L13-15: Building Blocks of Life

Question 1

What are the functions of DNA?

Answer 1

Genetic code
Storage within cell
Accessibility for transcription
Replication
Meiosis
Genome integrity

Question 2

How is DNA stored in the cell?

Answer 2

From DNA to histone to nucleosomes + chromatin to further condensation then duplicated chromosome

Question 3

How does DNA become more accessible for transcription?

Answer 3

Changes binding to histone proteins

Question 4

What are the 2 main types of variation from meiosis?

Answer 4

Crossing over and chromosome segregation

Question 5

Which bases are purines and which bases are pyrimidines?

Answer 5

Purines: Adenine, Guanine
Pyrimidines: Cytosine, Uracil and Thymine

Question 6

What are differences between ribose and deoxyribose?

Answer 6

Ribose has a hydroxyl group on C2

Question 7

What is a nucleoside composed of?

Answer 7

Base + sugar
Pyrimidine N1 attached to sugar C1

Question 8

What is a nucleotide composed of?

Answer 8

Base + Sugar + phosphate
Purine N9 attached to sugar C1
Pyrimidine N1 attached to sugar C1

Question 9

What is the polymeric structure of DNA and RNA?

Answer 9

Linear polymer formed by 3’-5’ phosphodiester bonds
Acidic sugar phosphate backbone
5’-3’ direction

Question 10

Is DNA or RNA more stable?

Answer 10

DNA >100x

Question 11

Why is DNA more stable than RNA?

Answer 11

Due to the attraction of the hydroxyl group on the RNA which increases the chance of the chain being broken

Question 12

What are Chargaff’s rules?

Answer 12

[A]=[T]
[G]=[C]
Number of bases vary between organisms

Question 13

Who used X-ray crystallography to visualise proteins?

Answer 13

Franklin and WIlkins

Question 14

Why were X-rays used?

Answer 14

As they have a high frequency and short wavelength

Question 15

What is the spacing between the inter-plane distance? (Franklin and WIlkins plate 51)

Answer 15

3.4 Angstrom (Å)

Question 16

How big is the radius? (Franklin & Wilkin plate 51)

Answer 16

10Å

Question 17

What are the properties of the Watson and Crick model?

Answer 17

2 anti-parallel strands
5’-3’
3’-5’
Right-handed double helix
Backbone outside
Specific base pairing
A-T
G-C

Question 18

Approximately how many base pairs are there per turn?

Answer 18

10

Question 19

What are the features of structural stability in DNA?

Answer 19

Hydrophobic effect
Base pair hydrogen bonds
Base pair stacking
Cooperativity

Question 20

Which part of the DNA is information-rich?

Answer 20

Major groove

Question 21

How wide is the major groove?

Answer 21

22Å wide

Question 22

How wide is the minor groove?

Answer 22

12Å wide

Question 23

What are the 3 types of DNA and what are their properties?

Answer 23

A-DNA: right handed (dehydrated DNA)
B-DNA: right handed
Z-DNA: left handed (lots of salt/supercoiling)

Question 24

What type of replication occurs in DNA?

Answer 24

Semi-conservative replication

Question 25

How are mistakes in DNA replication removed?

Answer 25

3'-5' exonucleases

Question 26

What is the origin or replication (oriC)

Answer 26

Circular genome Single origin in E.coli Five copies of DNA-A binding sequence AT-rich tandem array of 13mers DNA-A assembly stimulates unwinding of AT-rich array

Question 27

How does DNA-B helicase work?

Answer 27

Recruited by DNA-A Loaded around ssDNA ATPase-dependent translocation Strand exclusion model

Question 28

How does single stranded binding (SSB) protein work?

Answer 28

Loaded on to ssDNA ssDNA wrapped around SSB tetramers Prevents secondary structure forming

Question 29

What is the initiating step of the pre-priming complex?

Answer 29

DNA-A assembly stimulates unwinding of AT-rich array and recruits DNA-B

Question 30

What is the loading step of the pre-priming complex?

Answer 30

DNA-C is a loading factor that complexes with C-terminus of DNA-B. Following helicase closure around ssDNA, DNA-C hydrolyses ATP and dissociates

Question 31

What is the activation step of the pre-priming complex?

Answer 31

DNA-G synthesises short strands of RNA known as oligonucleotides during DNA replication

Question 32

What type of primer is used with the primase enzyme?

Answer 32

RNA

Question 33

What is primase?

Answer 33

Primase DNA-G, synthsises RNA primer and is recruited by DNA-B

Question 34

What is toopoisomerase I?

Answer 34

They are enzymes that release tension (relax) supercoiled DNA

Question 35

How does topoisomerase I work?

Answer 35

It cleaves (breaks) one strand Passes the cut end under the other strand Reseals the break

Question 36

What is topoisomerase II?

Answer 36

Catalyses untangling of the DNA duplexes

Question 37

How does topoisomerase work?

Answer 37

Cleaves both strands Passes separate duplex through break Reseals the break

Question 38

What are the components of DNA polymerase III? (at alpha unit)

Answer 38

Fingers Palm Thumb 5'-3' DNA synthesis Error rate 1 in 10^3-10^4

Question 39

What are the components of DNA polymerase III? (Exonuclease domain)

Answer 39

3'-5' exonuclease Proofreading Reduces error rate 1 in 10^6-10^7

Question 40

What are the components of DNA polymerase III? (Sliding clamp- beta 2)

Answer 40

35Å diameter hole accommodating dsDNA Keeps polymerase in contact with DNA Increases processivity 1-5kb added before falls off

Question 41

What is the lagging stand problem?

Answer 41

DNA polymerase synthesis 5'-3' but lagging strand grows 3'-5'

Question 42

What happens when lagging strand replicates?

Answer 42

It is separated into fragments called Okazaki fragments

Question 42

How is DNA polymerase III holoenzyme used?

Answer 42

2 DNA polmerases follow DNA-B helicase for coordinated synthesis of leading and lagging strands

Question 43

What is the Trombone model?

Answer 43

Looping of lagging strand Lets go after 1000 nts New loop then formed Loop lengthens then shortens like a trombone slide

Question 44

How are Okazaki fragments sealed?

Answer 44

Using DNA ligase and DNA polymerase I (synthesises degrading of DNA/RNA in front)

Question 45

What are the different DNA damaging agents?

Answer 45

DNA replication stress Oxygen radicals Ionising radiation Chemotherapeutics Polyaromatic hydrocarbons UV light

Question 46

What are the different types of DNA damage?

Answer 46

Base mismatches ssDNA breaks DNA adducts (intrastrand crosslinks) dsDNA breaks (Interstrand crosslinks)

Question 47

What are the 2 most common cancer genes?

Answer 47

BRAC 1&2 (breast cancer genes)

Question 48

What is homologous recombination?

Answer 48

Double strand DNA breaks another dsDNA interacts with the end resection so the invasion allows DNA synthesis which repairs the damage, ligation takes place and areas of DNA are crossed over

Question 49

What is dideoxy sequencing?

Answer 49

2',3' dideoxy analogues (ddNTPs) Form truncated products (chain stops when ddNTPs added)

Question 50

How did dideoxy sequencing help discover DNA base sequence?

Answer 50

Gel electrophoresis showed bands at the ddNTP areas which allowed for DNA sequencing (used fluorescent dyes)

Question 51

What are the 3 different types of sequencing methods?

Answer 51

Dideoxy sequencing with fluorescent ddNTPs Capillary DNA sequencing Next generation sequencing