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Biochemistry > Biochemistry of Nucleic Acids > Flashcards

Biochemistry of Nucleic Acids Flashcards

1
Q

what is the central dogma?

A

DNA > RNA > Protein

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2
Q

difference between ribose and deoxyribose?

A

ribose has 2 OH groups, deoxyribose only has 1

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3
Q

how are carbons numbered in nucleotides/nucleosides?

A

from amino end to phosphate end

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4
Q

DNA building blocks vs RNA building blocks?

A 
DNA = dATP, dCTP, dGTP, dTTP
RNA = ATP, CTP, GTP. UTP
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5
Q

how does polymerisation occur in DNA?

A

phosphodiester bond is formed between a free 3’ OH group on the above nucleotide and a 5’ triphosphate on ATP, leaving 2 diphosphate
consumes 2 high energy bonds

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6
Q

give an example of a nucleotide analogue used as a drug and describe how it works

A

ZDV/AZT/Retrovir (analogue of thymidine)

incorporated into growing viral DNA but lacks 3’ OH group so chain elongation is terminated

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7
Q

how many bond between A/T and C/G?

A 
A-T = double bond
C-G = triple bond
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8
Q

replication is conservative, true or false?

A

false

only semi conservative

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9
Q

what catalyses DNA replication?

A

DNA polymerase

can only add to existing nucleic acid and require an RNA primer to start replication

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10
Q

in which direction is DNA replicated?

A

bidirectional

always 5’ to 3’

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11
Q

building blocks of DNA replication?

A

dATP, dTTP, dCTP, dGTP

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12
Q

what synthesises an RNA primer?

A

primase

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13
Q

what is the exonuclease activity of DNA polymerase?

A

moves 3’ to 5’ removing incorrect nucleotides

improves error rate

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14
Q

most abundant RNA?

A

rRNA (80%)
forms ribosomes
tRNA = (15%)
mRNA = (5%)

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15
Q

describe structure and function of tRNA

A

clover leaf structure when flattened

specific amino acid is attached to 3’ end (dependant on anti-codon sequence)

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16
Q

what are the 3 types of eukaryotic RNA and how can they be distinguished?

A

Pol I, ii and iii (Pol ii makes all mRNA)

by sensitivity to toxins like alpha amanitin

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17
Q

what is TBP?

A

TATA box Binding Protein
recognises TATA box (present in promotor region)
part of TFIID
introduces kink into DNA providing landing platform for further transcription factors and RNA polymerase

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18
Q

what is TFIID?

A

general transcription factor required for all Pol ii transcribed genes

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19
Q

how is transcription initiated?

A

needs additional general transcription factors
Pol ii and TFIIF extend transcript on their own
TFIID remains at promotor, a new initiation complex can now assemble
allows transcription at low, basal rates

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20
Q

how is the transcribed strand elongated?

A

transcription bubble moves along DNA from 5’ to 3’ (DNA unwound in front of polymerase and rewound behind it)

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21
Q

how is transcription terminated?

A

new RNA makes a stem loop structure (followed by stretch of U’s)
specific enzyme cleaves the finished RNA
RNA released and polymerase dissociates

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22
Q

how is transcription regulated?

A

needs specific transcription factors (DNA binding proteins with DNA binding domain and transcriptional activation domain)
bind to specific DNA sequences in vicinity of promoter (enancers)

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23
Q

describe coordinated gene expression

A

a stress (e.g hormone stimuli, cellular stress etc) activates transcription of a regulatory protein through a stress sensitive transcription factor
binding of the regulatory protein to the stress regulatory element (SRE) stimulates transcription of genes A, B and C
Genes A, B and C produce different proteins which participate in the stress response

24
Q

give 2 examples of coordinated gene expression

A 
steroid receptors (on binding, ligand (steroid) moves to nucleus and binds to DNA at steroid response elements (SRE)
glucocorticoid receptors (free steroids enter target cells via diffusion, bind to inactive steroid receptor in cytoplasm, activates receptor, translocates to nucleus, binds to response elements as homodimer, coordinated regulation of set of genes)
25
Q

when does splicing take place?

A

after transcription, before translation

26
Q

what happens at the 5’ and 3’ ends of mRNA?

A

Poly(A) tail (AAAAA) added at 3’ end

modified GTP “cap” added at 5’ end

27
Q

what is the difference between transcription/translation in prokaryotes and eukaryotes?

A

compartmentalised in eukaryotes
- transcription in nucleus
- translation in cytosol
occurs anywhere in prokaryotes

28
Q

degenerate vs unambiguous?

A 
degenerate = amino acid has more than one codon
unambiguous = each codon has only one amino acid (or a stop)
29
Q

start vs stop codons?

A 
start = AUG
stop = UAA, UAG, UGA
30
Q

what are the 3 different reading frames of RNA (e.g if there are an extra 2 bases which cant complete a codon)?

A

2 bases at the right end
1 base either side
2 bases at the left end

31
Q

what are the components of translation?

A 
amino acids
tRNAs
Aminoacyl-tRNA synthetases
Specific protein factors for
- initiation of protein synthesis
- elongation
- termination
ATP and GTP (energy)
Ribosomes
mRNA
32
Q

what does aminoacyl tRNA synthetase do?

A

attaches amino acid to its tRNA via covalent bond

at least 1 per amino acid

33
Q

how many rRNA molecules are contained within each ribosome?

A

4

3 in bacteria

34
Q

what are the components of a ribosome?

A

4 rRNA molecules

proteins

35
Q

which has bigger ribosomes, prokaryotes or eukaryotes?

A

eukaryotes

36
Q

3 tRNA binding sites of ribosomes?

A

Exit
Peptidyl
Aminoacyl

37
Q

initiation of translation?

A

needs initiation factors (IFs)
energy from GTP hydrolysis
small ribosomal subunit binds to 5’ end of mRNA
moves along mRNA until start codon met
initiator tRNA with UAC anticodon base pairs with start (carries methionine)
large subunit joins assembly and initiator tRNA located in P site

38
Q

elongation of translated protein?

A 
elongation factor (EF-1alpha) brings next aminoacyl-tRNA to A site (anticodon-codon)
GTP hydrolysed, EF released from tRNA
second elongation factor (EF-1betagamma) regenerates EF1alpha
39
Q

what catalyses the peptide bond formation between amino acids and where does this occur?

A

peptidyl transferase

occurs in P and A sites

40
Q

how does the ribosome move along the mRNA?

A

elongation factor EF-2 moves it along by 1 triplet at a time

41
Q

what is the pathway a tRNA takes in a ribosome of a growing peptide?

A

moves from A to P and then the empty tRNA moves to the E site where it can exit and become reloaded with an amino acid

42
Q

where are the A, P and E sites located on a ribosome?

A 
A = furthest towards 3' end
E = furthest towards 5' end
P = in the middle
43
Q

how does termination occur?

A

when A site encounters a stop codon (no aminoacyl tRNA pairs with a stop codon)
release factor RF binds stop codon (GTP hydrolysis)
finished protein cleaved off tRNA
rRNA, mRNA and tRNA dissociate from each other

44
Q

what is a polysome?

A

mRNA with several ribosomes attached

45
Q

point mutation?

A

change in single DNA base

46
Q

missense mutation?

A

causes change in amino acid sequence

can change protein function (sickle cell anaemia)

47
Q

Nonsense mutation?

A

creates new termination codon

changes length of protein due to premature stop of translation

48
Q

silent mutation?

A

no change in amino acid sequence
due to degeneracy of genetic code
no effect on protein function

49
Q

frameshift mutation?

A

addition or deletion of single base (or 2)

changes reading frame of translation into protein

50
Q

types of chromosomal mutations? how are they different?

A 
deletions
duplications
inversions
translocations
affect larger portions of genome
51
Q

what are the 3 options for a finished protein?

A

targeting (moving to final cellular destination, depends on amino acid sequence)
modification (adding further functional groups)
degradation (unwanted or damaged proteins have to be removed)

52
Q

what do free ribosomes do and where are they found?

A 
make proteins for
- cytosol
- nucleus
- mitochondria
- translocated post-translationally
found in cytosol
53
Q

what do bound ribosomes do and where are they found?

A 
make proteins for
- plasma membrane
- ER
- Golgi apparatus
- secretion
- translocated co-translationally
found on rough ER
54
Q

what are the 2 destinations for newly synthesised proteins?

A

to organelles/cytosol

to rough ER

55
Q

give 4 examples of post translational modifications that can occur in the ER

A

glycosylation (adding/processing carbohydrates in ER an Golgi)
forming disulphide bonds
folding/multiunit assembly
proteolytic cleavage (in ER, Golgi and secretory vesicles)

56
Q

what results from misfolding of alpha1-antitrypsin in the ER?

A

hereditary emphysema

57
Q

give a clinical example of protein targeting

A

I-cell disease (recessive)
proteins destined for lysosomes not properly sorted and end up secreted from the cell
lysosomes cant digest material and become clogged
death before age 8

Biochemistry (7 decks)

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