RNA and Protein Flashcards Preview

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Flashcards in RNA and Protein Deck (42):
1

Kinds of RNA

- messenger RNA
- transfer RNA
- ribosomal RNA
- catalytic RNA

2

mRNA

- 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

tRNA

- decodes the message and loads the amino acid
- contains antidon complementary to codon
- charged with AA corresponding to anticodon

4

rRNA

- together with the ribosomal proteins make up the ribosome

5

catalytic RNA

- RNA enzymes involved in diverse processes.

6

RNA base pairs

- takes on the form of stem loops

7

greatest to least prevalence of RNA in cell

rRNA>tRNA>mRNA

8

RNA synthesis - transcription

- 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

RNA pol binds to which strand

- template strand

10

RNA produced has the same sequence as the

- coding strand

11

3 steps of transcription

- initiation - RNA pol binds to promotor
- elongation - RNA is polymerized
- termination - RNA polymerase detaches

12

RNA polymerase subunits

- alpha - chain initiation and interaction with regulatory protein
- beta - DNA binding and RNA elongation
- beta prime - DNA binding subunit
- sigma - promotor recognition

13

why multiple sigma factors

- each is used for different growth conditions and recognizes slightly different promotors.

14

holoenzyme

all 4 subunits together

15

core enzyme

consists of only a, b, and b'

16

promotor structure

- transcription initiated here. promotor not transcribed
- binding site for polymerase
- conserved sequences at -10 and -35
- transcription start site is +1

17

Pre-initiation

binding of sigma factor to RNA polymerase core converting polymerase to holoenzyme

18

Pol binding

- binding of holoenzyme (open hand) to promotor DNA sequence
- wrapped of DNA around holoenzyme (touches about 75-80 bp)

19

formation of open complex

- closing of open hand structure
- melting of about 10-15 bases
- incorporation of monomers into polymer until a length of about 10

20

elongation

- 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

termination

- elongation stops
- transcript RNA is released
- dissociation from DNA

22

two main classes of termination

- rho dependent
- rho independent
- both rely on formation of stem loop (inverted repeats)

23

rho independent termination

- 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

rho dependent termination

- 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