RNA and Protein Flashcards
1
Q
Kinds of RNA
A
- messenger RNA
- transfer RNA
- ribosomal RNA
- catalytic RNA
2
Q
mRNA
A
- template for protein synthesis
- contains the message (coding region) that is translated by the ribosome into protein, as well as some untranslated RNA involved in ribosome recognition and termination
3
Q
tRNA
A
- decodes the message and loads the amino acid
- contains antidon complementary to codon
- charged with AA corresponding to anticodon
4
Q
rRNA
A
- together with the ribosomal proteins make up the ribosome
5
Q
catalytic RNA
A
- RNA enzymes involved in diverse processes.
6
Q
RNA base pairs
A
- takes on the form of stem loops
7
Q
greatest to least prevalence of RNA in cell
A
rRNA>tRNA>mRNA
8
Q
RNA synthesis - transcription
A
- transcribed from DNA via a DNA-dependent RNA polymerase
- synthesizes RNA 5’ -> 3’
- RNA is transcribed from DNA
- RNA pol does not require a primer
9
Q
RNA pol binds to which strand
A
- template strand
10
Q
RNA produced has the same sequence as the
A
- coding strand
11
Q
3 steps of transcription
A
- initiation - RNA pol binds to promotor
- elongation - RNA is polymerized
- termination - RNA polymerase detaches
12
Q
RNA polymerase subunits
A
- alpha - chain initiation and interaction with regulatory protein
- beta - DNA binding and RNA elongation
- beta prime - DNA binding subunit
- sigma - promotor recognition
13
Q
why multiple sigma factors
A
- each is used for different growth conditions and recognizes slightly different promotors.
14
Q
holoenzyme
A
all 4 subunits together
15
Q
core enzyme
A
consists of only a, b, and b’
16
Q
promotor structure
A
- transcription initiated here. promotor not transcribed
- binding site for polymerase
- conserved sequences at -10 and -35
- transcription start site is +1
17
Q
Pre-initiation
A
binding of sigma factor to RNA polymerase core converting polymerase to holoenzyme
18
Q
Pol binding
A
- binding of holoenzyme (open hand) to promotor DNA sequence
- wrapped of DNA around holoenzyme (touches about 75-80 bp)
19
Q
formation of open complex
A
- closing of open hand structure
- melting of about 10-15 bases
- incorporation of monomers into polymer until a length of about 10
20
Q
elongation
A
- holoenzyme loses sigma factor and loses contact with -10 and -35 regions of promotor
- the core contacts 30-40 DNA bases and can incorporate 30-60 RNA monomers/sec
21
Q
termination
A
- elongation stops
- transcript RNA is released
- dissociation from DNA
22
Q
two main classes of termination
A
- rho dependent
- rho independent
- both rely on formation of stem loop (inverted repeats)
23
Q
rho independent termination
A
- RNA stem loop causes the polymerase to stall
- poly-U stretch behind the stem doesn’t have enough energy to hold RNA-DNA hybrid together and complex falls apart
24
Q
rho dependent termination
A
- Rho assembles as a hexamer on G-C rich RUTS on RNA. Stem loop forms
- translocates up RNA, catches up to RNAP, and dissociates RNA-DNA hybrid through helices activity.
25
RNA stability
- rRNA and tRNA stable due to large amounts of secondary structure
- mRNA is not stable
26
post-translational processing of protein
- cleavage
- insertion of non-protein ligands
- chaperon-mediated folding
- association with other proteins
27
protein primary structure
- sequence of amino acids
28
protein secondary structure
- alpha helix
- beta sheet
- fold due to R groups on primary sequence
29
protein tertiary structure
- how helices and sheets interact + co-factors
30
protein quartenary structure
- interaction of two or more polypeptides
31
protein folding
- all information required for proper folding of a protein resides in its primary sequence
- each protein has a thermodynamically defined stable structure
32
mis-foldings
- proteins often will not find the true thermodynamically favored structure without falling into "local" energy minima
33
chaperones
- help proteins fold
34
ways chaperones help fold
- proline peptidyl isomerase
- binding/release of hydrophobic regions of protein
- providing a safe surface/chamber for folding
- providing energy to escape a local minimum
35
GroEL
- provides a safe surface for protein to fold if it falls into a local min
36
GroES
- provides the energy
37
why proline needs it's on chaperone protein
- free rotation around all peptide bonds except protein
| - PPI breaks bonds to allow for isomerization then reforms
38
integral membrane protein
- spans membrane many times
| - inserted into membrane while being translated
39
secreted proteins
proteins targeted for secretion have a hydrophobic signal sequence which directs them to the sec secretion apparatus
40
sec system
- most proteins use
- proteins are secreted off the ribosome in a linear fashion before any folding as taken place.
- fold in the periplasm
- have signal sequence that contains charged residues following by a series of hydrophobic residues.
41
tat system
- can't fold in periplasm
- fold on inside then go outside
- signal sequence that is recognized by two consecutive arginine residues located near N-terminus of protein
42
open reading frame
- the coding region of DNA and RNA
