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Genetics > Chaptet 12 > Flashcards

Chaptet 12 Flashcards

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Biology 101 flashcards
1
Q

Gene

A

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

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2
Q

Transcription

A

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

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3
Q

Protein encoding genes, or structural genes

A

Carry the info for the amino acid sequence of a polypeptide

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4
Q

Flow of genetic material

A

DNA—>mRNA—>to polypeptide

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5
Q

Gene expression

A

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

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6
Q

Promoter vs. Terminator

A

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

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7
Q

Template strands

A

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

The opposite strand of DNA is the nontemplate strand

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8
Q

Coding strand

A

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

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9
Q

Template strand AKA

A

The non-coding strand or antisense strand

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10
Q

Ribosome binding site

A

mRNA site for ribosome binding, translation begins near this site

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

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11
Q

Start codon

A

The first amino acid on a polypeptide sequence, usually

Bacteria: formylmethionine
Eukaryote: methionine

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12
Q

Codons

A

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

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13
Q

Stop codon

A

The end of polypeptide synthesis

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14
Q

Transcription factors

A

Controls the rate of transcription

Some bind directly to the promoter and facilitate transcription

Others transcribe regulatory sequences or elements, regulating or inhibiting transcription

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15
Q

Transcription stages

A

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

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16
Q

Transcriptional start site

A

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

Bases before this site are numbered in a negative direction

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17
Q

Consensus sequence

A

The most commonly occurring bases within a specific type of sequence

Efficiently recognized by proteins that initiate transcription

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18
Q

E. coli, core enzyme subunits

A

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

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19
Q

Holoenzyme

A

Required to initiate transcription

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20
Q

Released sigma factor

A

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

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21
Q

ρ-dependent termination

A

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

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22
Q

ρ protein function

A

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

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23
Q

p independent termination or intrinsic termination

A

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

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24
Q

RNA Polymerase 1 function

A

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

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25
Q

RNA Polymerase 2 function

A

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

26
Q

RNA Polymerase 3

A

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

27
Q

Core Promoter

A

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

28
Q

TATA box

A

About 25 bp upstream from a transcriptional start site,

29
Q

Regulatory elements

A

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

30
Q

Enhancers

A

Activating sequences that are needed to stimulate transcription

31
Q

Silencers

A

DNA sequences that are recognized by transcription factor that inhibit transcription

32
Q

Cis-acting elements

A

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

33
Q

Trans-acting factors

A

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

34
Q

Proteins needed for basal transcription at the core promoter

A

RNA Polymerase 2

General transcription factors

Mediator

35
Q

General transcription factors (GTFs)

A

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

36
Q

Assembly of GTFs and RNA polymerase 2 at TATA box

A

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

37
Q

Nasal transcription apparatus

A 
TFIID
TFIIB
TFIIF
TFIIE
TFIH
RNA Pol 2
TATA Box
Transcriptional start site

DNA is then transcribed to RNA

38
Q

Mediator

A

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

39
Q

Allosteric model

A

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

40
Q

Torpedo model

A

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

41
Q

colinearity

A

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

42
Q

Exons

A

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

43
Q

Intervening sequences or introns

A

Found between exons

44
Q

RNA splicing

A

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

45
Q

Exonuclease

A

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

46
Q

Endonuclease

A

Cleaves the bond between two adjacent nucleotides within a strand

47
Q

Ribozyme

A

RNaseP for example, is a RNA molecule with catalytic activity

48
Q

Self splicing

A

Group 1 and Group 2 splices without requiring the aid of other catalysts

Instead RNA functions as its own ribozyme

49
Q

Group 1 introns

A

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

50
Q

Group 2 introns

A

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

51
Q

Maturases

A

Enhances the rate of splicing of group 1 and 2 introns

52
Q

Pre-mRNA

A

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

53
Q

Spliceosome

A

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

54
Q

Alternative splicing

A

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

55
Q

Constitutive exons

A

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

56
Q

Alternative exons

A

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

57
Q

Splicing factors

A

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

58
Q

Cap protein

A

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)

59
Q

polyA tail

A

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

transcribed by polydenylation

60
Q

RNA Editing

A

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

Genetics (9 decks)

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