Chaptet 12

Question 1

Gene

Answer 1

A segment of DNA that is used to make a functional product, either RNA or a polypeptide

Question 2

Transcription

Answer 2

The act or process of making a copy, or the process of synthesizing RNA from a DNA template

Question 3

Protein encoding genes, or structural genes

Answer 3

Carry the info for the amino acid sequence of a polypeptide

Question 4

Flow of genetic material

Answer 4

DNA—>mRNA—>to polypeptide

Question 5

Gene expression

Answer 5

He overall process by which the information within a gene is used to produce a functional product, such as a polypeptide

Question 6

Promoter vs. Terminator

Answer 6

Promoter provides a site for RNA polymerase binding at the beginning of transcription, and the terminator specifies the end of transcription

Question 7

Template strands

Answer 7

The base sequence in the RNA transcript is complementary to the template strand of DNA

The opposite strand of DNA is the nontemplate strand

Question 8

Coding strand

Answer 8

the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced. It is this strand which contains codons

Question 9

Template strand AKA

Answer 9

The non-coding strand or antisense strand

Question 10

Ribosome binding site

Answer 10

mRNA site for ribosome binding, translation begins near this site

In Eukaryotes, the ribosome scans the mRNA for a start codon

Question 11

Start codon

Answer 11

The first amino acid on a polypeptide sequence, usually

Bacteria: formylmethionine
Eukaryote: methionine

Question 12

Codons

Answer 12

a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule

The sequence of codons within mRNA determines the sequence of amino acids within a polypeptide

Question 13

Stop codon

Answer 13

The end of polypeptide synthesis

Question 14

Transcription factors

Answer 14

Controls the rate of transcription

Some bind directly to the promoter and facilitate transcription

Others transcribe regulatory sequences or elements, regulating or inhibiting transcription

Question 15

Transcription stages

Answer 15

Initiation: The specific binding of transcription factors to the promoter identifies the starting site for transcription

Elongation: RNA polymerase slides along the DNA in an open complex to synthesize RNA

Termination: causes RNA polymerase and the RNA

Question 16

Transcriptional start site

Answer 16

The first base used as a template for transcription and is denoted +1

Bases before this site are numbered in a negative direction

Question 17

Consensus sequence

Answer 17

The most commonly occurring bases within a specific type of sequence

Efficiently recognized by proteins that initiate transcription

Question 18

E. coli, core enzyme subunits

Answer 18

α, α, β´, β, and ω

With a sixth subunit called the sigma factor, which creates RNA polymerase holoenzyme and recognizes the promoter

The two α units are important in the proper assembly of the holoenzyme and in the process of binding to DNA

The β´and β subunits are needed for binding to the DNA and catalyzes RNA

ω important for proper core enzyme assembly

Question 19

Holoenzyme

Answer 19

Required to initiate transcription

Question 20

Released sigma factor

Answer 20

Marks the transition to the elongation phase of transcription, which allows the core enzyme to slide down the DNA to synthesize a strand of RNA

Question 21

ρ-dependent termination

Answer 21

This termination process first requires the rho utilization site to encode a sequence in the RNA that acts as a recognition site for the binding of ρ protein
Next, ρ protein binds to the RNA and moves in the direction of RNA polymerase

Secondly, at the termination site, the DNA encodes an RNA sequence containing several GC base pairs that form a stem loop structure, RNA synthesis terminates several nucleotides

RNA synthesis is paused by hairpin that binds to rna polymerase, p protein then catches up and breaks hydrogen bonds between DNA & RNA within open complex, finally the RNA is separated from DNA

Question 22

ρ protein function

Answer 22

Acts as a helicase, an enzyme that can separate RNA-DNA hybrid regions

Question 23

p independent termination or intrinsic termination

Answer 23

Does not require p protein, instead involves adjacent nucleotide sequences. One of the sequences forms a stem loop, another is a uracil rich sequence located at 3’ end of RNA that pauses RNA synthesis

The uracil rich sequence to the DNA template strand Is weak, causing the RNA transcript to spontaneously dissociate from DNA stopping transcription

Question 24

RNA Polymerase 1 function

Answer 24

Transcribes all of the genes for ribosomal RNA except for 5S rRNA

Question 25

RNA Polymerase 2 function

Answer 25

Transcribes all protein encoding genes, meaning it’s responsible for all mRNA synthesis Also transcribes most snRNAs for RNA splicing Lastly, it transcribes several non-coding RNAs like most microRNAs and snoRNAs

Question 26

RNA Polymerase 3

Answer 26

Transcribes all tRNA genes and the 5S rRNA gene lesser than RNA pol 2 Also transcribes few non-coding RNAs, such as snRNAs, long non-coding RNAs, microRNAs, and snoRNAs

Question 27

Core Promoter

Answer 27

Short DNA sequence that is necessary for transcription to take place Consists of a TATAAA sequence called the TATA box and the transcriptional start site, where transcription begins Produces a low level of transcription by itself

Question 28

TATA box

Answer 28

About 25 bp upstream from a transcriptional start site,

Question 29

Regulatory elements

Answer 29

Short DNA sequences that affect the ability of RNA pol to recognize the core promoter and begin the process of transcription They are recognized by transcription factors Two categories: Enhancers and Silencers Usually located: at -50 to -100 region

Question 30

Enhancers

Answer 30

Activating sequences that are needed to stimulate transcription

Question 31

Silencers

Answer 31

DNA sequences that are recognized by transcription factor that inhibit transcription

Question 32

Cis-acting elements

Answer 32

Regulate particular genes Located far from core promoter, and are always found within the same chromosome as the gene they regulate TATA BOX Enhancers Silencers

Question 33

Trans-acting factors

Answer 33

Protein factors that bind to die acting sequences to control gene expression

Question 34

Proteins needed for basal transcription at the core promoter

Answer 34

RNA Polymerase 2 General transcription factors Mediator

Question 35

General transcription factors (GTFs)

Answer 35

Five different proteins that are needed for RNA polymerase 2 to imitate transcription of protein-encoring genes

Question 36

Assembly of GTFs and RNA polymerase 2 at TATA box

Answer 36

Transcription factor IID first binds to the TATA box and thereby plays a critical role in recognizing the core promoter TATA binding protein directly bonds to TATA box and TBP associated factors Next it associates with TFIIB, promoting the binding of RNA pol 2 and TFIIF Lastly, TFIIE and TFIIH bind to the complex Completing the assembly of proteins to form a closed complex

Question 37

Nasal transcription apparatus

Answer 37

``` TFIID TFIIB TFIIF TFIIE TFIH RNA Pol 2 TATA Box Transcriptional start site ``` DNA is then transcribed to RNA

Question 38

Mediator

Answer 38

Mediates the interactions between RNA Pol 2 and regulatory transcription factors that bind to enhancers or silencers Interface between RNA pol 2 and many diverse regulatory signals Elliptically shapes and wraps around RNA pol 2 Phosphorylates CTD of RNA pol 2

Question 39

Allosteric model

Answer 39

RNA Pol 2 becomes destabilized after it has transcribed the polyA signal sequence, and it eventually dissociates from the DNA

Question 40

Torpedo model

Answer 40

RNA Pol 2 is physically removed from the DNA RNA is cleaved by an exonuclease that degrades the transcript in the 5’ to 3’ direction Lastly when the exonuclease catches up to the RNA Pol 2, this causes it to dissociate from the DNA

Question 41

colinearity

Answer 41

Correspondence between the sequence of codons in the DNA coding strand and the amino acid sequence of the polypeptide

Question 42

Exons

Answer 42

Where coding genes are found, which are regions that are contained within functional mRNA

Question 43

Intervening sequences or introns

Answer 43

Found between exons

Question 44

RNA splicing

Answer 44

To produce a functional mRNA, the sequences in the pre-mRNA that correspond to the introns are removed and the exons are connected or spliced together Common genetic phenomenon in eukaryotes, occasionally in bacteria

Question 45

Exonuclease

Answer 45

Cleaves a bond between two nucleotides at the end of a strand Starting at one end, an exonuclease digests a strand, one nucleotide at a time

Question 46

Endonuclease

Answer 46

Cleaves the bond between two adjacent nucleotides within a strand

Question 47

Ribozyme

Answer 47

RNaseP for example, is a RNA molecule with catalytic activity

Question 48

Self splicing

Answer 48

Group 1 and Group 2 splices without requiring the aid of other catalysts Instead RNA functions as its own ribozyme

Question 49

Group 1 introns

Answer 49

First, binding of a single guanosine to a guanosine binding site within the intron Guanosine breaks the bond between the first Exon and the intron and attaches to 5’end of the intron 3’—-OH group of exon 1 then breaks the bond next to a diff nucleotide Exon 1 forms a covalent bond with 5’ end of Exon 2, degrading the intron RNA

Question 50

Group 2 introns

Answer 50

2’—OH group on ribose in an adenine (A) nucleotide already within the intron strand behind the catalytic process

Question 51

Maturases

Answer 51

Enhances the rate of splicing of group 1 and 2 introns

Question 52

Pre-mRNA

Answer 52

Produced by the transcription of protein encoding genes, which is made in the nucleus Altered by splicing, required the aid of a spliceosome Spliceosome, needed to recognize the boundaries of the intron and to properly remove it

Question 53

Spliceosome

Answer 53

Large complex that splices pre-mRNA Composed of (U1, U2, U4, U5, U6): known as snRNPs Each snRNPs contains small nuclear RNA and a set of proteins Functions: recognizes the intron-exon boundary, catalysts the chemical reactions that removes introns and covalently linked exons

Question 54

Alternative splicing

Answer 54

Produces 2 or more polypeptides from the same gene that have differences in their amino acid sequences Allows an organism to carry fewer genes in its genome

Question 55

Constitutive exons

Answer 55

Encode polypeptide segments of the alpha-tropomyosin protein that are necessary for its general structure and function

Question 56

Alternative exons

Answer 56

The polypeptide sequences encoded by these exons May subtly change the function of alpha-tropomyosin to meet the needs of the cell type in which it is found Varies Regulated by splicing factors

Question 57

Splicing factors

Answer 57

Key role in the choice of particular splice sites and modulate the ability of a spliceosome to choose 5’ and 3’ sites Some inhibit (exon skipping) or enhance ^^ SR Proteins: A splicing factor

Question 58

Cap protein

Answer 58

Required for the proper exit of most mRNAs from the nucleus Recognized by Initiation factors Important in the efficiency of first intron splicing (5’ end)

Question 59

polyA tail

Answer 59

Important for mRNA stability, the exit of mRNA from the nucleus, and synthesizes polypeptide transcribed by polydenylation

Question 60

RNA Editing

Answer 60

The process of making a change in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular nucleotide or a conversion of one type of base to another, such as cytosine to a Uracil Effects, start and stop codon generation and Changing the code in sequence for a polypeptide