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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
Exon shuffling
Creating new genes
26
MicroRNA
Regulate gene expression
27
Transcription regulation
Enhancers and silencers
28
Post transcriptional modification
Modification of initial primary transcipt (preRNA) in eukaryotes that takes place in nucleus to generate mature RNA
29
Mature RNA
Have m7G cap on 5 end, introns are removed, and a poly-A tail is added to 3 end
30
Process by which eukaryotic mRNAs are processed
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
M7G cap and poly-A tail
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
Translation
Process of synthesizing a polypetide using genetic code in mRNA; takes place in ribosomes
33
Polypeptide
Amino acids linked together in a chain by peptide bonds
34
Components involved on translation
- ribosomes - mRNA - amino acids - tRNA - helper proteins - GTP
35
General structure of ribosomes
Small subunit, large subunit, E (exit) site, P (peptidyl) site, and A (aminoacyl) site
36
Ribosomes composed of:
Ribosomal proteins and ribosomal RNA (rRNA)
37
tRNA
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
Charged tRNA
Amino acid is attached by aminoacytl tRNA and synthases
39
Initiation of translation
Involves: mRNA, small and large ribosomal subunits, GTP, charged initiator tRNA, and initiation factors IF1, IF2, and IF3
40
IF1
Blocks A site from binding to tRNA
41
IF2
Enables initiator tRNA to associate with small subunit (P site) and stops other tRNAs from binding there
42
IF3
Binds to small subunit at E site to stop it from binding to large subunit too quickly
43
Initiation complex
When charged tRNA bonus to P site
44
Elongation of translation
Involves same factors as initiation but with elongation factors
45
Termination of translation
Stop coding is reaches and involves a release factor that cuts polypeptide at P site
46
Polyribosome
Complex of several ribosomes that simultaneously translate same mRNA molecule
47
Location of transcription vs translocation in prokaryotes vs eukaryotes
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
Difference in ribosomes components in eukaryotes vs prokaryotes
In euks, ribosomes are bigger and contain more proteins
49
Cap-dependant translation in eukaryotes
Assembly of eIGs, initiator tRNA, small subunit, and m7g cap that slides along mRNA till it finds start codon
50
Closed-loop translation
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
Life length of eukaryotic and bacterial mRNAs
Euks live longer (hours) than bacterial (minutes)
52
Elongation and release factors in eukaryotes
Homologous to bacterial elongation factors; only one release factors in euks, which recognizes three stop codons
53
Colinearity
Order of nucleotides in a gene correlates directly with order of amino acids in corresponding polypeptide chain
54
Function of protein is dependant on:
Form
55
Structure of amino acid
Amino group, carboxyl group, and R group (side chain), which varies and defines type of amino acid
56
Four main classes of amino acids
Nonpolar (hydrophobic), polar (hydrophilic), positively charged, and negatively charged
57
Peptide bonds
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
Levels of protein structure
Primary, secondary (alpha helix and beta sheet), tertiary, and quaternary (ex: hemoglobin)
59
Three main factors that determine tertiary structure of protein
Disulfide bonds (sulfur atoms that link two different amino acids), polar side chains, and nonpolar side chains
60
Posttranslational modification
Proteins are modified after they are made (crucial to function; ex: on/off switch)
61
Examples of posttranslational modifications
- 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
Example of individual amino acids being modified
Phosphorylation, which is the adding of a phosphate group by kinase, and dephosphorylation, which is removing a phosphate group by phosphatases
63
Role of chaperones in protein folding
Assist
64
Diseases caused by protein foldings incorrectly
Prions, sickle-cell anemia, cystic fibrosis
65
Protein functions
Structural or functionally active (such as enzymes or transcription facotrs Ex: hemoglobin, collagen, keratin, actin and tubulin, immunogloblin
66
Definition and role of enzymes
Cataylsts; lower energy of activation
67
Functional domain
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
Exon shuffling
Shuffling exons between different genes

Molecular Biology (10 decks)

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