Macromolecules (nucleic acid)

Question 1

Structure of nucleotide

Answer 1

• phosphate grp, 5-carbon sugar and nitrogenous base
• P grp and sugar bonded via phosphoester bond
• sugar and base bonded via glycosidic bond

Question 2

different types of nitrogenous base

Answer 2

• Purine (BIGGER): Adenine, Guanine
• Pyrimidine (SMALLER): Thymine/Uracil, Cytosine

Question 3

Difference between sugar in DNA and RNA

Answer 3

• 2’ C in RNA is OH, as compared to DNA which has H as 2’ C
• partial (-) charge in OH repels partial (-) charge of P
• thus preventing RNA chain from coiling in as tight a helix as in DNA
• thus RNA is more susceptible to chemical and enzyme degradation

Question 4

How nucleotides are joined tgt to form polynucleotide

Answer 4

via condensation reaction
between 5’-phosphate grp of one nucleotide
and 3’-OH grp of another
to form phosphodiester bond

Question 5

Structure of DNA

Answer 5

• consists of 2 polynucleotide strands/chains
  (- each strand forms a right-handed helix)
• which coil around each other to form a double helix
• one full DNA helix turn comprises 10 base pairs
• there is presence of major and minor groves along the length of DNA

Question 6

Reasons DNA is a device for stable storage of genetic information (resistant to mutations)

Answer 6

• extensive H bonds between base pairs
• hydrophobic interactions between stacked base pairs
  => stabilise the structure of the double helix
• hydrophobic nitrogenous bases safely tucked inside double helix (while hydrophilic phosphate grps are projected outside)
  / exposure to outside influences of only sugar-phosphate bb
  => protection of nitrogenous bases from degradation
• complementary base pairs between 2 strands
  => each strand serves a template to repair any DNA damage
• (Eukaryotes) double helix tightly wound around histones to form nucleosome
  -> folded into highly compact chromosome
  => DNA protected from thermal and physical damage

Question 7

reasons for complementary base pairing between DNA strands

Answer 7

1. steric restrictions
   - dna has regular helical structure
   -> double helix has uniform diameter of 2nm
   -> must always pair 1 purine to 1 pyrimidine
2. H bond factors
   - each nitrogenous base has side grps that can form H bonds with its appropriate partners
   - A with T (2 bonds),
   C with G (3 bonds)

Question 8

significance of complementary base pairing between DNA strands

Answer 8

1. maintains integrity of DNA
   - since base seq on 1 strand dictates base seq of other strand,
   - thus making genetic info redundant
2. DNA rep
   - where both parental DNA strands separate and act as templates for synthesis of daughter DNA strands

Question 9

gen 1 means after 1st replication

evidence for semi-conservative dna rep

Answer 9

• via density-gradient centrifugation
• gen 1: 100% of DNA mol are hybrid, resulting in only 1 band
• gen 2: 50% of DNA mol are hybrid and 50% are light, resulting in 2 separate bands

Question 10

gen 1 means after 1st replication

evidence for conservative rep

Answer 10

• via density-gradient dna centrifugation
• gen 1: both light and heavy DNA molecules, resulting in 2 separate bands

Question 11

gen 1 means after 1st replication

evidence for dispersive dna rep

Answer 11

• via density-gradient dna centrifugation
• gen 2: only hybrid DNA molecules present, resulting in only 1 band

Question 12

1st level of condensation of packaging of DNA in cell

Answer 12

• DNA is coiled around histone proteins, forming nucleosome core
• histones have (+)-charged residues, which form ionic bonds with (-)-charged sugar-phosphate bb of DNA
• nucleosome cores, together with linker DNA, forms 10nm chromatin fibre

Question 13

2nd level of condensation of packaging of DNA in cell

Answer 13

• DNA is further coiled to produce 30-nm solenoid
• histone H1 and linker DNA are involved in coiling

Question 14

3rd level of condensation of packaging of DNA in cell

Answer 14

• scaffold proteins are involved
• in condensing the 30-nm solenoid to form looped domains
• which further coil to produce the 1400-nm condensed chromosome

Question 15

Advantages of chromatin being dynamic molecule

Answer 15

1. When condensed …
   - more compact to fit into the nucleus
   - has ability to save space
   - helps to maintain the integrity of DNA
2. regulation of gene accessibility
   - ability to regulate gene accessibility
   - leading to differential gene expression
   - e.g. when chromatin is organised as euchromatin (diffused form), available for transcription
   - e.g. when chromatin is organised as heterochromatin (highly condensed form), transcriptionally inactive
3. regulation of cell cycle
   - condensation of chromatin to discret chromosomes so that DNA does not get entangles and break during separation at anaphase
   - uncondensed chromatin allows for ease of DNA rep during S-phase of interphase

Question 16

DNA methylation (control of transcription at chromatin level)

Answer 16

• addition of methyl grps to cytosine nucleotides in CpG dinucleotides in promoter region of genes
• catalysed by DNA methyltransferases
• thus changing 3D conformation of DNA
• and preventing the binding of transcription factors to the promoter
• thus preventing the formation of TIC
  -> preventing transcription initiation
• methylated DNA also serves as recognition signals to recruit histone deacetylases (HDACs)

Question 17

Histone deacetylation (control of transcription at chromatin level)

Answer 17

• removal of acetyl grps of lysine residues in in histone tails
• catalysed by histone deacetylases (HDACs)
• thus lysine residues regain their (+) charges, resulting in an increase in the affinity of the histone complex for DNA
• resulting in chromatin becoming more compact
• and preventing the binding of transcription factors to promoter
  -> preventing formation of TIC
  -> preventing transcription initiation

Question 18

silencer control element (control of transcription at transcription level)

Answer 18

• specific transcription factors known as repressor binds to it
• elaboration 1 (may or may not be needed):
  
  • EITHER competitive binding with activator
    
    • where binding of repressor to silencer region prevents binding of activator to enhancer region as repressor and activator competes for binding at the same DNA regulatory seq
  • OR interaction with activation domain of bound activator
    
    • where repressor binds to activator and prevents it from interaction with GTFs
  • OR interaction with GTFs
    
    • where repressor interacts with GTFs to prevent assembly of TIC
  • results in decreased affinity of general transcription factors and RNA pol for promoter
    -> prevention of formation of TIC
    -> thus decreasing rate of transcription
• elaboration 2 (may or may not be needed):
  
  • repressor recruits histone decacetylase which removes acetyl groups from lysine R grps of histones
    OR recruits histone methyltransferases which add methyl groups to histones
  • thus promoting chromatin condensation

Question 19

why different people have different phenotypes

Answer 19

• even if genes (i.e. DNA seq) are the same, different gene expression
  -> different genes being switched on
  -> different gens being expressed
  -> different proteins being produced at diff stages
  -> leading to diff phenotypes
• different environmental factors
• like diet, where consumption of different quality diets may result in differences in weight and height
• or lifestyle, where exposure to mutagens may lead to increase in gene mutations / risk for cancer
• or exposure to sunlight, where difference in production of melanin leads to difference in skin colour

Question 20

Reason it is necessary for 2 DNA pol enzymes to work together in a protein complex during DNA rep

Answer 20

• DNA pol is only able to synthesise from 5’ -> 3’ direction
• antiparallel nature of DNA strands, hence requiring 2 DNA pol to synthesise in the same direction
• 2 strands of DNA, thus require 2 DNA pol to increase efficiency

Question 21

significance of specific combinations of control elements and transcription factors in regulating gene expression

Answer 21

• allows for regulation of gene expression at a precise timing of development
  (temporal control)
• allows for regulation of gene expression in a specific cell type
  (spatial control)
• allows for correct amt of proteins/gene pdts produced

Question 22

secondary structure of tRNA

Answer 22

• 3 loops, held by complementary base pairing within the single-stranded molecule
• where 1 loop is the anticodon
  
  • which consists of 3 bases
  • and binds to specific mRNA codon via complementary base pairing
• also consists of the 3’ CCA stem (the part that is sticking out, opp the anticodon loop)
  
  • which is the attachment site for a specific amino acid

Question 23

how tRNA acts as an adaptor molecule for translation

Answer 23

• translates base/nucleotide seq in mRNA into amino acid seq in polypeptide by …
  
  • 3’ CCA stem binds via ester bond to specific amino acid
  • decided by the anticodon on tRNA
  • anticodon on tRNA then forms complementary bases pairs with codon on mRNA
  • tRNA then binds to the A and P site to bring the amino acid in close proximity to the growing polypeptide

Question 24

function of aminoacyl-tRNA synthetase

Answer 24

• catalyses formation of ester linkage between 3’ CCA stem and amino acid
• which requires the hydrolysis of ATP
• does so by having an active site that is
  complementary to the specific anticodon seq of tRNA
  and complementary to the specific 3d conformation of specific amino acid

Question 25

reason each amino acid can be carried by more than 1 tRNA

Answer 25

active site of aminoacyl-tRNA synthetase being complementary to the same amino acid but complementary to different anticodons

Question 26

enhancer control element (control of transcription at transcriptional level)

Answer 26

• specific transcription factors known as activators bind to it
• thus recruiting DNA-bending proteins causes looping of DNA, (thus bringing activator closer to promoter)
• activator then interact with mediator protein, resulting in
  a. increased affinity of TFIID and RNA pol for promoter to form** stable TIC**
  b. facilitation of proper positioning of TIC
  => rate of transcription increases
• may also recruit histone acetylase which add acetyl groups to lysine R groups of histone
  OR recruit chromatin-remodeling complexes
• thus resulting in **looser packing of chromatin **

Question 27

role of promoter and how it influences transcription

Answer 27

• serves as recognition site for binding of general transcription factors and RNA pol
• has critical element TATA box, to which general transcription factors bind to,
  and thus mediate binding of RNA pol to promoter to form TIC
• initiate transcription

Question 28

differences between chromosome and chromatin

Answer 28

• chromosome: highly condensed form of DNA
  chromatin: loosely-coiled and decondensed form of DNA
• chromosome: transcriptionally inactive
  chromatin: transcriptionally active
• chromosome: has 2 sister chromatids that are visible
  chromatin: do not have visible sister chromatids