Macromolecules (nucleic acid) Flashcards

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1
Q

Structure of nucleotide

A
  • phosphate grp, 5-carbon sugar and nitrogenous base
  • P grp and sugar bonded via phosphoester bond
  • sugar and base bonded via glycosidic bond
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2
Q

different types of nitrogenous base

A
  • Purine (BIGGER): Adenine, Guanine
  • Pyrimidine (SMALLER): Thymine/Uracil, Cytosine
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3
Q

Difference between sugar in DNA and RNA

A
  • 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
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4
Q

How nucleotides are joined tgt to form polynucleotide

A

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

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5
Q

Structure of DNA

A
  • 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
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6
Q

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

A
  • 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
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7
Q

reasons for complementary base pairing between DNA strands

A
  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)
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8
Q

significance of complementary base pairing between DNA strands

A
  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
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9
Q

gen 1 means after 1st replication

evidence for semi-conservative dna rep

A
  • 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
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10
Q

gen 1 means after 1st replication

evidence for conservative rep

A
  • via density-gradient dna centrifugation
  • gen 1: both light and heavy DNA molecules, resulting in 2 separate bands
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11
Q

gen 1 means after 1st replication

evidence for dispersive dna rep

A
  • via density-gradient dna centrifugation
  • gen 2: only hybrid DNA molecules present, resulting in only 1 band
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12
Q

1st level of condensation of packaging of DNA in cell

A
  • 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
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13
Q

2nd level of condensation of packaging of DNA in cell

A
  • DNA is further coiled to produce 30-nm solenoid
  • histone H1 and linker DNA are involved in coiling
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14
Q

3rd level of condensation of packaging of DNA in cell

A
  • scaffold proteins are involved
  • in condensing the 30-nm solenoid to form looped domains
  • which further coil to produce the 1400-nm condensed chromosome
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15
Q

Advantages of chromatin being dynamic molecule

A
  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
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16
Q

DNA methylation (control of transcription at chromatin level)

A
  • 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)
17
Q

Histone deacetylation (control of transcription at chromatin level)

A
  • 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
18
Q

silencer control element (control of transcription at transcription level)

A
  • 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
19
Q

why different people have different phenotypes

A
  • 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
20
Q

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

A
  • 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
21
Q

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

A
  • 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
22
Q

secondary structure of tRNA

A
  • 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
23
Q

how tRNA acts as an adaptor molecule for translation

A
  • 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
24
Q

function of aminoacyl-tRNA synthetase

A
  • 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
25
Q

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

A

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

26
Q

enhancer control element (control of transcription at transcriptional level)

A
  • 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 **
27
Q

role of promoter and how it influences transcription

A
  • 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
28
Q

differences between chromosome and chromatin

A
  • 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