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Biochemistry > Revison Lecture B29 > Flashcards

Revison Lecture B29 Flashcards

1
Q

What does the genome carry

A

Genetic information stored in the nucleotide sequence of the genome
Stored in the nucleotide sequnce of genome

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2
Q

What does the DNS nucleotide sequence determine

A

Amino acid sequnce of polypeptide chains and proteins

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3
Q

How is information of DNA transmitted

A

Via an intermediate rna

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4
Q

What si the process between
DNA –> rna
Rna –> protein

A

DNA – transcription –> RNA

RNA – translation –> protein

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5
Q

What are the components of DNA

A

4 bases - A C T G
Deoxyribose sugar
Phosphate

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6
Q

What are the bonds associated with DNA

A

Hydrogen bonds
Glycosidic bonds
Phosphodiester bonds

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7
Q

What si the structure of DNA.

A

Double helix
Sugar phosphate backbone
2- anti parallel chains
Run 5’-3’

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8
Q

What are the hydrogen bonds in DNA

A

A - 2 - T

C - 3 - G

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9
Q

What is a nucleoside

A

Base and sugar

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10
Q

What makes a nucleotide

A

Base
Sugar
Phosphate

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11
Q

What are the 2 types of sugar

A

Ribose

Deoxyribose

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12
Q

What are some RNA building blocks

A

ATP
CTP
GTP
UTP

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13
Q

What are some DNA building blocks

A 
dATP
dCTP
dGTP
dTTP
- deoxy adenosine triphosphate
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14
Q

What is another name for a nucleotide

A

Nucleoside triphosphate

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15
Q

What si the enzyme used for the formation of new polynucleotide chains

A

DNA polymerase

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16
Q

What dos each incoming nucleotide do when forming a phosphodiester bond

A

Forms appropriate base pair with a base in the template

DNA polymerase then links this to the 3’ end of new strand

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17
Q

What does DNA polymerase do

A

Catalyses a nucleophillic attack by deoxyribose 3’OH on the proximal phosphate of the dNTP

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18
Q

What si the reaction of phosphodiester bond deacon fuelled by

A

Breaking of the high energy bonds int he dNTPs

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19
Q

What end does dNTPs attach to

A

3’ end

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20
Q

What is released from a phosphodiester bond

A

Water and pyrophosphate

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21
Q

What reaction is a phosphodiester reaction

A

Polymerisation

Consuming 2 high energy bonds

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22
Q

What happens to the analogue of thymidine

A

Incorporate into the growing viral DNA

Lacks 3’ end therefore chain elongation terminated

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23
Q

What does the viral reverse transcriptase have a higher affinity for

A

ZDV than human DNA polymerase

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24
Q

What are nucleosides and nucleotides also used in

A

Chemotherapy

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25
Q

What is the analogue of thymidine used for

A

Retrovir

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26
Q

What are RNA polymerases

A

Multimeric enzymes very large

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27
Q

What does ecoli have in respect to RNA pol

A

One RNA pol which has 5 subunits

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28
Q

How many eukaryotic RNA pol are there

A

3

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29
Q

What are the three eukaryotic RNA polymerases

A

RNA polymerase
1 - pre rRNA
2 - mRNA
3 - tRNA

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30
Q

What does the RNA polymerases do

A

They use one strand of DNA as a template

Do not require a primer

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31
Q

What sit he fundamental reaction in RNA synthesis

A

Formation of OHOSPHODIESTER bond

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32
Q

How does the RNA phosphodiester bond form

A

The 3’ hydroxyl group of the last nucleotide nucleophilically attacks the proximal phsphoryl of incoming NTP releasing pyrophosphate

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33
Q

What does the RNA transcription formation f the phosphodiester bond require

A

Magnesium in the active site of the polymerase

Reaction is thermodynamically favourable

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34
Q

Where does RNA transcription reactions occur

A

In a complex of DNA called transcription bubble

Where DNA has been unwound by approx 17bp

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35
Q

Explain the transcription bubble action

A

Moves in one direction along the DNA

DNA unwound infrint of polymerase then would behind

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36
Q

What way is RNA syn

A

5’- 3’

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37
Q

What is the new RNA sequnce

A

Complementary to template strand

Identical except Uracil instead of thymine

38
Q

What are the three main stages of transcription

A

Initiation
Elongation
Termination

39
Q

What sit he initiation step of RNA transcription

A

RNA polymerase binding - RNA pol bind to a specific DNA sequnce in the promoter, helped by transcription factor - protiens bound to DNA

DNA chain seperation - local unwinding of a short stretch of double stranded DNA revealing a single stranded template (3’ - 5’)

40
Q

What si the elongation step of RNA transcription

A

Selection of correct nucleotide and catalysis of phosphodiester bond formation
Addition of nucleotides to RNA chain 5’ end for new RNA molecule is made first

41
Q

What is the termination step for RNA transcription

A

Detect termination signals which specify which transcript ends
Release new RNA molecules

42
Q

What are the 2 general typ of RNA processing

A

A - removal of excess sequences by the action of endonucleases and exonucleases - processing tRNA and rRNA

B - removal of excess sequences by action of endonucleases followed by rejoining of the required segments called splicing

43
Q

What’s re the products of transcription of DNA

A

mRNA
tRNA
tRNA

44
Q

Where are promoters

A

DNA sequences upstream in front of coding sequnce of the gene

45
Q

What does the promoter do

A

Tell RNA pol where to start transcription and which DNA strand to transcribe

46
Q

What is a TATA box

A

A promoter molecule
DNA sequnce 25bp upstream form start of transcription
An 8bp consensus sequenceusually entirely AT bases
Changes to this sequnce affect transcription efficiency

47
Q

What si the CAAT box

A

Promoter element

Upstream form TATA box
Control strength of promoter signal rather than tissue/time specific expression

48
Q

What si the GC box

A

Promoter element

GC boxes found in repeated throughout the promoter

49
Q

What doe promoters bind

A

Transcription factors

50
Q

What doe transcription factors do

A

Specifically recognise the DNS sequnce

Stimulate expression, some suppress, some ubiquitous

51
Q

What is TFIID

A

General transcription factor GTF

52
Q

What si TFIID needed for

A

RNA pol 2 than scribed genes

53
Q

What is TFIID composed of

A

Complex of proteins

One is tbp ( TATA box binding protein)

54
Q

What does TBP introduce to DNA

A

A kink in the DNA

Determines transcriptional start and direction

55
Q

What does TFIID provide

A

Landing platform for further transcription factors and for RNA polymerases 2

56
Q

What si the initiation of transcription for RNA pol 2

A

Formation of pre-initiation complex and most of the control of transcription occurs at this step

Complex contains RNA pol II and six general transcription factors including TFIID

Before transcription can start the pre initiation complex must form an open complex where RNA pol II is phosphorylated Nd the DNA strand s are sep

GTF required for all promoters and Evan has specific function

57
Q

What are some GTF functions

A

TATA box recognition by TFIID by tbp subunit

Recruitment of RNA pol II

58
Q

What sit he initiation of basal transcription

A

TFIID binds promoter as tbp revenues TATA box
RNA pol II and additional transcription factors bind
DNA is unwound locally to expose template 3’-5’
Open complex forms RNA pol II phsphorylated
Some tf released
RNA pol II and elongation factor extend transcript
TFIID remains promoter a new initiation complex can assemble
Pol II eventually dephos and recycled

59
Q

For higher levels of expression what are required

A

Activators
Eg
Gene sp transcription factors

60
Q

What happens in elongation

A

The phos RNA po II syn RNA
RNA pol II and emotion factor extend transcript
Leaving TFIID and promoter which initiate a new round of synthesis
Elongation factors stimulate the RNA synthesis
Elongation may be stopped leading to premature termination

61
Q

What is Rho-dependant termination

A

A protien called Rho unwinds the new RNA-DNA duplex catching up with RNA pol at the termination site (where RNA pol pauses) causing enzyme to dissociate

62
Q

What is Rho- indept termination

A

A hairpin loop upstream of s serious of U and dislodges RNA pol form the DNA template to,ringing transcription

63
Q

How does RNA pol 1 stop syn

A

Uses a transcript terminating factor

64
Q

How does RNA pol II stop syn

A

Sequnce AAUAAA

Once terminated the transcript is released in open form of RNA pol II released, dephos and recycled

65
Q

How does RNA pol III stop syn

A

Uses a method similar to the Rho- indept method in procarytoes

66
Q

How do procarytoes terminate

A

Via Rho- dept or indept termination

67
Q

Sat does specific regulation of transcription require

A

Specific transcription factors not GTP

68
Q

What are the specific regulation factors described as

A

Enhancers or silencers

69
Q

What doe the specific transcription factors do

A

Either regulate transcription positive or negative

70
Q

Where are the STP found

A

Either upstream or downstream form initiation site

71
Q

What does looping do

A

Brings enhancer and promoter together

72
Q

What so enhancers enhance

A

Formation of an initiation complex

73
Q

What are transcription factors

A

DNA binding protiens

74
Q

What are the 2 functional domains of transcription factors

A

DNA binding domain

Transcriptional activation domain

75
Q

What does the DNA binding domain do in transcription factors

A

Interacts with DNA via major or minor groove
Helix run helix motif
Leucine zipper motif
Zinc finger motif

76
Q

What does the transcriptional activation domain do in transcription factors

A

Stimulate the formation of an active transcription complex
May interact with the RNA pol complex
Indirect effect from interaction with coactivatirs and corepressors
May remodel chromatin

77
Q

How do transcription factors bind

A

Suing h bond
Electrostatic attraction
Hydrophobic interactions

Trans acting factors

78
Q

What si the Leucine zipper motif

A

Motif bind I the DNA major groove w/strong electrostatic charges between base and protein

Protein dimers form due to hydrophobic interaction of leucine rich areas

79
Q

What are zinc finger proteins

A

1/2 zinc ions tetrahedrally coordinated with cysteine, histidine side chains

80
Q

What are response elements

A

Enhancers which respond to detain metabolic factors

81
Q

What are some examples of response elements

A

Heat shock element
Glucocorticoid response element
Metal response element
Cyclic AMP response element

82
Q

What do response elements have bound to them

A

Transcription factors

83
Q

What are glucocorticoid response element

A

Steroids transported in blood bound to albumin or specific transport proteins

84
Q

How do glucocorticoid repose element get into target cell

A

Free steroids enter target cell by diffusion across mem

Bind to inactive steroid receptors in cyto

85
Q

What happens to the glucocorticoid response when in target cell

A

Receptor dimerises exposing nuclear lovalising signal
Complex trans located to nucleus where bind to so DNA activating promoter
Acts as transcription factor

86
Q

What does glucocorticoid repsonse element control pemit

A

The coordinated regulation of set of genes

87
Q

What is an epi genetic mechanism

A

Modifications of DNA that switch sp gene expression on or off

88
Q

What is chromatin structure

A

DNA in cell nucleus tightly packed with HISTONES so gene promoters not easy to get

Histone packing, Nucleosome stability and DNA accessibility tightly controlled by acetylation anddecactytleationg of lysine residues of core HISTONES

Some trans factors can do this themselves

89
Q

What is methylation of DNA

A

Affects gene expression
Methylation generally associated with regions DNA less active transcribing RNA
Usually shuts off expression
Cytosine tagged with ch3 group

90
Q

What does the total DNA constitue

A

The genome

Biochemistry (13 decks)

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