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Biochemistry > DNA replication, transcription, translation > Flashcards

DNA replication, transcription, translation Flashcards

1
Q

Nucleoside

A

pentose+base

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2
Q

Nukleotide

A

phosphate+pentose+base

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3
Q

Nucleic acid

A

DNA: sugar phosphate backbone and bases

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4
Q

Bond bw. bases

A

Hydrogen bonds (2 bw. A&T, 3 bw. G&C)

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5
Q

End of the strand

A
  • 3´end of the strand: free 3-OH-gr. of D-ribose

- 5´end of the strand: free 5-P-gr.

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6
Q

Bond be. sugar and P

A

Esterbond

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7
Q

Deoxyribonucleic acid

A

DNA. Long polymer of nucleotides as units, w. a backbone of sugar and phosphate.

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8
Q

What part of DNA encodes info.?

A

Sequence of the 4 bases

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9
Q

What is transcription?

A

Reading genetic information using genetic code, by copying stretches of DNA into RNA.

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10
Q

What is translation?

A

Gene expression. The process where mRNA is read and translated into a string of aa.

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11
Q

What is DNA replication?

A

duplication of chromosomes before the cells divide

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12
Q

Within chromosomes?

A

chromatin proteins such as histones

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13
Q

Watson-Crick model

A

conformation of double helix – tertiary structure

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14
Q

Chromosomes in prokaryotes

A

single circular chromosomal DNA

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15
Q

Plasmid

A

small circular extrachromosomal DNA

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16
Q

Chromosomes in eukaryotes

A

many nuclear chromosomes (extrachromosomal DNA: in mitochondria)

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17
Q

Types of proteins in chromosome

A

histone (alkaline proteins) and non-histone(regulatory and enzyme proteins)

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18
Q

Histone proteins

A

core 2x (H2A, H2B, H3, H4) and (H1) to stabilize the core histone octamer

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19
Q

Nucleosome

A

basic unit of eukaryotic DNA. Regularly repeating unit of chromatin

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20
Q

Primary structure of DNA

A

sequence (order and nr.) of nucleotides

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21
Q

Secondary structure of DNA

A

base-pairing (H-bonding bw. bases) and the double helix

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22
Q

Tertiary structure of DNA

A

conformation of double helix (B, A, Z conformation)

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23
Q

Quaternary structure of DNA

A
  • Prokaryotes: one circular chromosome w. superhelices

- Eukaryotes: nuclear chromosomes, containing regularly repeating units of chromosomal nucleoproteins=nucleosomes.

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24
Q

Tm

A

Define the temp. of which half of the DNA is melted. Melts into ss (single stranded) DNA. Varies on G+C content. If G+C content is more than T+A content, Tm is more. Reverse is A+T rich DNA

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25
Q

Conformation (tertiary structure)

A
  • B form: double helix - turn every 0,34 nm -> 10 base pairs
  • A form: structure change, in sol. w. higher salt conc. or alcohol added - 2,3 nm->11 base pairs
  • Z form: zigzag - 4,6 nm->12 base pairs
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26
Q

Type of conformation in prokaryotic DNA

A

Contains superhelix (double double helix). Positive (overtwisting) or negative (untwisting).

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27
Q

Topological isomers

A

-Coiled DNA

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28
Q

Type I topoisomerase

A

cuts one strand of ds DNA, relax the strand and then reanneal the strands. No ATP is needed.

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29
Q

Type II topoisomerase

A

cuts both strands of DNA helix, results in undwinding, neg. superhelix. ATP is needed. E.g. DNA gyrase (derived from Escherichia coli, bacterial).

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30
Q

Topoisomerase inhibitors

A

antimicrobial or antitumour agents

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31
Q

What encodes one aa?

A

3 bases (triplet=code) of DNA

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32
Q

Nr. of possibilities to prod. triplets?

A

64 possibilities to produce triplets from the 4 different nucleotides (A, G, C, T).

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33
Q

Are genes continious or discontinuous, and what does it consist of?

A

Discontinuous, consist of coding exons and non-coding introns.

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34
Q

Synthesis of DNA

A

Semiconservative replication

  • DNA helicase
  • Replication fork
  • DNA polymerase, 3´to 5´end
  • Complementary nucleotides, 5´to 3´end
  • Leading strand (5‘ to 3‘)
  • Lagging strand (3‘ to 5‘)
  • Okazaki fragments, DNA ligase
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35
Q

Diection of the new strand synt. in prokaryotes?

A

5´to 3´

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36
Q

Which side of the DNA synthesis is continious/discontinous?

A

On the leading strand the synthesis of the new strand is continuous, on the lagging strand is discontinuous.

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37
Q

Initiation of replication

A
  • Begins in the replication origo, recognized by DNA A protein.
  • Primer-start molec.
  • Synt. by primase
  • Helicase
  • All of these proteins form replisome.
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38
Q

Primer

A

Short DNA segment, start molecule, has a free 3´end.

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39
Q

Helicase

A

(in DNA B and C proteins) binds to ss. regions of DNA to prevent premature annealing of DNA strands.

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40
Q

Elongation of replication

A
  1. Primase synt. short RNA oligonucleotides copied from DNA.
  2. DNA polymerase III elongates RNA primers with new DNA.
  3. DNA polymerase I removes RNA at 5´end and fills gap
  4. DNA ligase connects adjacent fragments.
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41
Q

DNA polymerase isoenzymes in prokaryotes

A
  • DNA polymerase I and II: removal of primer, filling of the gaps. Repair of DNA.
  • DNA polymerase III: Synthesis of DNA. Found in enzyme complex, molecular machine (replisome) carries out replication.
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42
Q

DNA polymerase at eukaryotes

A
  • DNA polymerase alpha: synthesis of nuclear DNA
  • DNA polymerase beta: Removal of primer, filling of the gaps. Repair of DNA.
  • DNA polymerase gamma: synthesis of mitochondrial DNA.
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43
Q

Telomers

A

In Eukaryotic DNA replication, to the end of the chromosomes protecting telomeres (repeating DNA sequences) can be synt.

44
Q

Mutation

A

Change in base sequence of the gene results in mutant protein

45
Q

Types of mutation

A 
•Point mutation: 
-Substitution, such as transition: alternative pyrimidines (C, T) or purines (A, G) or transversion: purine pyrimidine (C/T, A/G).
-Same sense (silent)
-Missense
-Nonsense
•Insertion, such as duplication
•Deletion
Consequence: frameshift
•Multisite mutation: gene, chromosome, genom
46
Q

Functional difference bw. DNA and RNA

A

DNA to DNA: replication, DNA to RNA: transcription) of genetic info

47
Q

Which type of RNA has the largest molecular mass of all types?

A

Messenger RNA (mRNA)

48
Q

Which type of RNA transports covalently bound (activated) aa. to the protein synt.

A

Transfer RNA (tRNA)

49
Q

What is codes and codons?

A

Triplets of DNA=codes, triplets of mRNA=codons

50
Q

How many possible variations is there in gene expression?

A

64 possible variations -> 3 stop codons + 61 variations for 20 proteinogenic aa. (1 start codon – AUG – Met)

51
Q

Needed for transcription

A

•DNA template/non-coding/antisense strand
•Building stones for the synt. of RNA (ribonucleoside-triphosphate molecules, NTPs)
•Enzyme
-Prokaryote: DNA dependent RNA polymerase
-Eukaryote: DNA dependent RNA polymerase I, II and III

52
Q

Types of DNA dependent RNA polymerase in eukaryote

A
  • I: synt. of rRNA
  • II: synt. of mRNA and snRNA
  • III: synt. of tRNA (+rRNA and snRNA)
53
Q

What is the promotor region in prokaryotes?

A

pribnow-box and CAP-cAMP binding site

54
Q

What is the promotor region in eukaryotes?

A

GC-box and TATA-box (core promotor)

55
Q

Steps in transcription

A
  1. Initiation
  2. Elongation
  3. Termination
56
Q

Needed for initiation in transcription in prokaryotes?

A
  • RNA polymerase must bind sigma-factor

* cAMP-CAP site must be engaged by cAMP-CAP complex

57
Q

Needed for elongation in transcription in prokaryotes?

A
  • Transcription bubble
  • NTP -> NMP + PPin
  • RNA polymerase builds NMPs in the chain of mRNA being synt.
58
Q

Needed for termination in transcription in prokaryotes?

A 
•p(rho)-factor dependent 
-loop is formed in mRNA
-RNA polymerase
-ATP
•p(rho)-factor independent (rarely)
-loop
59
Q

is mRNA polycistronic/monocistronic?

A

Polycistronic

60
Q

Where can Shine-Dalgarno sequences be found?

A

bw. genes in Prokaryotic mRNA = ribosome binding site

61
Q

Where can Untranslated regions (UTR) be found?

A

on 5´and 3´ends of Prokaryotic mRNA

62
Q

Who has posttranscriptional modification?

A

Eukaryotes

63
Q

Regulation of prokaryotic transcription

A
  • Operon model

- CAP-cAMP binding site on promotor region

64
Q

Transcription in prokaryotes happens only if?

A
  1. CAP-cAMP complex is bound to CAP-cAMP binding site of promotor
  2. Repressor protein is not bound on the operator region
65
Q

Types of operons

A
  • Lac-operon: transcription of genes of enzymes needed for breakdown of lactose
  • Lac-operon: promotor region, operator region, structural genes: Z-gene (beta-galactosidase), Y-gene (permease), a-gene (transacetylase)
  • Tryptophan operon: transcription of genes of enzymes synt. tryptophan
66
Q

What is an operon?

A

distinct segment of DNA, a complete set of different regions

67
Q

Needed for initiation in transcription in eukaryotes?

A
  • Helicase subunit
  • RNA polymerase II
  • Protein kinase subunit
68
Q

Needed for elongation in transcription in eukaryotes?

A

•NTP -> NMP + PPin

-RNA polymerase II

69
Q

What does RNA polymerase II do?

A

Build NMPs

70
Q

When is termination in eukaryotes?

A

At cleavage sequence, after UTR

71
Q

What does helicase?

A

Uncoils DNA during initiation in transcription of eukaryotes, in the region of START site, by using 1 ATP

72
Q

What does Protein kinase?

A

During initiation in transcription of eukaryotes, hydrolyses 1 ATP for the phosphorylation of RNA polymerase II

73
Q

Steps in posttranscriptional modification?

A
  • 5´capping
  • Polyadenylation (polyA-tailing)
  • Splicing
74
Q

What is 5´capping?

A

7-methyl-GTP cap is built on the 5´end of mRNA (protection from enzymatic cleavage+transport)

75
Q

What is Polyadenylation (polyA-tailing)?

A

100-200 pcs of AMP is built on the 3´end of mRNA by polyA polymerase -> formation of polyA-tail (protection from enzymatic cleavage+transport)

76
Q

What is splicing?

A

removal of introns and ligation of exons to form mature mRNA

77
Q

Where does splicing happen?

A

Nucleus

78
Q

Types of splicing?

A
  • Alternative splicing

- Trans-splicing

79
Q

What is mature eukaryotic mRNA composed of?

A

7-methyl-GTP cap, UTR- exons (ligated), UTR, polyA-tail

80
Q

How does regulation of transcription happen in eukaryotes?

A
  • Altering chromatin structure (epigenetic regulation)
  • Histone acetylation
  • DNA-methylation
81
Q

Transcription factors

A

Proteins bound to the promoter region
•Activator protein -> incr. gene expression -> gene enhancing
•Repressor protein -> decr. gene expression -> gene silencing

82
Q

Synthesis of rRNA

A
  • Pre-rRNA -> rRNA by methylation

- DNA dependent RNA polymerase I (III)

83
Q

Synthesis of tRNA

A
  • Pre-tRNA -> tRNA by binding 3´CCA sequence (aa. binding site)
  • DNA dependent RNA polymerase III
84
Q

What does gene expression involve?

A

Transcription+translation.

DNA –(transcription)-> RNA –(translation)-> protein

85
Q

How does gene expression happen in the prokaryotic cell?

A

transcription and translation happens at the same time

86
Q

Loops in translation

A
  • 1st loop - DHU (dehydrouridine) loop: binds aminoacyl-tRNA synthetases.
  • 2nd loop - anticodon loop containing the complimentary triplet codon to that on the mRNA.
  • 3rd loop - pseudouridine loop (T, pseudouridine, C): binds tRNA to the ribosome
87
Q

Where will the aa. be bound to during translation?

A

The acceptor stem-3´end of the tRNA molecule

88
Q

What recognize which codon to bring an aa during translation?

A

tRNA, by anticodon on its mRNA-binding end that is complementary to the codon on the mRNA

89
Q

What is responsible for recharging tRNA with another aa. during translation?

A

aminoacyl-tRNA synthetases (ARS)

90
Q

Amount of swedbeg units in ribosomes of prokaryotes?

A

30 and 50S

91
Q

Amount of swedbeg units in ribosomes of eukaryotes?

A

40 and 60S

92
Q

Type of ribosome units?

A

Small (30 or 40S) and large (50 or 60S) subunits

93
Q

Start codon for prot. synt.?

A

AUG=codes for the aa. methionine. This aa. is used to start synt. of both prokaryotic and eukaryotic proteins.

94
Q

Needed in initiation in translation of prokaryotes?

A

Initiation complex: IF2 (initiation factor-2)-GTP-formylmethionyl-tRNA

95
Q

Needed in initiation in translation of eukaryotes?

A

Pre-initiation complex: IF2 (initiation factor-2)-GTP-methionyl-tRNA

96
Q

What is Kozaks-scanning?

A

Start codon scanning. Need 1 ATP/base.

97
Q

Elongation in prokaryotes?

A
  1. An aminoacyl-tRNA binds in A site. The anticodon loop binds to the codon of mRNA.
  2. Peptide bond is formed by peptidyl transferase, so Met will be bound to aminoacyl tRNA on the A site. Non-charged tRNA will be bound in the ribosomal E site, and then leaves the ribosome.
  3. Translocation occurs
98
Q

Required for aminoacyl-tRNA to bind in A site?

A

GTP and EF-1 alpha

99
Q

Required for translocation during elongation?

A

GTP, EF-2 and translocase

100
Q

Difference bw. eu- and prokaryotic elongation:

A

Instead of EF-1 alpha, EF-Tu exists

  • In prokaryotes transcription and translation on the same polypeptide chain happens at the same time
  • In prokaryotes poly(ribo)some is produced
101
Q

What is wobbling?

A

The third base of a codon is less important for id. the correct anticodon than the first two

102
Q

What are the stop codons?

A

UAA, UGA and UAG

103
Q

What is termination faciliated by?

A

By binding of protein called protein releasing factor (RPF) to the stop codon. RPFs recognize stop codons.

104
Q

When does termination occur?

A

when one of three special codons called stop codons appears in the A site of the ribosome

105
Q

Regulation of translation

A
  • If the complementarity of mRNA and small subunit of rRNA is big, the intensity of protein synt. is also big.
  • If an aa. is coded by a preferated codon of mRNA, the appropriate tRNA will be found quicker, so the intensity of prot. synt. is also bigger.
  • micRNA complementer to 5´end of mRNA can inhibit competitively binding of mRNA to the small subunit, so prot. synt. will decr.
106
Q

Posttranslation modifications

A

1.Splitting a peptide or an aa.
•Proinsulin becomes mature insulin
•Zymogens prod. active enzymes
•Met or fMet removal
2.Phosphorylation/dephosphorylation of OH in Ser, Thr, Tyr
3.Hydroxylation: OH-Lys and OH-Pro in collagen
4.Glycosylation of Ser-OH (in membrane)
5.Redox Rs: disulphide bond form.
6.Acetylation: histone proteins
•Transport of the modificated, final forms of proteins: bound to signal sequences

Biochemistry (16 decks)

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