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1

Messenger RNAs (mRNA)

encode the amino acid sequences of
all the polypeptides found in the cell

2

Transfer RNAs (tRNA)

match specific amino acids to triplet
codons in mRNA during protein synthesis

3

Ribosomal RNAs (rRNA)

is the RNA component of the
ribosome, interact with tRNA during translation

4

Micro RNA (miRNA)

post-transcriptionally regulate the
expression of genes, by binding to mRNA nucleotide sequences

5

Ribosymes

RNA can be catalytic

6

RNA Polymerase

Elongates an RNA strand in the 5'-3' direction, using the 3' hydrozyl to attack the a-phosphorous atom in the incoming nucleotide and release PPi

7

In Transcription: Where is the non-template strand traversing out of?

Active site

8

In Transcription: where is the template stand running through?

Active Site

9

Non-Template Strand

Coding Strand

10

Coding

Non-Template Strand

11

DNA/RNA hybrid size

8 bp in size

12

Transcription: NTP channels

Sampled in the active site (need right base matching the template)

-Right bases will incorporate
-Wrong bases will have poor Kd and get kicked out of the way

13

Elongation: Footprint size

35 bp worth of DNA

14

Initiation: Footprint Size

100 bp- when RNA polymerase is first associated with DNA

15

What is a footprint?

Extent of how much RNA polymerase covers on DNA

16

What is a template strand?

DNA Strand that serves as the template for RNA synthesis

-Other strand is called CODING because it has the same sequence as the newly made RNA molecule

17

Elongation occurs as a rate of...

50-90 bp/second

18

RNA Polymerase Core Subunits

a,a,B,B',w (omega), o(omega)

19

RNA Polymerase: Sigma Subunit

-Directs enzyme to the promoter
-The chaperone-takes the polymerase to the right promoter to the the right place where it needs to be polymerized
-Different sigmas can be used to turn on different genes all within same Core! To coordinate gene expression. they recognize own promoters

20

RNA Polymerase: alpha Subunit

(2) alphas. Functino is assembly and binding to UP elements (sequence upstream of promoter)

21

RNA Polymerase: Beta Subunit

Main catalytic subunit

22

RNA Polymerase: B' Subunit

Subunit responsible for DNA-building

23

RNA Polymerase: Omega (w) Subunit

appears to protect the polymerase from denaturationg
-Not catalystic role
-If you take away the RNA polymerase, dalls apart faster

24

Does UP element have specificity?

YES that interact with ALPHA subunits and Kd goes down when binding is favorable

25

Does RNA polymerase have proofreading ability?

NO so it makes mistakes every 10^4-10^5 nucleotides
-mistakes in RNA synthesis are not critical because many RNA copes are made from a single gene and they are rapidly degraded/ replaced

26

RNA polymerase binds to how many nucleotides?

100- stretching from 70 bp upstream (negative numbers) of the strat site and 30 bp downstream (positive numbers)

27

Start site is the

FIRST RNA RESIDUE that is incorporated in the RNA (+1 site)

28

Important promoter regions in E.Coli

-10 and -35

29

Pribnow Box

TATA sequence is found on -10 with a second sequence on -35.

-Sigma70 subunit binds to these seuqnces

30

A subunit binds to a third AT-RIch region. Where is it?

-AT rich region (UP element) is at position -40 to -60 in high expressed genes.
-THIS ENHANCES INTERACTION AND LOWERS Kd