Molecular Biology And Biochemistry DNA

Question 1

Characteristic components of nucleotides

Answer 1

Nitrogenous base
One or more phosphates
A Pentose sugar

Question 2

Why is ribose sugar more reactive the deoxyribose

Answer 2

It’s more reactive and unstable because of the OH group on the 2 carbon

Question 3

Which bases are purines

Answer 3

Adenine and guanine

Question 4

Which bases are pyrimidines

Answer 4

Thymine, uracil and cytosine

Question 5

What is a pyrimidine

Answer 5

Single ring nitrogenous base

Question 6

Structure of dna

Answer 6

Two anti parallel strands
Each strand has a 5’ (phosphate) and 3’ end (hydroxyl)
Held together by hydrogen bonds
Antiparallel nature allows for h bond formation
Bases planar to sugar phosphate backbone

Question 7

What evidence proved dna helical structure

Answer 7

X ray diffraction

Question 8

How does the x ray diffraction of dna show a helical structure

Answer 8

X shape which is indicative
Layer line which shows the length of one complete turn

Question 9

The common features of B-DNA

Answer 9

Right handed double helix
Hydrophobic core
Hydrophilic backbone
Major and minor groves

Question 10

Factors towards the stability and structure of the double helix

Answer 10

Backbones separated as far apart as possible to avoid electrostatic repulsion
Bases form stablizing h bonds
Bases stack to maximise aromatic ring interactions

Question 11

How many hydrogen bonds form between the bases

Answer 11

A +t 2
C + g 3 (

Question 12

Why doesn’t non standard base pairing work

Answer 12

Distorts the geometry of the double helix the bases are no longer 1.1 nm apart

Question 13

Why are their aromatic stack interactions

Answer 13

Benzene contains an e in all p orbitals which can delocalise and form a ring of electron density around the planar ring

Question 14

Why is displacement stacking better then eclipse stacking

Answer 14

Maximises attractive interactions between dipoles

Question 15

Why are there major and minor groves

Answer 15

The glycosidic bonds between bases are the same distance apart so nucleotides must be at an angle
They allow for dna bonding proteins to read dna without unwinding the helix

Question 16

Why does DNA have thymine not uracil

Answer 16

Cytosine can delaminate to uracil therefore uracil is identified and removed in dna repair processes

Question 17

Why does RNA have uracil not thymine

Answer 17

Thymine is more energetically costly to produce as a methylated uracil
There’s no bio synthetic pathway for it to be produced

Question 18

Why is rna less stable then dna

Answer 18

OH group on c2 acts as an internal nucleophile and causes the breakage of the phosphodiester backbone

Question 19

What end are nucleotides added to in replication

Answer 19

3’

Question 20

How does chain elongation occurs

Answer 20

The OH group on c3 has a nucleophilic attack on the primary phosphate group of another nucleotide. Hydrolysis of the other two phosphates provide energy for the reation

Question 21

What are the steps to separate the double helix

Answer 21

Helicase opens the helix by breaking the weak h bonds between bases
Topoisomerase releaves the tension in the helix by breaking the dna and reasealing to the right of the replication fork ahead of the helicase
Single stranded dna binding proteins bind to separate strands to prevent annealing

Question 22

How does dna get a 3’ OH end to start replication

Answer 22

Short rna primer is made by dna primase

Question 23

How does the antiparallrl nature of dna cause problems

Answer 23

Lagging strand is synthesised discontinuously

Question 24

What are the discontinuous stands of dna in the lagging strand called

Answer 24

Okazaki fragments

Question 25

How does replication occurs on lagging strand

Answer 25

Dna primase creates rna primers Dna polymerase III extends the dna from 3’ OH and makes Okazaki fragments Dna polymerase I removes RNA primase and fills gaps Dna Ligase joins discontinuous gaps

Question 26

What’s in place to prevent dna polymerase detaching

Answer 26

Sliding clamp protein complex

Question 27

Source of error in dna repl

Answer 27

Frameshifts Substitution mutations

Question 28

How are incorrect bases corrected

Answer 28

Dna polymerase has exonuclease activity that can remove the wrong base

Question 29

What different in the replication of circular dna

Answer 29

2 replication forks as single place of origin Dna has multipul origins of replication

Question 30

Base requirements of transcription

Answer 30

Ribonucleoside triphosphates (NTPs) A template Rna polymerase An energy source

Question 31

How is the correct place in the genome found for transcription

Answer 31

Promoter region containing specific sequences for rna polymerase and regulatory proteins

Question 32

How does rna polymerase bind to promoter

Answer 32

Sigma subunit between -35 and -10

Question 33

How does transcription stop

Answer 33

Rna polymerase has a hairpin structure of that are complementary to termination area causing release

Question 34

What the protein coding region also called

Answer 34

Open reading frame

Question 35

Transcription in prokaryotes

Answer 35

Proteins coded for that have similar function are located next to each other and transcribed together in a single mRNA called an operon

Question 36

Features of translation

Answer 36

Code must translate to one of twenty amino acids Involves ribosomes and tRNA mRNA read as triplet codons

Question 37

What are the three stop codons

Answer 37

UAA UAG UGA

Question 38

How are amino acids attached to tRNA

Answer 38

Aminoacyl-tRNA enzymes

Question 39

What are the three binding sites in ribosomes

Answer 39

Peptidyl Exit Aminoacyl

Question 40

How is translation initiated in prokaryotes

Answer 40

In the 5’ untranslated region, the shine-dalgarno pairs with the 16S rRNA which places the AUG in the p site of ribosome A modified methionine is used for the initiating amino acid

Question 41

How is translation initiated by eukaryotes

Answer 41

The small ribosomal subunit and initiating tRNAi-Met bonds to 5’ cap and scans until AUG

Question 42

Translation elongation

Answer 42

A charged aminoacyl tRNA enters the A site and pairs with anticodon Peptide bond is formed between the two amino acids which breaks the covalent bond between the amino acid and tRNA at p-site The tRNA that was in the p site leaves by e site and the tRNA with the peptide chain moved to P site freeing A site This repeatedly occurs untill a stop codon enters the a site Release factors stimulate hydrolysis of polypeptide from tRNA

Question 43

How is DNA amplified

Answer 43

Polymerase chain reaction (PCR) Created by Kary Mullis

Question 44

What process is PCR based on

Answer 44

Dna replication

Question 45

How many primer are needed for PCR

Answer 45

2 one for each stand of dna

Question 46

What is the process of PCR

Answer 46

Heated to 96 to denature and break hydrogen bonds Cool to approximately 55 to allow rna primers and extremophile dna polymerase (taq polymerase) to bond Heat to 72 for extention

Question 47

What type of DNA sequencing is used for dna tech

Answer 47

Sanger sequencing

Question 48

What can be inserted to prevent further extention

Answer 48

Dideoneucleotides because it has only hydrogen on c3 so sugar phosphate backbone can’t form

Question 49

How does Sanger sequencing work

Answer 49

A mixture of dNTP and ddNTPs are added the ddNTPs with Florescent tags Dna polymerase extends strand complementary to template Generated multipul fragments of different lengths different by one nucleotide so the sequence can be discovered Fragments are separated by size by capillary electrophoresis