DNA replication, transcription, translation Flashcards Preview

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Flashcards in DNA replication, transcription, translation Deck (106):
1

Nucleoside

pentose+base

2

Nukleotide

phosphate+pentose+base

3

Nucleic acid

DNA: sugar phosphate backbone and bases

4

Bond bw. bases

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

5

End of the strand

-3´end of the strand: free 3-OH-gr. of D-ribose
-5´end of the strand: free 5-P-gr.

6

Bond be. sugar and P

Esterbond

7

Deoxyribonucleic acid

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

8

What part of DNA encodes info.?

Sequence of the 4 bases

9

What is transcription?

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

10

What is translation?

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

11

What is DNA replication?

duplication of chromosomes before the cells divide

12

Within chromosomes?

chromatin proteins such as histones

13

Watson-Crick model

conformation of double helix – tertiary structure

14

Chromosomes in prokaryotes

single circular chromosomal DNA

15

Plasmid

small circular extrachromosomal DNA

16

Chromosomes in eukaryotes

many nuclear chromosomes (extrachromosomal DNA: in mitochondria)

17

Types of proteins in chromosome

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

18

Histone proteins

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

19

Nucleosome

basic unit of eukaryotic DNA. Regularly repeating unit of chromatin

20

Primary structure of DNA

sequence (order and nr.) of nucleotides

21

Secondary structure of DNA

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

22

Tertiary structure of DNA

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

23

Quaternary structure of DNA

-Prokaryotes: one circular chromosome w. superhelices
-Eukaryotes: nuclear chromosomes, containing regularly repeating units of chromosomal nucleoproteins=nucleosomes.

24

Tm

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

25

Conformation (tertiary structure)

-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

26

Type of conformation in prokaryotic DNA

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

27

Topological isomers

-Coiled DNA

28

Type I topoisomerase

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

29

Type II topoisomerase

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

30

Topoisomerase inhibitors

antimicrobial or antitumour agents

31

What encodes one aa?

3 bases (triplet=code) of DNA

32

Nr. of possibilities to prod. triplets?

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

33

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

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

34

Synthesis of DNA

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

35

Diection of the new strand synt. in prokaryotes?

5´to 3´

36

Which side of the DNA synthesis is continious/discontinous?

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

37

Initiation of replication

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

38

Primer

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

39

Helicase

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

40

Elongation of replication

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.

41

DNA polymerase isoenzymes in prokaryotes

•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.

42

DNA polymerase at eukaryotes

•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.

43

Telomers

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

44

Mutation

Change in base sequence of the gene results in mutant protein

45

Types of mutation

•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

Functional difference bw. DNA and RNA

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

47

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

Messenger RNA (mRNA)

48

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

Transfer RNA (tRNA)

49

What is codes and codons?

Triplets of DNA=codes, triplets of mRNA=codons

50

How many possible variations is there in gene expression?

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

51

Needed for transcription

•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

Types of DNA dependent RNA polymerase in eukaryote

-I: synt. of rRNA
-II: synt. of mRNA and snRNA
-III: synt. of tRNA (+rRNA and snRNA)

53

What is the promotor region in prokaryotes?

pribnow-box and CAP-cAMP binding site

54

What is the promotor region in eukaryotes?

GC-box and TATA-box (core promotor)

55

Steps in transcription

1.Initiation
2.Elongation
3.Termination

56

Needed for initiation in transcription in prokaryotes?

•RNA polymerase must bind sigma-factor
•cAMP-CAP site must be engaged by cAMP-CAP complex

57

Needed for elongation in transcription in prokaryotes?

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

58

Needed for termination in transcription in prokaryotes?

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

59

is mRNA polycistronic/monocistronic?

Polycistronic

60

Where can Shine-Dalgarno sequences be found?

bw. genes in Prokaryotic mRNA = ribosome binding site

61

Where can Untranslated regions (UTR) be found?

on 5´and 3´ends of Prokaryotic mRNA

62

Who has posttranscriptional modification?

Eukaryotes

63

Regulation of prokaryotic transcription

-Operon model
-CAP-cAMP binding site on promotor region

64

Transcription in prokaryotes happens only if?

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

65

Types of operons

-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

What is an operon?

distinct segment of DNA, a complete set of different regions

67

Needed for initiation in transcription in eukaryotes?

•Helicase subunit
•RNA polymerase II
•Protein kinase subunit

68

Needed for elongation in transcription in eukaryotes?

•NTP -> NMP + PPin
-RNA polymerase II

69

What does RNA polymerase II do?

Build NMPs

70

When is termination in eukaryotes?

At cleavage sequence, after UTR

71

What does helicase?

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

72

What does Protein kinase?

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

73

Steps in posttranscriptional modification?

-5´capping
-Polyadenylation (polyA-tailing)
-Splicing

74

What is 5´capping?

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

75

What is Polyadenylation (polyA-tailing)?

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

What is splicing?

removal of introns and ligation of exons to form mature mRNA

77

Where does splicing happen?

Nucleus

78

Types of splicing?

-Alternative splicing
-Trans-splicing

79

What is mature eukaryotic mRNA composed of?

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

80

How does regulation of transcription happen in eukaryotes?

-Altering chromatin structure (epigenetic regulation)
-Histone acetylation
-DNA-methylation

81

Transcription factors

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

82

Synthesis of rRNA

-Pre-rRNA -> rRNA by methylation
-DNA dependent RNA polymerase I (III)

83

Synthesis of tRNA

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

84

What does gene expression involve?

Transcription+translation.
DNA –(transcription)-> RNA –(translation)-> protein

85

How does gene expression happen in the prokaryotic cell?

transcription and translation happens at the same time

86

Loops in translation

-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

Where will the aa. be bound to during translation?

The acceptor stem-3´end of the tRNA molecule

88

What recognize which codon to bring an aa during translation?

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

89

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

aminoacyl-tRNA synthetases (ARS)

90

Amount of swedbeg units in ribosomes of prokaryotes?

30 and 50S

91

Amount of swedbeg units in ribosomes of eukaryotes?

40 and 60S

92

Type of ribosome units?

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

93

Start codon for prot. synt.?

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

94

Needed in initiation in translation of prokaryotes?

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

95

Needed in initiation in translation of eukaryotes?

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

96

What is Kozaks-scanning?

Start codon scanning. Need 1 ATP/base.

97

Elongation in prokaryotes?

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

Required for aminoacyl-tRNA to bind in A site?

GTP and EF-1 alpha

99

Required for translocation during elongation?

GTP, EF-2 and translocase

100

Difference bw. eu- and prokaryotic elongation:

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

What is wobbling?

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

102

What are the stop codons?

UAA, UGA and UAG

103

What is termination faciliated by?

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

104

When does termination occur?

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

105

Regulation of translation

•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

Posttranslation modifications

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