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AP Bio 1 > Gene Expression & Regulation > Flashcards

Gene Expression & Regulation Flashcards

Ch. 17, 18

1
Q

3 differences between RNA and DNA

A

RNA is:
1. single stranded
2. has a uracil base
3. has a ribose sugar
DNA is:
1. double stranded
2. has a thymine base
3. has a deoxyribose sugar

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2
Q

What is transcription
What is the first product of transcription

A

The synthesis of RNA using DNA information.
The first product of transcription is the primary transcript or pre-mRNA

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3
Q

What is translation

A

The synthesis of a polypeptide using mRNA

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4
Q

What is a triplet code

A

The genetic instructions for a polypeptide chain written in DNA as 3-letter words

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5
Q

True or False:
During transcription, for each gene, only 1 strand acts as the template strand

A

True. Only one strand can be the template to code for a protein

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6
Q

True or False:
The same strand will always be used for any specific gene. The opposite strand may, however, become the template strand for a different gene

A

True. This is determined by enzymes that transcribe the gene

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7
Q

True or False:
RNA synthesis is in antiparallel direction

A

True

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8
Q

What is a codon

A

An mRNA triplet code
One codon codes for one amino acid

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9
Q

What is the coding strand also known as

A

The non-template DNA strand

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10
Q

What is the sense strand also known as

A

The template DNA strand

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11
Q

What is the reading frame

A

The frame in which triplet codes are read together properly so that they produce the proper amino acid

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12
Q

What is RNA polymerase

A

An enzyme that unwindes the DNA double helix and synthesizes the pre-mRNA, and finally closing the DNA strands back together

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13
Q

What is a promoter

A

Sequence of non-coding DNA where RNA pol. and other transcription factors bind to DNA and begin transcription

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14
Q

What is a transcription unit

A

DNA sequence downstream from the promoter to the terminator

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15
Q

What is the start point

A

The nucleotide pair where RNA pol. begins mRNA synthesis

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16
Q

Describe initiaion of transcription in 3 parts

A
  1. Eukaryotic promoter includes TATA box ~25 nucleotide pairs upstream from the start point
  2. Transcription factors bind to DNA (some recognize TATA box) before
  3. Additional transcription factors along with RNA polymerase bind and for Transcription Initiation Complex
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17
Q

Describe transcription in terms of
1. Initiation
2. Elongation
3. Termination

A
  1. After RNA polymerase binds to DNA, it unwinds strands and begins mRNA synthesis at start point on template strand
  2. RNA pol. moves downstream, building mRNA. DNA reforms double helix
  3. pre-mRNA transcript is removed and RNA pol. detaches
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18
Q

What is a transcription factor

A

A protein that mediates the binding of RNA pol. to DNA

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19
Q

What is the TATA box

A

DNA sequence in promoter of As and Ts that helps binding of transcription factors

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20
Q

What is polyadenylation

A

The addition of the poly-A tail to the pre-mRNA

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21
Q

What is RNA processing

A

both ends of the primary transcript are altered and some interior parts are cut out

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22
Q

What are the benefits of the 5’ cap and poly-A tail

A

F. acilitates exportation out of nucleus
A. ttachment to ribosomes is easier
P. rotectes mRNA from degradation

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23
Q

What changes are made during RNA processing

A

Introns and cut out by spliceosomes and a 5’ GTP end cap as well as a poly-A tail are added

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24
Q

What is alternative RNA splicing

A

The different splicing sequences of one gene
(this is determined by enhancers and inhibitors)

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25
Q

What is tRNA

A

An RNA molecule that transfters an amino acid from the cytoplasm to a growing polypeptide chain at a ribosome

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26
Q

What is an anticodon

A

A specific nucleotide triplet sequence that base pairs with an mRNA codon

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27
Q

What is an aminoacyl-tRNA synthetase

A

An enzyme that catalyzes the bonding of a specific tRNA to its specific amino acid (this results in a charged tRNA because the reaction requires an ATP)
There is a specific aminoacyl-tRNA synthetase for each amino acid

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28
Q

Explain the E, P, A sites of a ribosome

A

A. The aminoacyl tRNA binding site is where the next tRNA comes into the ribosome
P. The peptidyl tRNA binding site is where the amino acid chain grows
E. The exit site is where uncharged tRNAs leave the ribosome

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29
Q

Describe translation initiation

A

A small ribosome subunit binds to mRNA
An initiator tRNA (Methionine) will bind to 5’ cap and read along until it finds START codon.
tRNA anticodon hydrogen-bonds to start codon
Big subunit will bond

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30
Q

Describe translation elongation

A

tRNA molecules enter at the A site
Amino acids are added one-by-one to the chain (at the C-terminus) on the previous amino acid
(This requires GTP)

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31
Q

Describe translation termination

A

When a STOP codon is reached, a release factor comes into the A site instead of a tRNA molecule.
This causes hydrolysis between amino acid chain and tRNA.
Chain leaves and remaining complex dissociates.

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32
Q

What is a signal recognition particle (SRP)

A

A particle that escorts the ribosome to the ER during protein synthesis

33
Q

What is a polyribosome (polysome)

A

A string of ribosomes all translating the same mRNA strand

34
Q

What is a mutation
What is a pointshift mutation

A

A mutation is a change to the genetic info. (DNA) of the cell
A pointshift mutation occurs on only 1 nucleotide base pair

35
Q

What is a substitution mutation
What are the 3 types

A

The changing of 1 nucleotide base pair
The 3 types are:
1. Silent - no change to protein being coded
2. Missense - change to amino acid but order of amino acids is not important in nonsense proteins
3. Nonsense - changed mutation now produces STOP codon ; protein may not function

36
Q

What is a frameshift mutation
What are the 2 types

A

A frameshift mutation is a deletion or addition of one nucleotide base pair
The 2 types are:
1. Insertion - the addition of a base pair
2. Deletion - the removal of a base pair

37
Q

What is a control element

A

A non-coding DNA strand that serves as binding sites for transcriptions factors

38
Q

What are the two ways in which metabolic pathways are controlled

A
  1. Cells can adjust activity of enzymes in the cell
  2. Cells can adjust production of enzymes
39
Q

In the tryptophan repressor metabolic pathway, describe the feedback inhibition

A

Activity of the 1st enzyme in the pathway will be inhibited by the end product
Tryptophan is an amino acid that must be produced by cell enzymes if there is none in the environment. When there is enough tryptophan in the cell, it will inhibit the production of new tryptophan-synthesizing enzymes so the cell cannot produce a surplus of the amino acid that will go to waste

40
Q

Describe the operon model of the tryptophan repressor metabolic pathway

A

Cells can regulate the expression of the genes coding for the necessary enzymes
If the environment provides all the necessary tryptophan, the cell will cease production of the enzymes that catalyze tryptophan synthesis

We would see a decrease in mRNA synthesis coding for these enzymes

41
Q

What are coordinately controlled genes

A

In prokaryotic cells, these are grouped genes of related function that will be transcribed into 1 transcription unit, but still become multiple proteins

Coordinately controlled genes have 1 operator for the transcription unit

42
Q

What is an operator

A

The “on/off” switch segment of DNA in prokaryotic cells

Found within promoter or between promoter and regulatory genes

Controls RNA pol. access to genes

43
Q

What is an operon

A

A segment of DNA including the operator, the promoter, and the genes in the transcription unit

44
Q

What is a repressor protein

A

A protein that can bind to an operator, inhibiting RNA synthesis (in both repressible and inducer operons)

Repressors are specific to the operator of each operon

45
Q

What is a regulatory gene

A

A gene located upstream from the operon that codes for repressor proteins

A regulatory gene is continuously expressed, usually at low rates

46
Q

Most repressor proteins (inducer/repressor) are allosteric. What does this mean

A

The shape change of a protein due to activation through the binding of a molecule at a specific site

47
Q

What is a corepressor molecule
What is an inducer molecule

A

Corepressor = A molecule that binds to a repressor protein causing activation
Inducer = A molecule that binds to a repressor protein causing deactivation

48
Q

Describe in short the repressible tryptophan operon when the operon is on and off

A

On
1. Tryptophan is absent in the cell, so
2. The operon is on, coding for tyrptophan-synthesising enzymes therefore
3. The repressor is inactive and unbound
Off
1. Tryptophan is present in the cell, so
2. The operon is off, not producing enzymes, therefore
3. The repressor protein is active with help from the corepressor (tryptophan molecule) and is bound to the operator

Negative Control Operon

49
Q

Describe in short the inducible lac operon when the operon is on and off

A

Off
1. Lactose is absent, so
2. The repressor is active and bound to operator but unbound by inducer, therfore
3. The operon is off, not producing enzymes for lactose digestion
On
1. Lactose is present, so
2. The repressor protein is deactivated by inducer molecule (allolactose) and unbinds from operator, therefore
3. Operon turns on, and lactose-digesting enzymes are synthesized

Negative Control Operon

50
Q

Describe the difference between a “Negative Control” operon and a “Positive Control” operon

A

Negative control = An operon that is turned off by an active repressor protein
Positive control = An operon that is enhanced by an active activator protein

Opposites if you think

51
Q

What is an activator protein

A

A protein that binds to DNA that stimulates gene transcription

Ex. cAMP receptor protein (CRP)

52
Q

Describe in short the positive gene regulation seen in the lac operon

A

On
1. Lactose is present and glucose is scarce, so cAMP levels increase, meaning that
2. cAMP will bind to CRP, causing it to activate and bind to promoter, leading to
3. Increase in RNA’s affinity to bind to and transcribe lactose-digesting enzymes
Off
1. Lactose and glucose are present, so cAMP levels decrease, meaning that
2. cAMP will not be bound to CRP and will not bind to promoter
3. Lactose-digesting enzyme synthesis is not enhanced, but is still happening

Lac repressor is inactive in both senarios

53
Q

What is differential gene expression in eukaryotic cells

A

The different expression of genes by cells within the same genome (they have the same DNA)

54
Q

In what 3 ways is gene transcription affected

A
  1. Location of a gene’s promoter
  2. Histone modification and DNA methylation
  3. Epigenetic inheritance
55
Q

Describe histone acetylation

A

The N-terminus of each histone protein sticks out where the addition of an acetyl group (-COCH3) can be added
This promotes transcription by opening the chromatin strucure into euchromatin

56
Q

Describe DNA methylation

A

The addition of methyl groups to certain nucleotide bases in the DNA
This leads to condensed chromatin in the form of heterochromatin that is hard to transcribe

Genes are more mythylated in cells where they are not transcribed

Daughter DNA strands are methylated with each new replication

57
Q

Describe epigenetic inheritance

A

The inheritance of traits past down to daughter cells that are not DNA-sequence based

Ex. Methylation/acetylation, DNA scaffolding, positive operon function

58
Q

In eukaryotic cells, what are the 4 ways in which initial transcription is regulated

A
  1. General transcription factors (GTFs) at the promoter
  2. Enhancers and specific transcription factors (STFs)
  3. Combinatorial control of gene activity
  4. Nuclear architecture
59
Q
A
60
Q

Describe how GTFs at the promoter affect initial gene transcription

A

GTFs must bind to/around the promoter before RNA polymerase can bind to DNA and begin synthesis of mRNA

GTFs act as glue between DNA and RNA polymerase

61
Q

Describe how STFs and enhancers affect initial gene transcription

A

Gene expression can be increased or decreased by the binding of STFs to enhancers

STFs here are activators / repressors

Enhancers are control elements

62
Q

Describe how enhancers can still affect a gene even if they are 1000s of nucelotides away

A
  1. Activator proteins bind to enhancers
  2. DNA bending protein bends DNA to bring enhancers close to promoter
  3. Activators bind to mediator proteins and GTFs which relay the message - This is an Active Transcription Initiation Complex
63
Q

Describe how combinatorial control of gene activity affects initial gene transcription

A

Eukaryotic genes that are co-expressed are typically scattered over chromosomes
Coordinate gene expression relys on genes having the same sequence of enhancers
Activator proteins in the nucleus bind simultaneously, causing transcription at the same time

64
Q

Describe how nuclear architecture affects initial gene transcription

A

Transcription factors, RNA polymerase, proteins, etc. are most common in the middle of the nucleus
Chromosomes are also positioned so that the most commonly expressed genes are facing the middle of the nucleus

65
Q

What are the 3 ways in which post-transcription mRNA and proteins are regulated

A
  1. RNA processing
  2. Initiation of translation / mRNA degradation
  3. Protein processing / degradation
66
Q

How does RNA processing regulate post-transcription mRNA

A

Alternative RNA splicing allows different mRNA molecules to be produced from 1 primary transcript

67
Q

How does initial translation and mRNA degradation regulate post-transcription mRNA and proteins

A

During translation initiation, some mRNA can be blocked by regulatory proteins that bind to UTR sequences, preventing ribosomal attachment and leading to degradation

68
Q

How does protein processing and degradation regulate post-transcription proteins

A

Protein processing includes assembly, activation, packing, shipping, etc. (what happens in golgi)
Proteins can be marked for destruction by cell by adding molecules (ubiquitin) to the protein
Big protein complexes (proteasomes) recognize ubiquitin and destroy protein

69
Q

What are some examples of mutagens

A
  • Chemical carcinogens
  • X / UV rays
  • radiation
  • some pathogens
70
Q

What is a proto-oncogene
What is an oncogene

A

Proto-oncogene = A normal gene that codes for cell division
Oncogene = A mutated proto-oncogene that codes for rapid cell division

71
Q

Mutations can lead to 2 problems. What are they

A
  1. Increase in the amount of proto-oncogene protein production
  2. An increase in activity of these proteins
72
Q

The 3 main ways proto-oncogenes become oncogenes:

A
  1. Movement of DNA within the genome
  2. Amplification of proto-oncogenes
  3. Point mutation in the control element / gene itself
73
Q

How does DNA movement within the genome contribute to cancer formation

A

Cancer cells may have broken / incorrectly joined chromosomes. If a proto-oncogene is accidentally placed next to a hyperactive promoter, more cell dividing proteins will be produced

74
Q

How does amplification of proto-oncogenes contribute to cancer formation

A

Amplification of a proto-oncogene can lead to an increase in the amount of cell-dividing proteins in the cell

75
Q

How do point mutations contribute to cancer formation

A

A mutation in the control element can lead to an increase in transcription factors and RNA pol. binding to DNA and thus increase in cell-division proteins
A mutation in the gene itself can code for hyperactive cell-division proteins, causing increased cell division

76
Q

What is a tumor-suppressor gene

A

A normal gene that codes for proteins to inhibit cell division

77
Q

Proteins from proto-oncogenes and tumor-supressor genes are usually part of the…

A

Cell signalling pathway

78
Q

What happens when a Ras G-protein is mutated in a signal transduction pathway

A

Although growth factors are not present to transmit a signal to divide, the mutated Ras protein overexcessively issues the signal to other kinases into the nucleus that the cell must divide. Activators enhance the transcription of proteins that are now overexpressed and the cell divides too much.

79
Q

What happens when a P53 gene is mutated in the cell cycle-inhibiting pathway

A

P53 codes for STFs that synthesize cell-cycle-inhibitor proteins.
If damaged DNA is found, this will be relayed through kinases to the cell-cycle-inhibitor proteins. If the P53 is mutated and cannot make these proteins, there is nothing to stop the damaged DNA from being reproduced during cell division. This can lead to cell division with damaged DNA.

AP Bio 1 (7 decks)

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