genetics chapter 12

DNA transcription

genes

genes

Instead of transcribing the whole DNA strand, RNA transcribes single _____ one at a time.

m

Which RNA carries genetic code to proteins in both eukaryotic and prokaryotic?

same

In prokaryotes, translation and transcription take place at the ____ place and time.

Nucleus

In eukaryotes, transcription takes place in the ______, while translation takes place in the cytoplasm. (one must occur before the other)

shapes

RNA is usually single stranded and can acquire different _____ by forming bonds with itself or other RNA or DNA

pyrimidine

Is uracil a pyrimidine or a purine?

catalytic

RNA can be ______ using ribonzymes

selective

Transcription is ____ meaning only bits of the genome are ever transcribed into RNA

single

the template that RNA uses is only a _____ strand of DNA

triphosphate

Just like DNA replication, transcription requires a ribonucleoside __________ substrate

template

The strand being used for transcription is called the _______ strand

coding

The strand not being used for transcription is called the _____ strand

copy

The RNA strand is an exact _____ of the coding strand (except U for every T)

promoter

DNA sequence that transcriptional apparatus recognizes, indicates which strand of DNA will be transcribed. Determines start site and is not usually transcribed!

downstream

To the right of the promoter is ______

upstream

The promoter and left is _______

CORE

Makes up 4 subunits (2 alpha, 1 beta, 1 beta prime and 1 omega).

holoenzyme

CORE + sigma = _______ which will initiate transcription at the promoter

sigma

____ factor will show CORE the promoter and initiate transcription, different ones will initiate at different promoters.

initiation

____ phase- machinery assembles on promoter, begins synthesis of RNA

elongation

_______ phase- RNA polymerase reads DNA, adds ribonucleotide to growing RNA

termination

______ phase- end of transcription, separation of RNA from DNA template.

yes

Is the terminator usually transcribed?

no

is the promoter usually transcribed?

0

Think of the transcription start site as the origin (_)

triphosphate

The first nucleotide on the strand is a ______ but the rest are monophosphates

pribnow

upstream 10 consensus sequences is the _____ box of the promoter. (more t/a: less hydrogen bonds)

-35

upstream ___ consensus sequences is still part of the promotor (more t/a, less hydrogen bonds)

strong

a ______ promotor is one that attracts a lot of sigma factors and needs to be replicated a lot.

weak

A _____ promoter is one that attracts only a few sigma factors and doesn’t need to be replicated a lot.

5-3

What direction does the RNA polymerase move in?

intrinsic

_____ termination - contains inverted repeat sequences, hair-pin forms and causes the line of U/As to disconnect (rho independent)

rho

This protein causes RNA to release from DNA

rho-dependent

_________ termination - required DNA sequences that causes a pause in transcription (hairpin). stretch of DNA upstream of termination site (rho utilization site)

rut

Rho utilization site is also called the ___

3

How many RNA polymerases do eukaryotic cells have?

RNAP2

What polymeraase is present in pre-mRNA, other RNAs?

RNAP1

Which polymerase is present in rRNA?

RNAP3

Which polymerase is present in tRNA?

cis-acting

regulatory elements located on the template DNA strand which binds to trans-acting factors

promoter

_____ elements: needed to start transcription, must be intact, found within or adjacent to gene

enhancers, silencers

Two types of gene production influencers, affect how much, can be far away from gene!

transcription

________ factors: bind to core promoter, form PIC (pre-initation complex)

TATA

____ box: (goldberg-hogness box) similar to pribnow box, AT rich, good place to start unwinding, TFIID binds

TFIID

protein which binds to Tata box to position RNAP2 correctly

activators, repressors

Two types of transcriptional influencers which influence rate. bind to proximal-promoter elements

folds

When a chromosome _____ the repressors/activators can effect even though far away

Rho-dependent

RNAP1 termination is much like _________ termination because it has a factor that binds to the DNA downstream of the termination site

intrinsic

RNAP3 uses _______ termination by having a string of Us at the end (requires no secondary structure)

RNAP2

______ termination is coupled to cleavage in the 3’ UTR (untranslated region), overachiever, translates past the end of the gene, AAUAAA is incorporated into RNA causing cleavage, recognition causes RNA to be cut (destabilizes and terminates)

nucleus

Where does RNA transcription occur?

5’

__ capping is an addition of an extra nucleotide (backwards guanine) at the 5’ end and methyl group to the end of that

transfer

The 5 prime cap facilitates _____ out of the nucleus and is very important in translocation

poly-A

most eukaryotic DNA has a ______ tail on the end of their 3’ tail, gets binding proteins coat, (polyadenlyation)

exon

coding region (expressed), only mature in mRNA

intron

intergenic region (not expressed)

different

each gene has different introns/exons

GU, AG

The 5’ and 3’ splice cite for introns are usually defined by __ and end in __

branch point

The _____ ____ is usually defined by an A right next to a pyramindine at the end, needs to be fairly close to 3’ end

snRNP

small ribonucleoprotien particles, rely in RNA seq, marks edges of introns

splicosome

Where splicing occurs, pre-mRNA cuts at 5’ site, intron folds back to form a lariat w A, pre-mRNA is cut at 3’ site

transesterification

forming a lariat requires ___________

5’

Which RNA strand is attached to the A to form a lariat?

self-excision

Group 1 introns are found in rRNA and can ________ (ribosomes, transesterification reactions), catalytic reaction

mitochondria, chloroplast

Two organelles where group 2 introns are found. (self-excision) (Fungi, Plants, protists, and bacteria)

introns, exons

All ___ should NOT be included, however some _____ can be excluded (variations of genes)

3’

Which end gets the poly-a tail?

editing

RNA ____ includes either substitution or insertion/deletion editing

guide

post-transcriptional processing editing uses _____ RNA to substitute

trymanosome

Mitochondria and chloroplasts use RNA editing as well as the _______ (ASS)

crick

WHO solved how many nucleic acids make up a codon

codon

3 nucleotides that specify one amino acid

frame shift

anything that interrupts or disrupts the reading frame is called a _____ _____

nirenburg, matthaei

(1961)- accidentally found the first codon by using a line of uracil in a different experiment, found which one had all UUU with radioactive label. only worked with homopolymers tho.

ochoa

WHO discovered the polynucleotide phosphorylase

nirenburg, leder

(1964)- found heteropolymers with triplet binding!, used synthetic mRNA with one codon, three tRNA and used ribosome and then filtered out the rest, found which tRNA bound with mRNA in ribosome, found amino acids

5-3

WHICH way do you read codons???!

isoaccepting

______ tRNA means that they can carry different codons because the third nucleic acids is a wobble

degenerate

means that different codons can code for the same amino acid (many seq = one amino acid) (one seq = one amino acid)

3

which position is the wobble? _rd (3’ codon, 5’ end tRNA)

nonoverlapping

experiments prove that the ___________ code is true rather than the overlapping code

aug

Which codon is the universal start? (Met)

UAA,UAG,UGA

what three codons code for stop? (no tRNA bind with these)

overlapping

In viruses, they have _______ genes which means it has multiple start points. can be beneficial for small amount of info but if a mutation happened it would effect a lot of proteins