hypoxia).

4-Four hemoproteins and mention the function of each.

- Hemoglobin; O₂ transporter in blood
- Myoglobin; O₂ storage in muscle
-Cytochrome P450; for hydroxylation reactions
-Nitric oxide synthase; synthesis of nitric oxide.

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 Chemistry of Nucleotides & Nucleic acids
II-Enumerate:
1. Four adenine containing nucleotides; mention their functions.
- ATP > source of energy
- cAMP > hormone second messenger
- SAM > Methyl doner
- PAPS > Sulfate doner
2. Four coenzymes that act as hydrogen carriers.
NAD, NADP, FMN, FAD
3. Two adenine containing nucleotides: one which acts as a second hormone
messenger and one which acts as a sulfate donor.
cAMP > hormone second messenger
PAPS > Sulfate doner
4. A pyrimidine found only in RNA.
Uracil
5. Two oxy purines.
Xanthine, Hypoxanthine
6. Two methylated purines.
Caffeine, Theophylline
7. Two nucleotides that act as secondary hormone messengers.
cAMP, cGMP

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8. The functions of methylated purines.
Act as CNS stimulant
Act as Diuretics
Their catabolism is not uric acid
9. Two free uracil nucleotides & mention their functions.
UDP Glucose > synthesis of Glycogen & Glycoprotein
UDP Galactose > synthesis of Lactose & Glycoprotein
10. Two free adenine nucleotide act as chemical group donors.
SAM > Methyl doner
PAPS > Sulfate doner
11. Two coenzymes containing adenine.
NAD, NADP, FMN, FAD
12. Two small RNA species & mention their functions.
- mRNA, carries a message from DNA in nucleus to ribosomes in cytoplasm, it
directs protein synthesis
- tRNA, Carries the aa that needed for protein synthesis to ribosome
III-On biochemical basis explain:
1. Methylated purines are not contraindicated in diet in case of gout
(hyperuricemia).
Because the catabolism of these purines is not producing uric acid.

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2. cAMP acts as a hormone second messenger.
As Many enzymes involved in certain metabolic pathways are regulated by
phosphorylation and dephosphorylation.
Hormone binds to receptor in cell membrane → Activation of
G protein → Activation of Adenylate cyclase → ↑ cAMP → Activates protein
kinase A → Phosphorylation of the enzyme.
Glucagon and adrenaline activates adenylate cyclase → ↑ cAMP → Activates
proteinkinase A → Phosphorylation of the enzyme.
Dephosphorylation occurs by another enzyme (Protein phosphatase)
Protein phosphatase is activated by insulin and inhibited by cAMP
Insulin activates Phosphodiesterase and protein phosphatase →↓ cAMP level
→Dephosphorylation of the enzyme.
Glycogen synthase: The active form is dephosphorylated
Glycogen phosphorylase kinase: The active form is phosphorylated

3. Methylated purines of dietary origin have biological importance (explain and

mention two examples of methylated purines).
Act as CNS stimulant
Act as Diuretics
Their catabolism is not uric acid so it’s allowed in case of Gout
e.g .
Caffeine > present in coffee
Theophylline > present in tea

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4. Different effects of glucagon and insulin on CAMP
Glucagon activates adenylate cyclase → ↑ cAMP → Activates protein kinase A →
Phosphorylation of the enzyme.

Insulin activates Phosphodiesterase and protein phosphatase → ↓ cAMP level

→Dephosphorylation of the enzyme.

5. The role of nitric oxide as a vasodilator.

Nitric oxide activates guanylate Cyclase, thus, cGMP leading to vasodilation
smooth muscle relaxation because cGMP acts as a 2nd hormone messenger,
antagonist to cAMP.

6. Myopathies are maternally inherited diseases.

Mitochondria are provided by the ovum, thus, mtDNA is maternal inherited.
Mutation in mtDNA leads to myopathies , replication by DNA polymerase

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IV-Compare between:
1. DNA and RNA

2. A & Z forms of DNA

3. Monocistronic & polycistronic mRNA.

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 Replication
III-Enumerate:
1-Eukaryotic DNA polymerase enzymes & mention their functions.
- DNA polymerase -primase complex: for synthesis of RNA primers and short
DNA stretches connected to the RNA primers.
- DNA polymerase  : for DNA repair.
- DNA polymerase  : for mitochondrial DNA synthesis.
- DNA polymerase δ : for synthesis of lagging strands.
- DNA polymerase ε : for synthesis of leading strands
2- Prokaryotic DNA polymerase enzymes & mention their functions.
DNA polymerase I: filling of the gaps and proofreading and DNA repair
DNA polymerase II: proofreading and DNA repair
DNA polymerase III: synthesis of both leading and lagging strands.

3-The functions of single strand binding (SSB) proteins, dna A, dna B & dna C.
1- A unique origin (ori C) (rich in AT base pairs)
2- Binding of dna A protein to ori C produces local opening and unwinding of DNA.
B- Formation of Prepriming Complex at the Two Replication Forks:
1- A complex of dna B and dna C also binds to ori C, dna B is a helicase that
produce
unwinding of DNA double helix.
2- Single strand binding (SSB) proteins bind to the single strand cooperatively to
prevent rewinding and protect the single strand from nucleases

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IV- On biochemical basis explain:
1.The importance of telomerase enzyme in replication.

2.Cancer cells do not age.

Cells that do not age (for example, germ-line cells and cancer cells) contain an
enzyme called telomerase that maintain telomere ends.

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3. Telomeres have a protective role in chromosomes.
DNA at the parent 3'-end is a few hundred nucleotides longer than the
complement lagging strand forming single stranded region. The single-stranded
region folds back on itself forming a structure that is stabilized by protein to
protect the ends of the chromosomes from nucleases

4. Topoisomerases play an important role in replication.

5. Telomeres are a target for cancer chemotherapy.

In cancer cells, telomerase is reactivated so it is target for chemotherapy.

6. DNA replication is semi-conservative

The newly formed DNA molecules contain one of the original strands and a new
complementary strand. This process is called semi conservative replication.

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V-Compare:
1.DNA polymerases of replication in prokaryotes and eukaryotes.

33
2. Type I and Type II topoisomerases.

3.The function of DNA polymerase β and DNA polymerase ε in eukaryotic

replication.
- DNA polymerase  : for DNA repair.
- DNA polymerase ε : for synthesis of leading strands

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 Transcription
III-Enumerate:
1. Types of RNA polymerases in eukaryotes referring to their functions.
- RNA polymerase I: It transcribes 18S, 5.8S and 28S ribosomal RNA genes.
- RNA polymerase II: It transcribes mRNAs, and most
small nuclear RNAs (sn RNAS), miRNA.
- RNA polymerase III: It transcribes, tRNAs, 5S rRNA, one sn RNA

2.post-transcriptional modifications of mRNA mentioning the importance of each.

- Methyl guanosine cap is added at 5' end in cytosol.
- RNA triphosphatase is involved in 5' cap formation.
- It hydrolyzes terminal -phosphate of nascent pre mRNA to form diphosphate.
- Then it is capped with GMP by the enzyme RNA guanylyl transferase.
- Then GMP is methylated at position 7 by SAM.

IV-On biochemical basis explain:

1.RNA editing changes mRNA after transcription.
- Coding information in mRNA is changed by editing as follow:
- in liver apoB gene is transcribed to mRNA to give apoB-100 protein
- in intestine the same gene is transcribed to mRNA then by cytidine deaminase
CAA codon is converted to UAA which is stop codon, so apoB-48 is formed

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2.The sigma factor (σ) and the rho factor (p) have different roles in prokaryotic
RNAsynthesis.

3. The role of σ subunit (sigma factor) in initiation of transcription.

It works during intiation
It binds TATA box for intiation of transcription
No ATP is needed

36
4. The estimated number of proteins exceed the number of genes.
1- It decreases the incidence of mutations.
2- Alternative splicing may lead to the formation of different types or new types
of mRNA molecules or proteins.
N.B:
-. Systemic Lupus erythematosus (SLE) is an autoimmune disease characterized by
autoantibodies against Small nuclear ribonucleoproteins (snRNPs).
-. One type of ß-thalassemia results from a nucleotide change at the intron-exon
junction leading to failure to remove the introns and hence decreased synthesis
of the  globin chain.

5.TFIIH has bifunctional activity.

- TFIIH has a kinase activity that activates RNAP by its phosphorylation and a
helicase activity and separates the two strands of DNA for initiation.
- This is followed by release of TFII A, B, E & H. Then, Pol II-TFIIF complex leaves
the promoter region, moves towards the +1 nucleotide and starts to synthesize a
complementary transcript of the template DNA strand.

6.The ribonuclease does not attack the 5' end of the mature mRNA
- Methyl guanosine cap is added at 5' end in cytosol.
- RNA triphosphatase is involved in 5' cap formation.
- It hydrolyzes terminal -phosphate of nascent pre mRNA to form diphosphate.
- Then it is capped with GMP by the enzyme RNA guanylyl transferase.
- Then GMP is methylated at position 7 by SAM.

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V-Compare:
1.The importance of capping and splicing of mRNA.
Importance of capping (explain):
- It protects the 5 -end from ribonucleases which are specific for 3`-5
phosphodiester bonds.
- It Facilitates initiation of protein synthesis through binding with a specific cap
binding proteins

Importance of splicing (explain):

- It decreases the incidence of mutations.
- Alternative splicing may lead to the formation of different types or new types of
mRNA molecules or proteins.

2.Sigma(σ)and Rho(p)factors.

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3.Prokaryotic and eukaryotic promoters.

4.Prokaryotic and eukaryotic RNA polymerase(s).

- RNA polymerase holoenzyme in prokaryotes synthesis of all types of RNA except
RNA primer
*There are three types of RNA polymerases in eukaryotes:
- RNA polymerase I: It transeribes 8S 5 8S and 28S ribosomal RNA genes.
- RNA polymerase I: It transcribes mRNAS, and most small nuclear RNAS (sn
RNAS), miRNA
- RNA polymerase I: It transcribes, IRNAS, 5S rRNA. one sn RNA

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5.Termination of transcription in prokaryotes and eukaryotes.

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 Translation
IV- Enumerate:
1. Four causes of mutations.
- Error of replication
- Error of recombination events
- Exposure of chemical mutagens
- Exposure of irradiation
2. Four characteristics of the genetic code.
Specificity
Degeneracy
Universality
Reading frame
3. Four requirements for translation.
1. rRNA and Ribosomes (which contain the enzyme peptidyl transferase).
2. Amino acids.
3. mRNA
4. tRNA: carry the activated amino acid.
5. Aminoacyl tRNA synthetase.
6. Source of energy (ATP and GTP).
4. Three differences between eukaryotic and prokaryotic translation.

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5. Four posttranslational covalent modifications, giving an example for each.
Phosphorylation > serine
Glycosylation > serine
Acetylation > chromatin remodeling by histone
Hydroxylation > proline
6. Four causes for gene mutation.
- Error of replication
- Error of recombination events
- Exposure of chemical mutagens
- Exposure of irradiation
7. Two mechanisms that may lead to errors in replication.
Base substitution mutation
Deletion of one or more base
8. Three effects of point mutation.
Mis sense
Non sense
Silent mutation

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V-On biochemical basis explain:
1. tRNA can recognize more than one codon for a specific amino acid.
20 aa charge 50 tRNA: As some aa have more than 1 tRNA
A charged tRNA may recognize more than 1 codon: This is due to Wobble theory
There is close apposition between the 1st 2 bases on mRNA & the corresponding
2 bases on tRNA
While there is no close apposition between the 3rd base on mRNA & that on tRNA
(Unusual base pairing) this allows some tRNA to recognize more than 1 codon
2. The three classes of RNA are required for translation.
As
- rRNA and Ribosomes contain the enzyme peptidyl transferase.
- mRNA template which is read by the ribosome for the correct addition of aa
- tRNA carry the activated amino acid.

3. IF4 plays an important role in translation.

As Initiation requires 4 IFs (1, 2, 3 & 4)
The 40S subunit of the 80S ribosome binds to the 5` cap of the mRNA with the help
of IF-4. It scans the mRNA to reach the initiation codon (AUG).

4. The two binding sites on the 80S ribosome play important role in translation.
• The 40S subunit of the 80S ribosome binds to the 5` cap of the mRNA with the
help of IF-4. It scans the mRNA to reach the initiation codon (AUG).
• The 60S subunit of the 80S ribosome binds to the 40S subunit forming the
completed Initiation step.
• The 60S subunits contains the enzyme peptidyl transferase in Elongation step

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5. Release factor plays an important role in translation.
Release factor (RF) binds to the A site in Termination step
6: Trimming is a very important posttranslational modification
-Many proteins secreted from the cell are made of large precursor molecules that
are inactive.
-Part of the large protein is removed by endoproteases for activation.
-The site of trimming differs from protein to another one.
Intracellular: As insulin ....Preproinsulin →Proinsulin → Insulin
Extracellular: -as Pepsinogen: Activated to pepsin in the stomach.
-as Trypsinogen: Activated to trypsin in the intestine.

7. Covalent modification is very important posttranslational process.

- Alter the activity or stability of the protein.
- Direct the protein to the cellular compartments.
- Prepare the protein for secretion from the cell.
Covalent modifications include:
• Phosphorylation:
occurs by kinase… Phosphate is added to OH of serine, threonine, or tyrosine.
• Glycosylation:
forming glycoproteins or proteoglycans.
O-linked glycoproteins: CHO is linked to OH of serine or threonine.
N-linked glycoproteins: CHO is linked to amide group of asparagine.
• Acetylation or methylation:
The N-terminal amino acid is sometimes acetylated or methylated.
e.g. chromatin remodeling by histone acetylation.

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8. DNA contains thymine but not uracil.
DNA uses thymine instead of uracil because thymine has greater resistance to
photochemical mutation, making the genetic message more stable. ... Outside of
the nucleus, thymine is quickly destroyed. Uracil is resistant to oxidation and is used
in the RNA that must exist outside of the nucleus.

9. Base substitution (point mutation) may have no effect or may cause serious
effects.
• Mis-sense mutation:
Depending on the amino acid changed mis-sense mutation may
have no effect or serious effect as in sickle cell anemia.
• Non-sense mutation:
This leads to premature termination of translation and the
resulting protein is non-functioning as in thalassemia
• Silent mutation:
Leads due defective termination of translation and production of abnormal large
protein.

10. Deletion mutation may or may not result into frame shift.
Depends on number of deletion bases
- If it 1 or 2 bases, then will result Frame shift mutation
- If it 3 or multiply 3 bases, then leads to no change in frame shift mutation and it
is less severe

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VI-Compare:
1. The effect of a missense mutation and a nonsense mutation

2. Eukaryotic and prokaryotic translation

3. Missense & silent mutations

4. Silent & nonsense mutations

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