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biochemistry > LM5 DNA and molecular biology > Flashcards

LM5 DNA and molecular biology Flashcards

1
Q

how is DNA organised in bacteria

A

in the nucleoid in plasmids
bacterial chromosomes are usually circular and occupies more than 1/4 of the volume of the cell

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2
Q

how is DNA arranged in most eukaryotes

A

Nuclear DNA is in linear chromosomes and the mitochondrial genome is circular.

In plants the DNA is in the nuclei, mitochondria and chloroplasts

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3
Q

how does mitochondrial and chloroplast DNA differ

A

mitochondrial DNA is 5 times smaller

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4
Q

describe histone proteins

A

they are positively charged proteins that interact with DNA

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5
Q

what is the average structure of a nucleosome

A

it is around 150bp and 8 histone proteins

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6
Q

what are the types of eukaryotic chromosomal DNA packaging

A

DNA double helix - nucleosome

chromatin - scaffold associated chromatin - condensed chromatin - compacted chromosome

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7
Q

describe chromatin

A

nucleosomes pack into a coil that twists into another large coil forming these fibres

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8
Q

describe scaffold- associated chromatin

A

the chromatin fibre fold to form loop domains attached to a protein scaffold

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9
Q

describe condensed chromatin

A

further condensed

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10
Q

describe the compacted chromosome

A

during mitosis the loops coil even further

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11
Q

describe DNA packaging in prokaryotes

A

supercoiling compacts bacterial DNA and the DNA is attached to a protein core

the E.coli genome has 50 supercoiled domains

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12
Q

what are nucleotides comprised of

A

a pentose sugar 2’ deoxyribose

nitrogenous base

phosphate group

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13
Q

what are the nitrogenous bases

A

cytosine, thymine, adenine, guanine

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14
Q

what are purines

A

purines have 2 rings - Adenine guanine

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15
Q

What are pyrimidines

A

one ring - thymine and cytosine

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16
Q

how many hydrogen bonds occur between the bases

A

A=T two bonds
C-=G three bonds

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17
Q

What is Chargaff’s rule

A

abundance of purines is equal to the abundance of pyrimidines

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18
Q

who discovered the structure of DNA

A

Rosalind Franklin working with Maurice Wilkins produced x-ray crystallography images from purified DNA

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19
Q

what did the x-ray crystallography suggest about the structure of DNA

A

bases were on the inside and the sugars and phosphates on the outside and it also suggested the molecule was helical with 10 nucleotides per turn and anti-paralles

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20
Q

what are the 4 key features of DNA

A

it is a double stranded helix of uniform diameter

it is antiparallel

has major and minor grooves

usually right handed

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21
Q

what does it mean when DNA is right handed

A

curves in the direction of the fingers on the right hand when the thumbs point upwards

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22
Q

describe the antiparallel nature of the DNA strands

A

it is determined by the sugar-phosphate bonds

phosphate groups connect to the 3’C of one sugar and the 5’C of the next sugar by phosphodiester bonds, the two chain ends differ, one has a free 5’ phosphate group and the other is a free 3’ OH group

the 5’ end of one of the strands is a base paired to the 3’end of the other strand in a DNA double helix

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23
Q

describe why the helix is of a uniform diameter

A

Chargaff’s rule

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24
Q

describe major and minor grooves

A

minor grooves occur when the backbones of two strands are closer together on one side of the DNA helix

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25
Q

what is the significance of major and minor grooves

A

DNA bonding proteins often bind in the major grooves

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26
Q

when does DNA replicate

A

during the S phase in the cell cycle

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27
Q

define semiconservative replication

A

produces molecules containing one parent strand and one new daughter strand

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28
Q

define conservative replication

A

produces one completely new molecule and preserves the original molecule

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29
Q

define dispersive replication

A

produces two molecules with old and new DNA interspersed along each DNA strand

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30
Q

where does the initiation of DNA occur

A

replication origins

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31
Q

how are replication origins bound

A

bound by replication proteins to initiate replication

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32
Q

what occurs once replication is initiated

A

the replication origins are recognised by a replication complex and two replication forks are formed moving in opposite directions

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33
Q

describe the differences in replication origins between different chromosomes

A

humans have large linear chromosomes and can have many hundreds of replication origins, whereas small circular chromosomes have a single replication origin

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34
Q

what drives DNA replication

A

loss of phosphate groups on the deoxynucleotide triphosphates releasing energy to drive reactions once the DNA polymerase adds it to the strand

35
Q

describe DNA replication and the enzymes catalysing it

A

Helicase unwinds the double helix exposing the bases

RNA primer us made which is complimentary to the DNA template and primase synthesises RNA one nucleotide at a time

DNA polymerase synthesises DNA in the 5’3’ directions

RNA primer is later removed and DNA fragments are joined by ligase

36
Q

what is the leading strand

A

3’end of the strand as the synthesis of this strand is continuous

37
Q

what is the lagging strand

A

5’ start and the synthesis of this strand is discontinuous and Okazaki fragments are formed.

38
Q

what is the end replication problem

A

the lagging strand cant be completed right to the end and the end of chromosome =s will get shorter with each round of replication

39
Q

what are telomeres

A

chromosome ends

40
Q

what is the alternative method of replication of telomeres

A

telomerase uses an RNA template made by primase to extend the telomere and telomerase moves to the new end and DNA polymerase fills the gap and this process can be repeated multiple times to lengthen the telomere

41
Q

what is the purpose of the sliding clamp in DNA processivity

A

sliding clamp helps to keep DNA polymerase attached to the template and it can incorporate more nucleotides before detaching compared to without a clamp

42
Q

define transcription

A

copies information from a DNA sequence to a complementary RNA sequence

43
Q

what are the main differences between DNA and RNA

A

The sugar is ribose instead of deoxyribose

uracil is present instead of thymine

single stranded

can base pair with itself and DNA

44
Q

what are the different classes of RNA

A

mRNA
tRNA
rRNA

45
Q

define transcriptome

A

all RNA molecules produced from a genome. Not all of these are translated, some are non-coding RNAs

46
Q

what is a gene

A

unit of inheritance and a stretch of DNA that encodes a functional product

47
Q

how are genes orientated

A

they can be orientated in either direction in the genome so the coding strand be either the top or bottom one but by convention we write it as the 5’3’ strand

48
Q

define promoter sequence

A

directly upstream of genes and contain binding sites for transcription machinery

49
Q

what are enhancers

A

regulatory sequences located far from genes and can be millions of base-pairs away from the gene

50
Q

how do enhancers and promoters interact

A

the 3D conformation of eukaryotic chromosomes.
DNA bending allows transcription factors to interact with RNA polymerase

51
Q

how can genes be regulated

A

transcription - which genes can transcribe and when

transcript stability - rate of transcript degradation

RNA processing

translation initiation

post-translational protein modification

52
Q

what is the major gene control point

A

transcription initiation

53
Q

how can DNA sequences instruct protein binding

A

DNA binding proteins contain domains that can interact with DNA in a sequence-specific manner

for example the helix-turn-helix motif binds to the major groove and first helix interacts with the sugar-phosphate backbone to orient the DNA-binding helix which interacts with the bases

54
Q

where does protein sequence specificity come from

A

comes from the protein having a surface that is chemically complementary to the DNA

55
Q

what kind of effect can transcription factors have

A

activating or repressing

56
Q

what are the components of transcription

A

RNA polymerase
DNA template
Ribonucleoside triphosphates

57
Q

how does RNA polymerase differ in prokaryotes and eukaryotes

A

Prokaryotes have one RNA polymerase

Eukaryotes have RNA polymerases

58
Q

what are the three RNA polymerases in eukaryotes

A

1 - ribosomal RNA
2- messenger RNA
non-coding RNAs
small nuclear RNA
3- transfer RNA
rRNA and snRNA

59
Q

what are the three stages of transcription

A

initiation
elongation
termination

60
Q

describe the initiation stage of transcription

A

it initiates at promoters which is a sequence that controls the expression of a gene

promoters contain binding sites for transcription factors and RNA polymerase

directly upstream 5’ of a protein coding sequence

promoters dictate the direction of transcription

DNA helix is unwound

61
Q

describe the elongation stage of transcription

A

about 10bp are unwound at a time

RNA polymerase reads the template and uses ribonucleoside triphosphates to generate the RNA strand in a 5’3’ direction

no proofreading

62
Q

describe the synthesis of RNA

A

it doesnt require a primer

ribonucleotides are added to the 3’ end of the transcript

63
Q

describe the termination of transcription

A

formation of phosphodiester bonds stops and RNA-DNA hybrid dissociates

RNA polymerase dissociates from DNA

64
Q

describe prokaryotic gene organisation

A

transcription unit contains a coding region which is linear complementarity between DNA and mRNA

1 protein is produced from 1 gene

65
Q

describe polycistronic gene organisation

A

multiple genes are controlled by a single promoter (operon)

multiple proteins are produced and there is a mechanism for the co-regulation of these genes

66
Q

describe how transcription is coordinated with transcription factors

A

genes to be regulated simultaneously may be far apart or on different chromosomes and co-regulation can be achieved by having related regulatory sequences

67
Q

describe eukaryotic gene organisation

A

transcription units produce pre-mRNA after transcription which contains introns and exons and after splicing a strand of mRNA is produced which contains only exons which are the base sequences that code for proteins

68
Q

what is splicing

A

it turns pre-mRNA with introns and exons to mRNA with only exons

69
Q

how is splicing catalysed

A

spliceosome in the nucleus

70
Q

when are introns removed

A

removed by splicing prior to translation

71
Q

describe the action of splicing

A

small nuclear ribonuclear protein particles bind to consensus sequences in RNA near the 5’ donor end and 3’ acceptor splice sites

binding of snRPs recruits other proteins and a cut is made between the 5’ exon and the intron

72
Q

what kind of structure does tRNA form

A

cloverleaf where about half the nucleotides are base paired
contain many modified nucleotides such as pseudo uridine

73
Q

what kind of attachment sites do tRNA have

A

they are covalently attached to a single charged amino acid

they bind to mRNA with their anticodon

74
Q

what are aminoacyl -tRNA synthetases

A

they attach amino acids to tRNAs

75
Q

what is wobble

A

reduces the number of tRNAs needed by enabling one tRNA to read more than one codon

76
Q

what are non-Watson Crick base pairs

A

G-U base pairs
Inosine can base pair with A,C,U

77
Q

how are the ribosomal components held together

A

hydrophobic forces

78
Q

describe the three tRNA binding sites in ribosomes

A

A - tRNA anticodon binds mRNA codon

P-amino acid added to the polypeptide chain

E- exit site - uncharged tRNA is released from here

79
Q

what subunit of ribosomes is mRNA associated with

A

the small subunit

80
Q

what are the stages of translation

A

initiation
elongation
termination

81
Q

What do most chains initiate with

A

AUG methionine

82
Q

Describe translation initiation

A

5’ cap interacts with the small ribosomal unit kozak consensus sequence used to find the initiation codon and position the ribosomes

tRNA binds to AUG start codon completing the initiation complex then the large ribosomal sub unit joins the complex and occupies the p site

83
Q

describe translation elongation

A

bond between the tRNA and its amino acid is broken in the p site and a peptide bond is formed between the amino acid that has just been released from the P site and the one attached to the tRNA in the A site

the ribosome shifts along one codon at a time

84
Q

describe translation termination

A

a release factor binds to the complex when a stop codon enters the A site the release factor disconnects the polypeptide from the tRNA in the P site

biochemistry (6 decks)

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