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Molecular Biology > Quiz 4 > Flashcards

Quiz 4 Flashcards

1
Q

Transcription

A

Synthesizing an RNA molecule using DNA as a template

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2
Q

RNA polymerase

A

Enzyme that carries out transcription

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3
Q

Similarities between DNA polymerase and RNA polymerase

A

DNA template strand, nucleotides, 5 -> 3 direction, phosphodiester bonds

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4
Q

Dissimiliarities between DNA polymerase and RNA polymerase

A

No primer needed, uses RNA nucleotides

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5
Q

Initiation is done by:

A

In e. Coli, sigma subunit, in eukaryotes, three types

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6
Q

Template strand

A

DNA strand that serves as template for RNA synthesis

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7
Q

Coding strand

A

DNA strand that doesn’t serve as template

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8
Q

Template binding

A

Initial binding by RNA polymerase to DNA where gene is located

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9
Q

Promoter

A

Where template binding occurs (can vary, affecting how well RNA polymerase binds)

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10
Q

Transcription start site

A

Where RNA polymerase adds first nucleotide; it flows “downstream” from there

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11
Q

Consensus sequences

A

Similar DNA sequences; different promoters but share common sequences (ex: TATAAT or TTGACA in e. Coli promoters)

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12
Q

Cis-acting elements

A

Short portions of DNA that are next to a gene

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13
Q

Trans-acting factors

A

Proteins that bind to cis-acting elements and influence transcription

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14
Q

Initiation in e. Coli

A

Initial binding of sigma subunit which recruits rest of RNA polymerase; bubble formation as strands separate to make template accessible

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15
Q

Elongation in e. Coli

A

5-3 direction at 50mlcls/second, carried out by core RNA polymerase; sigma subunit leaves soon

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16
Q

Intrinsic termination in e. Coli

A

Occurs for about 80% of genes; transcription reaches termination sequnmence and mRNA forms hairpin that forces RNA polymerase to stall and dissociate from template strand

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17
Q

Rho-dependant termination in e. Coli

A

20%; termination involves Rho-dependent factor (an RNA helicase) and a rut in the template–Rho binds to rut and moves towards 3 end so RNA stalls and forms hairpin; Rho then moves through hairpin causing RNA polymerase to dissociate

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18
Q

Differences in transcription between prokaryotes and eukaryotes

A

More complex and more regulated:
- occurs in nucleus and not coupled to translation
- three different RNA polymerase
- chromatin remodeling is required
- more cis-acting elements and trans-acting factors
- termination is different
- mRNA is processed after transcription

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19
Q

Four cis-acting elements that affect transcription in eukaryotes:

A

Core promoter, where RNA polymerase II binds and transcription starts; proximal-promoter elements, which regulates level of transcription; enhancers, which increase efficiency of transcription; silencers, which decrease efficiency of transcription

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20
Q

General transcription factors

A

Proteins that affect RNA polymerase II binding to promoters; necessary

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21
Q

Transcriptional activators and repressors

A

Bind to enhancers and silencers to regulate efficiency

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22
Q

Cycle of transcription

A

Initially, RNA polymerase is unstable and makes several attempts to get going; during elongation, it is stable and transcription is a steady process; no specific termination sequence happens in eukaryotes, and instead mRNA contains AAUAAA which is cut by enzyme making it unstable

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23
Q

Introns

A

Intragenetic regions with no genetic code

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24
Q

Exons

A

Expressed regions with genetic code; both introns and exons are in initial mRNA, so introns must be removed before translation

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25
Q

Exon shuffling

A

Creating new genes

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26
Q

MicroRNA

A

Regulate gene expression

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27
Q

Transcription regulation

A

Enhancers and silencers

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28
Q

Post transcriptional modification

A

Modification of initial primary transcipt (preRNA) in eukaryotes that takes place in nucleus to generate mature RNA

29
Q

Mature RNA

A

Have m7G cap on 5 end, introns are removed, and a poly-A tail is added to 3 end

30
Q

Process by which eukaryotic mRNAs are processed

A

M7G cap is added to the 5 end, introns are removed and exons are put together to make continous coding sequence, and poly-A tail is added to 3 end

31
Q

M7G cap and poly-A tail

A

Protects mRNA from being destroyed by nucleus, facilitates transport between nucleus and cytoplasm, and essential for initiation (m7g) and process (poly-A tail) of translation

32
Q

Translation

A

Process of synthesizing a polypetide using genetic code in mRNA; takes place in ribosomes

33
Q

Polypeptide

A

Amino acids linked together in a chain by peptide bonds

34
Q

Components involved on translation

A
  • ribosomes
  • mRNA
  • amino acids
  • tRNA
  • helper proteins
  • GTP
35
Q

General structure of ribosomes

A

Small subunit, large subunit, E (exit) site, P (peptidyl) site, and A (aminoacyl) site

36
Q

Ribosomes composed of:

A

Ribosomal proteins and ribosomal RNA (rRNA)

37
Q

tRNA

A

75 to 90 nucleotides long, folded like a four leaf clover with an anticodon (that recognizes codon in mRNA and brings right amino acid) and amino acid at other

38
Q

Charged tRNA

A

Amino acid is attached by aminoacytl tRNA and synthases

39
Q

Initiation of translation

A

Involves: mRNA, small and large ribosomal subunits, GTP, charged initiator tRNA, and initiation factors IF1, IF2, and IF3

40
Q

IF1

A

Blocks A site from binding to tRNA

41
Q

IF2

A

Enables initiator tRNA to associate with small subunit (P site) and stops other tRNAs from binding there

42
Q

IF3

A

Binds to small subunit at E site to stop it from binding to large subunit too quickly

43
Q

Initiation complex

A

When charged tRNA bonus to P site

44
Q

Elongation of translation

A

Involves same factors as initiation but with elongation factors

45
Q

Termination of translation

A

Stop coding is reaches and involves a release factor that cuts polypeptide at P site

46
Q

Polyribosome

A

Complex of several ribosomes that simultaneously translate same mRNA molecule

47
Q

Location of transcription vs translocation in prokaryotes vs eukaryotes

A

In euks., they are separate and take place inside nucleus, while in proks., takes place at same time and ribosomes access mRNA as it markers from RNA polymerase during transcription

48
Q

Difference in ribosomes components in eukaryotes vs prokaryotes

A

In euks, ribosomes are bigger and contain more proteins

49
Q

Cap-dependant translation in eukaryotes

A

Assembly of eIGs, initiator tRNA, small subunit, and m7g cap that slides along mRNA till it finds start codon

50
Q

Closed-loop translation

A

Advantageous because it’s more efficient for ribosome recycling; poly-A binding proteins bind to poly-A tail and eIF4G protein, which then binds with eIF4E, closing loop

51
Q

Life length of eukaryotic and bacterial mRNAs

A

Euks live longer (hours) than bacterial (minutes)

52
Q

Elongation and release factors in eukaryotes

A

Homologous to bacterial elongation factors; only one release factors in euks, which recognizes three stop codons

53
Q

Colinearity

A

Order of nucleotides in a gene correlates directly with order of amino acids in corresponding polypeptide chain

54
Q

Function of protein is dependant on:

55
Q

Structure of amino acid

A

Amino group, carboxyl group, and R group (side chain), which varies and defines type of amino acid

56
Q

Four main classes of amino acids

A

Nonpolar (hydrophobic), polar (hydrophilic), positively charged, and negatively charged

57
Q

Peptide bonds

A

Form between carboxyl group of one amino acid and the amino group of another; N-terminus is amino group side and C-terminus is carboxyl group side

58
Q

Levels of protein structure

A

Primary, secondary (alpha helix and beta sheet), tertiary, and quaternary (ex: hemoglobin)

59
Q

Three main factors that determine tertiary structure of protein

A

Disulfide bonds (sulfur atoms that link two different amino acids), polar side chains, and nonpolar side chains

60
Q

Posttranslational modification

A

Proteins are modified after they are made (crucial to function; ex: on/off switch)

61
Q

Examples of posttranslational modifications

A
  • individual amino acids can be modified
  • N-terminus
  • sugars can be attached to protein
  • trimming polypeptide chain (ex: insulin)
  • removing signal sequences
  • prosthetic groups
62
Q

Example of individual amino acids being modified

A

Phosphorylation, which is the adding of a phosphate group by kinase, and dephosphorylation, which is removing a phosphate group by phosphatases

63
Q

Role of chaperones in protein folding

64
Q

Diseases caused by protein foldings incorrectly

A

Prions, sickle-cell anemia, cystic fibrosis

65
Q

Protein functions

A

Structural or functionally active (such as enzymes or transcription facotrs

Ex: hemoglobin, collagen, keratin, actin and tubulin, immunogloblin

66
Q

Definition and role of enzymes

A

Cataylsts; lower energy of activation

67
Q

Functional domain

A

Regions of specific amino acids in proteins (50-300 AAs long) that confer unique functions

Ex: catalytic domains (enzymes), DNA-binding domains (transcription factors)

68
Q

Exon shuffling

A

Shuffling exons between different genes

Molecular Biology (10 decks)

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