Assignment 1

/100 marks

Due: At the end of Unit 5

Weight: 20% of the final grade

Questions 1 to 20 are related to material selected from Units 1 to 5 of the Study Guide and

pertinent reading material from the textbook. The remaining questions refer to the paper

below, which you can access through the CHEM 301 Digital Reading Room.

Talhaoui, I., Shafirovich, V., Liu, Z., Saint-Pierre, C., Akishev, Z., Matkarimov, B.T., Gasparutto,

D., Geacintov, N.E., and M. Saparbaev. (2015). Oxidatively Generated Guanine (C8)-

Thymine(N3) Intrastrand Cross-links in Double-stranded DNA are Repaired by Base Excision

Repair Pathways. Journal of Biological Chemistry, 290: 14610.

(3 marks)

1. What is a redox reaction? Why are redox reactions common in biological systems?

Give an example of a redox reaction.

An oxidation-reduction (redox) reaction is a type of chemical reaction that involves a transfer of

electrons between two species. An oxidation-reduction reaction is any chemical reaction in

which the oxidation number of a molecule, atom, or ion changes by gaining or losing an

electron. Redox reactions are common and vital to some of the basic functions of life,

including photosynthesis, respiration, combustion, and corrosion or rusting.

Cellular respiration is a biological process in which organic compounds are converted into

energy. ... We shall soon see how the cell uses a series of redox reactions to break down

glucose to release energy. That energy is used to change ADP into ATP that can be used to

power biological processes throughout the cell.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 1

 (5 marks)

2. Calculate G for the following reaction:

Glutamate  NH3 glutamine  H2O

Where the reaction occurs at 293 kelvin, the change in heat is 19,070 calories, and

the change in entropy is 90 cal/k.

Is this reaction endergonic or exergonic?

Chemistry 301: Introduction to Biochemistry :: Assignment 1 2

 (6 marks)

3. Outline the three forms or states of ATP synthase, and indicate the function of

each.

Atp synthase generally occurs in the inner membrane of bacterial cells, present in both

mitochondria and chloroplast. Its main function is to produce ATP ,necessary to power all the

cellular processes. ATP is produced through three different methods like one is through cellular

respiration in mitochondria, during photosynthesis in chloroplasts of plants and across the

inner membrane of bacteria and archaea. The binding model of the ATP synthase shows the

state of it,

ADP and Pi open to the binding site.

passage of protons causes change conformation

The loose site with ADP and Pi becomes the tight site.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 3

finally ATP released from the open site ,ADP and Pi form ATP in the tight site.

this helps in releasing ATP and binding more ADP and phosphate ,ready for the next cycle of

ATP production.

(5 marks)

4. Draw the following amino acids linked by peptide bonds:

a. aspartate

b. lysine

c. cysteine

d. tryptophan

Indicate the letter designation for each amino acid.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 4

5. The amino acid sequence shown below represents a portion of a peptide obtained

from a large protein.

1 2 3 4 5 6 7 8 9 10 11 12 13 14

15 16 17 18

Leu---His---Ile---Thr---Arg---Phe---Phe---Pro---Cys---Met---Gly---Glu---Ala---Ile---Pro---His---Thr---

Glu-

19 20 21 22 23 24 25 26 27 28 29 30 31 32

--Asp---Cys---Gln---Met---Ile---His---Cys---Pro---Arg---Lys---Gln---Pro---Tyr---Leu---

(2 marks)

a. Discuss where in this sequence one would find cross-linked disulfide bonds.

(2 marks)

b. Would you consider this molecule to be in an α-helix formation? Explain your answer.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 5

6. List two roles for proteins in vivo. Give a specific example of a protein for each.

1: Plasma proteins : Plasma proteins, also termed serum proteins or blood proteins, are proteins

present in blood plasma. They serve many different functions, including transport of lipids,

hormones, vitamins and minerals in the circulatory system and the regulation of acellular

activity and functioning of the immune system.

example-- Serum albumin

2: Cytoskeletal proteins: These are proteins that make up the cytoskeleton, flagella or cilia of

cells. Generally, cytoskeletal proteins are polymers, and include tubulin (the protein component

of microtubules), actin (the component of microfilaments) and lamin (the component of

intermediate filaments).

example-- Actin, keratin

(5 marks)

7. Draw the structures of all of the nitrogenous bases found in DNA and RNA

Chemistry 301: Introduction to Biochemistry :: Assignment 1 6

 DNA contains adenine, thymine, cytocine and guanine. instead of thymine RNA contains uracil hence RNA is

made up of adenine, cytocine, guanine and uracil

(4 marks)

8. If a DNA molecule comprised the following sequence, what would be the

complementary sequence? If the DNA sequence was transcribed to RNA, what would

be the mRNA sequence?

5-ATGCAACGCTTCAAGATAGGCATCTAA-3

Chemistry 301: Introduction to Biochemistry :: Assignment 1 7

9.

9.Using the standard genetic code described on page 132 of the textbook, interpret

the following questions:

(5 marks)

a. An mRNA molecule was found with the following sequence:

5-ACAGCUAAGCUAGCAAUGAGGAGUCUGGUAGCAAGAUGA-3

What amino acid sequence is represented here following the translation of this mRNA

molecule?

The translation of the mRNA gives the following amino acid sequence:

mRNA 5'-ACA GCU AAG CUA GCA AUG AGG AGU CUG GUA GCA AGA UGA-3'

Amino acid Thr-Ala-Lys-Leu-Ala-Met-Arg-Ser-Leu-Val-Ala-Arg-Stop

Chemistry 301: Introduction to Biochemistry :: Assignment 1 8

 (4 marks)

b. Describe how the amino acid sequence would change if the 20th base (G) was mutated to

C.

If 20th base G was mutated to C, the amino acid sequence changes in the following way,

mRNA 5'-ACA GCU AAG CUA GCA AUG ACG AGU CUG GUA GCA AGA UGA-3'

Amino acid Thr-Ala-Lys-Leu-Ala-Met-Thr-Ser-Leu-Val-Ala-Arg-Stop

Here, the 7th amino acid, Arg change to Thr.

(2 marks)

(4 marks)

10. Draw the structures of the -anomer and the -anomer of D-glucose.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 9

Glucose contain both carbonyl and alcoholic functions, the hemiacetal or hemiketacal.

A cyclic hemiacetal is formed by the reaction between one of the hydrotyl groups in the chain

and carbonyl groups at Cl.

Formation of cyclic structure introduces another chiral center resulting in two diastereomers

known as anomers.

Asymmetry is introduced at anomeric carbon. Two anomers of D-glucose are -D-glucose and -

D-glucose.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 10

 (3 marks)

11. Identify the structure below, and indicate its role or significance.

The structure given in the question is glycogen molecule. Glycogen is made up of several

glucose molecules linked to each other by a-1,4/1,6 linkages. Glucose molecules are linked

linearly by a-1,4 bond and branching is by a-1,6 bonds. Glycogen is the major storage form of

carbohydrates. The excess glucose molecules gets converted into glycogen and stored in liver.

When there is requirement of energy, the glucose molecules are produced from glycogen by the

process called as glycogenolysis.

(2 marks)

12. What type of molecule are bile acids? What is their function?

Ans)Bile acids are part of the bile system ,these are steroid acids and are Amphipathic in nature having both

hydrophilic and hydrophobic parts .They help in lipid digestion,glucose metabolism .

(6 marks)

13. Describe the structure of a biological membrane, and name three functions of a

membrane.

Structure of biological membrane

Chemistry 301: Introduction to Biochemistry :: Assignment 1 11

The biological membrane is a sandwich model, also referred to as the phospholipid bilayer,

which consists of proteins that are embedded in the bilayer, in the form of integral proteins as

well as peripheral proteins. These proteins are used in transportation of ions and chemicals and

in transportation.

Functions of the biological membrane:

Helps in selective permeability.

Helps in fluidity maintenance of the bilayer.

Helps in cell signaling.

There is a phospholipid bilayer. Phospholipids contain hydrophobic tails as well as hydrophilic

heads. This implies that the phospholipid molecules are amphipathic. The tail would be pointing

on the inner side and the head would be pointing on The outer side. These molecules are not

bound together, rather, staying together provides a complete stability to the molecule. The non

polar molecules, that are smaller in size, squeeze through the bilayer and these do not get

repelled by the hydrophobic tails.

(4 marks)

14. What type of transport is responsible for allowing glucose across the membrane?

Does this process require ATP?

Glucose transport is a secondary active transport. The GLUT or SLC2A family are a protein

family that acts as glucose transporter. Glucose transport is said to be secondary active

transport as this transport is driven by some ion carriers like Na+ ions. Hence energy released

from hydrolysis of ATP is not directly used, so it is not primary active transport. ATP-driven

carriers are said to mediate primary active transport.

In the plasma membrane Na+ is the usual co-transported ion whose electrochemical gradient

provides a large driving force for the active transport of a second molecule like glucose. The

Chemistry 301: Introduction to Biochemistry :: Assignment 1 12

Na+ that enters the cell during transport is subsequently pumped out by an ATP-driven

Na+ pump in the plasma membrane which by maintaining the Na+ gradient indirectly drives

the transport.

(2 marks)

15. Cataracts are associated with a deficiency in which vitamin? Is this a water-

soluble or fat-soluble vitamin?

Answer-:Cataract disease of eye is caused due to deficiency of Vitamin B2 (Riboflavin),

This is Water-Soluble Vitamin,

Riboflavin is a constituent of flavin mononucleotide and flavin adenine dinucleotide,FMN is

synthesize after the addition of phosphates in riboflavin and FAD formed by the transfer of an

AMP moiety from ATP to FMN,

FMN and FAD are each capable of reversibly accepting two hydrogen atoms, forming FMNH2

(or) FADH2,

The oxidized form of the isoalloxazine structure absorbs light

around 450nm,The color is lost,and ring is reduced ,

(5 marks)

16. What is feedback inhibition? What type of enzymatic control is it? Give an

example of feedback inhibition of an enzyme.

Feedback inhibition is an event where the output of a process is used as an input for control the

process of behavior itself.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 13

It is a type of cellular control mechanism in which an enzyme’s activity is inhibited by the

enzyme’s end product. It permits cells to regulate how much of an enzyme’s end product is

formed. It acts on the first enzyme unique to a given pathway. This inhibition is completed by

the help of allosteric site, which is a site on an enzyme that alters the shape of an enzyme and

the behavior of the active site. Binding of the end product to the allosteric site slows down or

stops the enzyme’s activity .

Feedback inhibition prevents waste, when more of a product is made than the requirement of

cell. It also prevents harm when too much of the pathway’s end product may actually be

harmful to the organism.

Examples of Feedback Inhibition: Feedback inhibition controls the production of amino acids.

The advantages of feedback inhibition are that the building blocks are essential to other

processes such as the Calvin cycle and glycolysis are used optimally and without waste.

Cholesterol in little amounts is useful to the cell membranes, but in large amounts, it can build

up in veins and arteries and become very harmful.

17. An experiment was performed to determine the effects of an inhibitor on the

breakdown of glycogen by an enzyme. In an accompanying experiment, the inhibitor

was added to the glycogen-enzyme suspension and reacted using the same

experimental conditions. The data obtained from these experiments is tabulated

below.

Glycogen Product Formed Glycogen onlyProduct Formed Glycogen and

(mM) (mM/min) Inhibitor (mM/min)

0.5 22.6 15.9

1.0 32.1 24.9

1.5 38.1 28.2

2.0 41.2 35.1

Chemistry 301: Introduction to Biochemistry :: Assignment 1 14

 2.5 44.7 40.0

3.0 48.5 43.3

(6 marks)

a. Draw the Michaelis-Menten and Lineweaver-Burke plots of these data.

(3 marks)

b. Determine the form of inhibition observed from these results, and explain your rationale

for this form.

(4 marks)

c. Determine the values for Km and Vmax from these results.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 15

Chemistry 301: Introduction to Biochemistry :: Assignment 1 16
 (3 marks)

18. What are Okazaki fragments?

Okazaki fragments are short , newly synthesized DNA fragments formed on the lagging strand

during DNA replication. Okazaki fragments are joined together by DNA ligase .They were

discovered by OKAZAKI in 1968. (3 marks)

19. In the absence of lactose, where does the lac repressor protein bind in the lac

operon? What happens when lactose is present?

Allolactose (modified form of lactose) is required for removing the lac repressor that is bound to

the operator region of the lac operon. Only if the repressor is removed, the RNA polymerase

can transcribe the lac genes by binding to the promoter region.

(2 marks)

20. What hypothesis do the authors propose?

Lactose or lac operon is a constitutive type of operon which is actively engaged in metabolism

and transport of lactose across the cells. It is a constitutive operon by nature which suggests

that the operon is "switched on" in the presence of repressor. The operon constitues an

operator onto which the RNA polymerase binds. The operator can be masked by the repressor

under certain conditions and thus the RNA polymerase cannot bind to it and hence, no

Chemistry 301: Introduction to Biochemistry :: Assignment 1 17

transcription and translation of lactose metabolizing enzymes takes place. This leads to

accumulation of lactose in the cells. Thus the primary site of binding for the repressor is the

operator site of the lac operon.

When there is excessive lactose present in the cells, a regulatory protein called activator is

required for essential binding and support to the RNA polymerase. The RNA polymerase then

gets stabilized since no free repressor is available to bind to the operator site. Hence, free

movement of RNA polymerase takes place on the operon thus leading to active transcription

and translation of lactose metabolizing genes. This ultimately leads to metabolism of excessive

lactose present in the cells.

(3 marks)

21. Describe the DNA damage that occurs in human cells as a result of oxidative

damage.

Oxidative damage due to reactive oxygen intermediates causes the intrastand and interstand

cross linked Lesions in DNA helix. These are difficult to remove by DNA repair

mechanism.These lesions are as result of covalent coupling of two nucleotides on opposite DNA

strands, while the coupling of two nucleotides on the same strand gives rise to intrastrand

cross-linked (IntraCL) lesions.

(3 marks)

22. How did the authors determine that base excision repair corrected errors from

oxidative damage?

Base excision repair corrected errors from oxidative damage: The author has investigated

various eukaryotic and prokaryotic bifunctional DNA glycosylases/lyases and PAGE and MALDI-

TOF/MS show that the G*[C8-N3]T* lesions in 17-mer duplexes are incised on either side of G*

Chemistry 301: Introduction to Biochemistry :: Assignment 1 18

and no fragment is recovered with G*, simultaneously T* is converted to a normal T in the 3′-

fragment cleavage products. This capability of DNA glycosylases to incise the DNA strand

adjacent to G* indicates the versatility of these base excision repair proteins.

23. What did the authors conclude about BER and NER repair systems?

The author concluded that 8,5′-cyclo-2′-deoxypurine lesions are not repaired by DNA

glycosylase-mediated BER mechanisms, but are excellent substrates of mammalian NER and

prokaryotic NER repair pathways. And both BER and NER can function in parallel in incising

the G*T* and G*CT* intrastrain cross-links in DNA.

Chemistry 301: Introduction to Biochemistry :: Assignment 1 19