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BIOL 1020 FINAL > Topic 10: gene expression > Flashcards

Topic 10: gene expression Flashcards

1
Q

Who worked on the haploid Neurospora (bread mould)?

A

George Beadle and Edward Tatum

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2
Q

What is transcription?

A

-RNA made is a copy of one strand of DNA (template strand)
-DNA template strand read 3’ to 5’
-RNA is synthesized 5’ to 3’
-RNA made is complementary to the DNA template strand
-U’s instead of T’s in RNA
-non template strand can be used to determine the amino acid sequence in the RNA

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3
Q

What is translation?

A

-ribosomes read mRNA in 5’ to 3’ direction
-groups of three bases are read out as triplets called a codon by the ribosome
-each triplet codes for an amino acids, or a stop signal to end translation
-occurs in the cytosol

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4
Q

How many triplets are there?

A

64 possible triplets, only 20 amino acids

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5
Q

How to read the genetic code?

A
  1. start at the 5’ end of the mRNA and find the first AUG. Translation by the ribosome starts here.
  2. this is the “reading frame”. Read out the next codon.
  3. Keep going until you hit a STOP signal, where ribosome will stop translating the mRNA
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6
Q

Where does Transcription start? (STEP 1)

A

“Upstream” is a promoter, where RNA polymerase will attach and initiate transcription.

-“TATA” box approx. 25 base upstream from start
NONTEMPLATE STRAND: TATA box 5’ to 3’
TEMPLATE STRAND: 3’ to 5’

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7
Q

What is the end point of transcription?

A

“termination”, located “downstream” of the start site

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8
Q

What are transcription factors and what role to they play? (STEP 2)

A

are proteins that bind to the DNA at specific locations, such as the TATA box
-role: initiating transcription of all genes
-can bind to other transcription factors via protein-protein interactions

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9
Q

What is step 3 of transcription initiation?

A

more transcription factors bring in RNA polymerase II
-positioning of transcription factors at the TATA box is just right that it brings RNA polymerase II to the right position, allowing transcription at the exact correct site
-transcription factors and RNA polymerase form the transcription initiation complex
-once RNA polymerase II has left the initiation site, another can bind and start transcribing.
-Continues as long as GENE IS ACTIVE!

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10
Q

Describe Transcription Elongation?

A

RNA Polymerase II
-unwinds the DNA strands (10-20 nucleotides exposed)
-read template strand 3’-5’
-catalyses the polymerization of ribonucleotides in a 5’ to 3’ direction
*adds base to 5’ phosphate to the 3’ hydroxyl of previous base
-uses ATP, GTP, CTP, UTP as substrate

a single gene can be transcribed by multiple molecules RNA polymerases (follow like ducks)

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11
Q

What happens at transcription termination?

A

Occurs when RNA Polymerase hits a specific sequence of nucleotides that tells it to stop

PROKARYOTES: “terminator” sequence
EUKARYOTES: “polyadenylation signal” (AAUAAA), RNA polymerase keeps going for a bit, but enzyme cleaves the RNA just after the signal, releasing pre-mRNA for further processing

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12
Q

What are the steps of transcript processing?

A
  1. 1 5’ cap is added that protects 5’ end (helps translation). Formed from Guanine.
  2. Introns are “spliced” out and the axons are stitched together to give a full coding statement.
  3. right after the polyadenylation signal, a poly-A tail is added. This gives mRNAs stability in the cytosol and helps in translation.
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13
Q

What is pre-mRNA ?

A

has to be processed before leaving the nucleus , after transcription its called pre-mRNA

-undergoes RNA processing, both ends of transcript are altered and internal parts gets spliced out (introns) and stitched together (axons)

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14
Q

What happens to introns?

A

gets spliced

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15
Q

What happens to Exons?

A

gets stitched together

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16
Q

What happens to the processed transcribed RNA ?

A

we can convert back to DNA
-called complementary DNA (cDNA)… includes axons spliced together without the introns

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17
Q

What is Genomic DNA (gDNA)?

A

includes all the axons spliced together and the introns still intact

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18
Q

What is RNA splicing?

A

carried out by enzyme: spliceosome
-an enzyme complex binds to several short sequences along an intron, which includes key sequences at either end
-intron is then cut by spliceosome and rapidly degraded
-spliceosome stitches (ligates) the axons together

spliceosome activity is an example of ribozymes, RNA molecules with enzymatic functions

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19
Q

a single gene can encode for multiple polypeptide, which polypeptide is produced is dependent on what?

A

which introns get spliced out and axons get stitched together

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20
Q

What is Alternative RNA splicing?

A

process by which different introns and axons are spliced out within a single transcript to yield different polypeptides
-results: number of proteins that can be made being higher than the number of genes present within the genome

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21
Q

What are protein domains?

A

functional regions where stuff happens (active sites for catalytic reactions, protein to integrate into the plasma membrane)

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22
Q

How do introns facilitate evolution?

A

Due to exon shuffling
-crossing over of the exons of an allele during meiosis
-non-homologous mixing and matching of axons between different genes
-novel combination of a.a. –> novel proteins –> novel funtions

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23
Q

What are the components needed for translation:

A
  1. mature mRNA exported from the nucleus
  2. tRNAs that recognize the codons on the mRNA with their anticodons on the tRNA
    -written 3’ to 5’
  3. Ribosomes (made from rRNA and proteins)
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24
Q

What are tRNA structure and functions?

A

translation occurs by transfer RNAs
-transfer a.a. from the cytoplasm to the growing polypeptide chain in the ribosome
-a.a. in the cytoplasm are stocked by synthesis or recycling them from other cellular processes

SHAPE: small RNA twisted into ‘cloverleaf’ shape (2D shape) with some intra-molecule base pairing

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25
Q

What is amino-acid tRNA?

A

tRNA + the proper amino acid attached

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26
Q

How are tRNAs matched with their correct amino acids?

A

via an aminoacyl-tRNA synthetase
-20 specific amino acids
-20 specific aminoacyl-tRNA synthetases

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27
Q

Steps for tRNA matching with their correct amino acids?

A
  1. the amino acid and the appropriate tRNA enter the active site of the specific synthetase (covalent bond)
  2. Using ATP, the synthetase catalyzes the covalent bonding of the amino acid to its specific tRNA
  3. the tRNA charged with its amino acid is released by the synthetase
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28
Q

What are ribosomes composed of?

A

-rRNA (ribosomal RNA)
-proteins

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29
Q

What are ribosomes 2 subunits?

A

large and small
-synthesized in the nucleus and then exported to the cytoplasm
-fully formed when mRNA is threaded through

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30
Q

What are ribosomes functions?

A

-facilitate codon-anticodon matching (on binding sites)
-from peptide bonds

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31
Q

What are the three tRNA sites?

A

LOCATED ON RIBOSOMES
E (step 3)= exit (‘spent’) tRNAs are ejected)
P (step 2)= peptide (the tRNA holding the polypeptide is)
A(step 1)= aminoacyl (charged tRNAs attach)

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32
Q

Steps to building a polypeptide?

A
  1. ribosome is made of rRNAs and bunch of associated proteins
  2. binds an mRNA at the 5’ end and finds the first AUG codon
  3. read out triplet codons, matching codons with appropriate anticodon of the appropriate tRNA
  4. catalyzes the attachment of the single amino acid of the ‘newly’ matched tRNA with the previously attached Amino acids to form a polypeptide with the proper a.a sequence
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33
Q

Describe Initiation of Translation?

A
  1. small ribosomal subunit binds to the 5’ end of mRNA and looks for first AUG codon
  2. the first tRNA carrying (start) codon attaches by codon/anticodon binding
  3. after GTP is hydrolyzed, large ribosomal subunit attaches (completes the initiation complex)
  4. ribosome then starts ‘reading’ rest of mRNA codons 5’ to 3’ direction
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34
Q

Describe Elongation of Translation?

A

** lecture 25 slide 14 ***

35
Q

Describe Termination of Translation?

A

1.)
- when a ribosome reaches a stop codon on mRNA site
-a release factor is a protein that recognizes stop codons by a.a / base interaction

2.)
-release factor causes the ribozyme to hydrolyze the polypeptide form the tRNA in the P site
(2 GTP –> 2 GDP + 2Pi

3.) ribosomal subunit dissociates

36
Q

What are some post-translation modifications?

A

-As a polypeptide is synthesized it already begins to be folded based on its amino acid sequence (primary structure) with secondary (alpha helix or beta pleated sheets) and tertiary (3D) structures
*genes determine the primary structure
*primary structure determines shape

-AMINO ACIDS may be chemical modified by attaching sugars, lipids, phosphate groups etc.

-ENZYMES may remove one or more amino acids from the leading end

-ENZYMES. may also cleave the polypeptide into smaller chains or join two or more polypeptides into a single chain

37
Q

What are the two kinds of ribosomes?

A

CYTOPLASMIC: free ribosome are in the cytosol and synthesis polypeptides that will stay in the cytosol

MEMBRANE: bound ribosomes are attached to the cytosolic side of the rough ER/ nuclear envelope
-make proteins for endomembrane system

38
Q

Polypeptides destined for the endomembrane system (or secretion) are marked by a single peptide, how does the signal-recognition particle work?

A

SRP escorts the ribosome to a receptor protein in the ER membrane, locks it on and polypeptide synthesis continues there.

39
Q

lecture 25 slide 19****

A
40
Q

What happens if there are changes in a genetic code?

A

Mutations

41
Q

What are point- mutations ?

A

change in a single nucleotide

42
Q

What are nucleotide-pair substitution mutations?

A

replacement of a nucleotide and its partner with another nucleotide pair

43
Q

What are silent mutations?

A

no observable effect on phenotype since the amino acid didn’t change

ex. change one nucleotide in a codon triplet results in the same amino acid being coded

44
Q

What is a missense mutation?

A

one amino acid is changed for another

45
Q

What is Nonsense mutation?

A

a point change results in a stop codon, resulting in premature termination

46
Q

What is a frameshift mutations?

A

insertions or deletions of nucleotides can change the polypeptide sequence
-may alter the reading frame (if not in multiples of three)
-results in extensive missense mutation

47
Q

Mutations arise in mulitple ways?

A

Mutagens: chemical or physical agents that alter DNA

48
Q

When do prokaryotes express genes?

A

only when they need to be expressed

EXAMPLE: E. coli can produce their own Tryptophan

49
Q

What happens when there is an abundance of tryptophan in the environment?

A

a.) cells reduce the activity of the enzymes that make tryptophan (fast response)

b.) inhibit the expression of the genes that encode the tryptophan enzymes (slower response)

50
Q

What happens if E. coli is in a low tryptophan environment

A

-they can activate a metabolic pathway to produce their own tryptophan

51
Q

What is an Operon and how are they regulated?

A

a group of genes with a common function

regulated by: regulatory genes elsewhere in the genome. These genes encode either activator (turns it on) or repressor (turns it off) proteins that regulate whether the operon will be transcribed

52
Q

What happens if there is no tryptophan ?

A

the repressor isn’t functional. thus, RNA polymerase can bind to the promoter and transcribe the trap to true genes to make the tryptophan biosynthetic enzymes

53
Q

What are repressor proteins?

A

bind to the operator, this preventing RNA polymerase from binding to the promoter to initiate gene transcription
-they are specific for the operator within a specific operon
-encoded by a regulatory gene, which sits upstream from the trp operon
-constantly expressed and produced in its inactive form, but only works when tryptophan binds to it, hence its an ALLOSTERIC protein

54
Q

What happens if the concentration of tryptophan is high?

A

-tryptophan binds to the repressor protein, activating it (acts as a corepressor)
-the active repressor binds to the operator sequence in the trp operon promoter
-there it blocks the binding of RNA polymerase, so the operon isn’t transcribed
-thus, the tryptophan biosynthetic enzymes aren’t produced

55
Q

Why is the trp operon a repressible operon?

A

it is always on but can be inhibited when a molecule binds to it

56
Q

What is the lactose (lac) operon?

A

an inducible operon (off, but can be turned on when a specific molecule binds to a regulatory protein)

57
Q

Why is the lac operon normally off?

A

E. coli doesn’t normally use lactose as an energy source, so the lac operon is normally off

-the lac repressor protein is made in an active form and prevents the lac operon genes from being transcribed

-thus the genes that allow the bacteria to use lactose are transcribed

58
Q

If lactose is abundant in the environment what happens?

A

allolactose (an inducer) binds to the repressor and inactivates it

59
Q

Inducible operon are usually associated with what?

A

Catabolic processes

60
Q

How does the cell turn gene expression on or off?

A

-signal transduction pathways help the cell to sense when the environment changes and genes need to be expressed to fulfill a need

-cAMP binds to a cAMP receptor protein which binds to the DNA at a specific location upstream of the lac promoter

61
Q

If glucose concentration increase, what happens to cAMP concentrations?

A

as glucose concentration increases, cAMP concentration falls (due to less signal transduction), which reduces binding of CRP, which reduces the amount of RNA polymerase that binds to the operon (reducing transcription)

62
Q

Approximately how many genes are there in humans?

A

20 000 genes and only about 20% are expressed in any specific cell type

63
Q

What are housekeeping genes?

A

genes that are expressed in most cells all the time (actin, tubulin, ATP synthase, glycolysis etc.)

64
Q

What are differential gene expression?

A

the rest of the genes is regulated as differential gene expression

SPATIAL EXPRESSION: different cell types express a set of genes so that cell can do its job
ex. liver cells expressing thin degrading enzymes

TEMPORAL EXPRESSION: expressed at different times
ex. response to the cell perceiving a hormone

65
Q

What are the two ways for differential expression at the transcriptional level?

A
  1. whether the gene is in a heterochromatin (inactive) or euchromatin (active) area of the genome. Done through chromatin modification
  2. Whether specific transcription factors are present in the cell that will allow for the transcription of a specific gene

mRNA processing level: alternative splicing
Translation level: how long the mRNA is active
Protein Level: how long the protein is active before degradation, protein modification affecting activity (phosphorylation)

66
Q

What is Chromatin?

A

-DNA is associated with proteins to form chromatin
-histone tails can be chemically modified by enzymes to alter how tightly the chromatin is packed

67
Q

What is Heterochromatin?

A

tighter packed
-genes in that area are unable (less likely) to be transcribed

68
Q

What is Euchromatin?

A

looser packed
-genes in that area are able to be transcribed

69
Q

What does Acetylation (-COCH3) do?

A

acetylation of the histone tails promotes looser chromatin structure (i.e. euchromatin)
-permits transcription

70
Q

What does Methylation (-CH3) do?

A

of the tails compacts the chromatin into a heterochromatin state. Barr bodies are super methylated

71
Q

What are “epigenetic” marks?

A

-the DNA sequence has not changed and has little to do with this level of regulation
-these marks are replicated through cell division and passed on to progeny

EXAMPLE: why some identical twins have different traits or genetic diseases even though their genomes are the same!

72
Q

What happens to the TATA box alone?

A

on its own it will give very low-levels of transcription

73
Q

Where are control elements located and what are they ?

A

-approx. 2000bp upstream from the TATA box are control elements
-specific nucleotide sequences contained within enhancer regions

74
Q

What are enhancer regions?

A

-short region of DNA that can increase transcription of genes

75
Q

What is a repressor?

A

any protein that binds to DNA and thus regulates the expression of genes by decreasing the rate of transcription

76
Q

What is an activator?

A

any chemical or agent which regulates one or more genes by increasing the rate of transcription

77
Q

What is a DNA bending protein?

A

if the activator transcription factors bind the enhancer elements, the DNA bending protein bends the DNA, placing the enhancers + activators close to the TATA box and transcriptional start site

78
Q

What is the mediator complex?

A

the DNA bending proteins interacts with a group of proteins that form the mediator complex, which ‘mediates’ the interaction of the activators and the initiation complex

-mediators help bring in the general transcription factors and RNA polymerase II to form the initiation complex

-this increases the rate at which RNA polymerase II is recruited to the transcriptional start site, so the rate of transcription is much higher

79
Q

All cells carry how many genes?

A

20 000 genes

80
Q

How do liver cells works?

A

the gene that encodes albumin is expressed in liver cells and has a specific combination of enhancer elements

-a liver cell expresses activators that will recognize each of these, so the albumin gene is turned on

-the cystallin gene has different enhancer elements that the liver activator proteins don’t recognize, so that crystalline gene isn’t transcribed

81
Q

What is alternative RNA splicing?

A

different RNA transcripts are produced depending on which axons and introns are spliced out

-an intron in one transcript may be an exon in another depending on the gene needing to be transcribed

82
Q

what happens to exons and introns during mRNA splicing ?

A

they are spliced out

83
Q

What is a photo-oncogene?

A

a gene that has a normal function (usually in triggering cell division)
-through mutation or errors, the proton-oncogene becomes an oncogene can lead to cancer

84
Q

What are tumour suppressor genes?

A

encode proteins that stop cell division if something is wrong (DNA damage)

BIOL 1020 FINAL (5 decks)

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