Exam 5 part 3

Biochemistry 401 with Foley at Michigan State University

About this deck

By: Kara Brockhaus
Textbook: Biochemistry (Looseleaf)
Created: 2010-11-16
Size: 86 flashcards
Views: 22

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non-template strand aka:

•Coding Strand

•Sense Strand

•(+) Strand

template strand aka:

•Non-Coding Strand

•Anti-Sense Strand

•(-) Strand

Regions of the strand that are upstream are from the

5’ to the coding region

Regions of the strand that are downsteam are from the

3’ to the coding region

RNA synthesis has what 3 steps?

initiation
elongation
termination

details of initiation

-Polymerase finds, and binds to initiation site (promoter)

-Unwinds DNA duplex to allow access of NTPs to template

From closed promoter complex to open promoter complex

details of elongation

NTPs are polymerized,complement template DNA

-DNA template read 3’ to 5’

-RNA polymerized 5’ to 3’

-3’ OH attack on alpha phosphate, PPi loss, hydrolysis to 2Pi.

details of termination

signals instruct the polymerase to dissociate from the DNA and transcription stops

neg. supercoiling by topoisomerase II can facilitate in unwinding and thus

initiation

what is NOT needed for RNA transcription ?

primer

RNA __NT/sec, DNA __dNT/sec

50
800

what are the functions of the two Magnesiums in RNA pol

1. remains in the RNAPol active site = Activates 3´OH
2.leaves with PPi, and a new one enters with the next NTP

the core of the RNA pol is made up of

alpha
beta
beta'

σ decreases core affinity for ____but at the same time allows the core to recognize ___

random DNA
specific promoter sequences

Without σ, the core does not ____

Rather, it binds indiscriminately and tightly to __

initiate transcription
DNA

σ Factor Supplies ___ to the polymerase and

Different σ factors Target __promoters

Specificity
different

alpha subunit of RNA pol core =

structural

beta and beta' of RNA pol core =

active site

initiation of RNA syn almost always begins with

a purine

after initiation of 9-12 residues, what dissociates from RNA syn process?

sigma

sigma 70 is the

standard promoter
(house keeping genes)

sigma 32 is the

heat shock promoter

sigma 54 is the

nitrogen starvation promoter

-35 and -10 are considered

upsteam

anything beyond the imitation site =

downstream

the promoters most similar to the___ will provide the most optimal interaction for the DNA with the __and therefor makes the strongest promoters

consensus sequence
sigma factor

-10 is AKA:

pribnow box

simga touches the DNA at what two spots?

-35 and -10

the Up element is found upstream of ___ and is found in genes that are especially ___

-35
highly expressed like tRNAs

characteristics of the UP element

*binds alpha subunit of RNA pol
*rich in AT dNTPs

Flexibility of DNA in this region to wrap around polymerase

if no rho in RNA transcript how many species?

23S

if rho is at the start of the synthesis in RNA transcript how many species?

10S

if rho is added 30 sec after syn how many species?

13S

if rho is added a minute later how many species?

17S

the rho protein is a ___protein and

Follows Pol and using ___, unwinds the DNA-RNA hetero-duplex

hexameric
ATP hydrolysis

___ cleave RNA at specific sites to make products like rRNA and tRNA

Ribonucleases

Most___ mRNAs are not post-transcriptionally modified

prokaryotic

rRNA and a tRNA are cleaved from one ___

RNA transcript

Some Bases are also modified after transcription

Especially

tRNA

___ binds β subunit of RNA polymerase to prevent transcription

Rifampicin

Antibiotics work by targeting

prokaryotic RNA Polymerases

prokaryotes transcribe and translate in

the same place

in eukaryotes transcription and translation are not___ or in ____

concurrent
the same space

type 1 of eukaryotic RNA pol is found in

the nucleolus

type 1 of eukaryotic RNA pol has what cellular transcripts?

18S
5.8S
28S (rRNA)

type 1 of eukaryotic RNA pol with effects on alpha amanitin

insensitive

type 2 and 3 of eukaryotic RNA pol is found in

nucleoplasm

type 2 of eukaryotic RNA pol has what cellular transcripts?

snRNA
mRNA precursors

type 2 of eukaryotic RNA pol with effects on alpha amanitin

strongly inhibited

type 3 of eukaryotic RNA pol has what cellular components

5S rRNA
tRNA

type 3 of eukaryotic RNA pol with effects on alpha amanitin

inhibited by high concentrations

Polymerases in Eukaryotes:

8-14 subunits
Larger & More diverse and complex than prokaryotes via :

In structure and regulation

RNA pol 2 in eukaryotes is the most ___ and usually has a ___

complex
TATA box

upstream regulatory sequences in eukaryotes

CAAT box
GC box

*can be on coding or template strand
*can be -150 - -40 bp away from start site

TBP Binds and Deforms ___bc of ___interactions

minor groove DNA
hydrophobic
(bends DNA is due to the concentration of A-T in this region)

TBP is a __binding protein

TATA

TBP is not fully ___ and it depends on

symmetric

- Directionality in further GTF additions

- Directionality of transcription itself.

TBP also serves as a ___ for other transcription factors

docking platform

TFIIA binds TBP in the

upstream direction

TFIID

recognizes and binds the TATA box and recruits other members of the basal machinery.

TATA-binding protein (TBP), and TBP-associated factors (TAFs)

TFIIA

binds to TBP

Stabilizes TBP binding to DNA

May serve as an anti-repressor

TFIIB

binds to TBP, stabilizes TBP binding.
May be bound by transcriptional activators that help to activate transcripton at specific promoters

TFIIF

Helps recruit RNA pol II Thought to bind TFIIB

TFIIE

Recruits TFIIH to initiation complex

Required for promoter escape

TFIIH

Contains many subunits,

Phosphorylates the Pol II CTerminalDomain (beings elongation)

*Helicase, Kinase necessary for for promoter escape.

7-methylguanylate 5’ capping does what?

Protects mRNA

Allows recognition by ribosomes for translation

As the__ is synthesized, the 5' cap is added

mRNA

steps in eukaryotic termination

Cleavage signal (at 3' end)
Polyadenylation site
Addition of poly-A tail

wtih ___the ribosome can become a functional mature ribsome via___

18S, 5.8S, 28S, 5S and ribosomal proteins
Pol I

amino acid attachment site in Pol III

CCA at 3' end

steps in Pol III transcripts

Base modification

clip

CCA

(for Pol III)

Intron consensus sequence

begins with __

ends with __

and an internal __
*these 3 things must be retained for proper ___

GU
AG
Adenylate
splicing

size of snRNA in U1

165

size of snRNA in U2

185

size of snRNA in U5

116

size of snRNA in U4

145

size of snRNA in U6

106

role of U1 snRNA

binds to 5' splice site

role of U2 in snRNA

binds the branch site and forms part of the catalytic center

role of U5 in snRNA

binds 5' splic esite then 3' splice site

role of U4 in snRNA

maskes catalyic activity of U6

role of U6 in snRNA

catalyzes splicing

Splicing occurs in two ___and do not require __ input

transesterifications
ATP

Riboprotein particle RNA makes contact with target RNA through

complementary base pairing

Mutation of splice recognition sites can result in

disease

About this deck

By: Kara Brockhaus
Textbook: Biochemistry (Looseleaf)
Created: 2010-11-16
Size: 86 flashcards
Views: 22

About StudyBlue

“I have used this website for three exams, and I see a huge difference in my test results.”
Naj