DNA and genomics

Question 1

What are the monomers of nucleic acid?

Answer 1

Nucleotides

Question 2

What are the two types of nucleotides and what do they form when joined together respectively?

Answer 2

Deoxyribonucleotides -> deoxyribonucleic acid (DNA)

Ribonucleotides -> ribonucleic acid (RNA)

Question 3

What are the structures of nucleotide?

Answer 3

1. Pentose sugar
   - Ribose and Deoxyribose
   - H atom found at 2’ carbon atom in deoxyribose while OH atom found in ribose
2. Phosphate group
   - makes DNA negatively charged
3. Nitrogenous base
   - purines (2 fused ring) : Adenine and Guanine (AG)
   - pyrimidines (1-ringed structure) : Cytosine, Uracil and Thymine (CUT)

Question 4

What is located at the 3’ carbon atom of both DNA and RNA?

Answer 4

OH group

Question 5

Is DNA or RNA more chemically reactive?

Answer 5

RNA. Presence of extra OH group makes the RNA more polar and reactive.

• so DNA is more stable -> storage of genetic info
• RNA is temporary molecule meant to be broken down

Question 6

How is the nucleotide formed?

Answer 6

The 3 components are linked up to form a nucleotide via condensation reaction.

Question 7

What and how is the bond formed when a phosphate group join the pentose sugar?

Answer 7

Phosphoester bond (O-P=O) is formed when phosphate joined the sugar molecule at the 5’ carbon atom via condensation rxn

Question 8

What and how is the bond formed btw pentose sugar and base?

Answer 8

Glycosidic bond (R-C-O-R) is formed when nitrogenous base is joined to 1’ carbon atom via condensation rxn

Question 9

How is a polynucleotide formed?

Answer 9

A condensation rxn btw the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another to form a phosphodiester bond (O=POOO) and this process is repeated to form a polynucleotide.

Question 10

What is a sugar-phosphate backbone?

Answer 10

It is made up of alternating sugar and phosphate group with the bases projecting from the backbone.

Question 11

What is the structure of DNA?
(7 points but only 2 are here)

Answer 11

1. DNA molecule consists of 2 polynucleotide strands twisted around each other to form a double helix
2. The 2 strands are antiparallel
3. One complete turn of the DNA double helix comprises 10 base pairs and spans a distance of 3.4nm. Sugar-phosphate backbone face outside while nitrogenous base faces centre

Question 12

How are bases joined together btw opposite strands in DNA?

Answer 12

Hydrogen bonding.

Purine always pair with pyrimidine.
A pairs with T to form 2 H bonds while C pairs with G to form 3 H bonds via complementary base pairing.

Question 13

What is the ratio of pairings btw bases like?

Answer 13

Ratio of A : T is 1 and the ratio of C : G is also 1.

Question 14

What is the width between the 2 strands of polynucleotides?

Answer 14

Constant width (2nm) btw the sugar phosphate backbone of DNA molecule which equals to the width of a purine and pyrimidine.

Question 15

What is the bond formed between stacked nitrogenous bases?

Answer 15

Hydrophobic interactions

Question 16

What is the bond formed btw nucleotides?

Answer 16

Phosphodiester bond

Question 17

How can H bonds, phosphodiester bond and hydrophobic interactions help the molecule?

Answer 17

They help to stabilize the structure of the double helix.

Question 18

Which mechanism allows DNA replication?

Answer 18

Semi-conservative mechanism

Question 19

How does the semi-conservative replication occur?

Answer 19

Through this mechanism, both strands of a DNA molecule separate and act as templates for the synthesis of new daughter strands

Hydrogen bond formed between bases of parental strand and newly-synthesized daughter strand to form a daughter DNA molecule.

Question 20

Briefly state the steps for semi conservative DNA replication.

Answer 20

1. Before the replication, free nucleotides are synthesized in the cytoplasm and transported into the nucleoplasm via nuclear pores into the nuclear envelope.
2. Initiation of DNA replication
3. Synthesis of new DNA strands.

Question 21

What are the roles of proteins and enzymes involved in the initiation of DNA replication?

(5 proteins involved)

Answer 21

1. Helicase - binds to origin of replication, causing DNA to unwind and unzip
2. Topoisomerase - prevent supercoils by making transient double-stranded breaks in the DNA molecule and reseals it
3. Single-stranded binding protein (SSBP) - prevent reannealing (reformation of H bonds) and degradation of ssDNA
4. DNA polymerase III - unable to synthesize polynucleotide by its own and can only add deoxyribonucleotides to the free 3’OH end of the growing DNA strand
5. Primase - synthesize RNA primer

Question 22

what is a gene mutation?

Answer 22

permanent change in the nucleotide sequence of a gene (found in a DNA)

Question 23

what is the link between nucleotide, nucleic acid, mRNA, amino acids, proteins… etc ?

Answer 23

nucleotides -> nucleic acids (e.g DNA) -> mRNA -> amino acids (in a polypeptide) -> protein

gene is a specific segment of DNA that determines amino acids sequence in polypeptide which determine the function and stucture of protein.

Question 24

what is the difference between polynucleotide and nucleic acid?

Question 25

How does alteration of a nucleotide sequence affects an organism | link to a.a -> protein...

Answer 25

change in sequence of nucleotides in a gene -> change in codon sequence in mRNA -> change the sequence of amino acids in a polypeptide -> (if change in physical and chemical properties of amino acid's R group) -> change in 3D conformation of the protein and function (types of bonds)-> change in phenotype of an organism

Question 26

what is point mutation?

Answer 26

change in only one base

Question 27

1 codon is made up of _ bases

Answer 27

3

Question 28

What are the types of mutations in DNA

Answer 28

1. Base substitution 2. Base deletion 3. Base insertion

Question 29

What are the effects of mutation in DNA? | 4 types

Answer 29

1. silent mutation - Due to** degeneracy of the genetic code** -> ...changed codon codes for the same amino acid -> no change in amino acid sequence coding for protein -> no obervable change in phenotype 2. missense mutation - Change in nucleotide sequence -> codon that codes for diff a.a -> phenotype altered 3. nonsense mutation - change in nucleotide sequence change codon that codes for a.a into a stop codon -> translation will be terminated prematurely -> polypeptide formed truncated -> non-functional protein - * may result in frame-shift 4. frameshift mutation - change in the *reading frame* of the mRNA template during translation -> ribosomes begin to read incorrect triplets from the point of deletion or insertion -> non-functional protein formed

Question 30

Why is sickle-cell anaemia formed?

Answer 30

- haemaglobin S (HbS) is produced due to single-base substitution where thymine is replaced by adenine in the gene coding for B-globin chain - in the mRNA produced, one of the codon changed from GAA (coding for a.a glutamate) to GUA (coding for a.a valine)

Question 31

what codes for what?

Answer 31

*codon* codes for *amino acids*

Question 31

how does glutamate differ from valine?

Answer 31

glutamate is hydrophilic while valine is hydrophobic

Question 32

What causes the HbS to form fibres?

Answer 32

**At low O2 concentration**, the **hydrophobic** portions of the HbS molecules stick together, causing the **HbS moleucles to polymerise into fibres**. This causes the **red blood cell** to *change from circular biconcave chape to sickle-shape*.

Question 33

What causes the sickle-shaped?

Answer 33

RBC forms the sickle-shape due to the fibres formed inside the cell

Question 33

What is the problem of sickle-cell RBC? | 3 big ones

Answer 33

- obstruct blood capillaries -> deprives multiple organs fo O2 -> cause damage - more rigid and fragile thatn normal RBC -> shorter life span -> haemolyse readily resulting in anaemia - accumulate in spleen for destruction -> enlargement of the spleen

Question 34

wha is nuclease?

Answer 34

enzyme that break down nucleic acid