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BIO 303 > Exam 4 > Flashcards

Exam 4 Flashcards

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1
Q

transcription

A
  • process where RNA polymerase synthesizes one strand of RNA from a DNA template
  • begins when DNA in a chromosome unwinds near gene to be transcribed
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2
Q

ribonucleotides

A
  • assemble along the unwound DNA strand in a complementary sequence
  • only one strand in a gene is transcribed
  • but dif genes may be transcribed from dif strands
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3
Q

both eukaryotic and prokaryotic genes contain…

A
  • transcriptional units made up of:
  • promoter
  • RNA-coding sequence(s)
  • terminator region
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4
Q

promoter

A
  • DNA sequence that the transcription apparatus recognizes and binds to
  • located in the 5’UTR (upstream)
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5
Q

bacterial transcription

A
  • many genes transcribed at once
  • genes and proteins are almost always colinear
  • 3 steps:
  • initiation
  • elongation
  • termination
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6
Q

initiation of transcription

A
  • first step in bacterial transcription
  • RNApol binds to DNA at the gene’s promoter
  • DNA helix unwinds
  • RNA synthesis begins
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7
Q

elongation of transcription

A
  • second step in bacterial transcription
  • DNA threaded thru RNApol at transcription bubble
  • RNA strand growing 5’ -> 3’
  • A in DNA [paired with U in RNA
  • 30-50 nucleotides per second
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8
Q

termination of transcription

A
  • 3rd step in bacterial transcription

- RNApol reaches “bumps” in terminator region and falls off

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9
Q

polycistronic RNA

A
  • in bacterial cells many genes can be transcribed at once

- RNA that codes form multiple proteins

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10
Q

genes and proteins are almost always ______ in bacteria

A

-colinear

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11
Q

eukaryotic transcription

A
  • additional step to transcription after initiation, elongation, and termination
  • final step= RNA processing
  • step modifies newly synthesized RNA (heterogeneous nuclear RNA)
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12
Q

complex internal organization of eukaryotic genes

A
  • promoter region
  • introns (noncoding nucleotides that are transcribed but not translated into amino acid sequence of protein)
  • exons (intervene between coding sequences)
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13
Q

RNA processiong

A
  • final step of transcription of eukaryotic cells
  • modifies heterogeneous nuclear RNA:
  • caps added for initiation of translation and stability
  • poly adenine tail (30-100 A’s long) added
  • slicing removes introns
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14
Q

why transcription is a highly regulated process

A
  • initiation of transcription (ex lac operon)
  • splicing (alternative splicing yields dif proteins from same gene)
  • nuclear export (mature mPNA hidden in nucleus and released w signals like first responders)
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15
Q

mutations to splice sights

A
  • cause genetic disorders
  • ex. beta-thalassemia inherited blood disorders
  • improper splicing results in defective form of hemoglobin and anemia
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16
Q

translation of mRNA

A
  • mRNA is translated from language of nucleic acids to amino acids (protein)
  • enzymes and RNA translate mRNA
  • euk: mature mRNA exported out of nucleus into cytoplasm to be translated by ribosomes
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17
Q

ribosomal RNA (rRNA)

A

-major component of ribosomes/ organelles that construct proteins

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18
Q

transfer RNA (tRNA)

A
  • interpreters that read mRNA code and insert amino acids into growing protein
  • cloverleaf structure
  • amino acid attachment site at 3’ end (always CCA)
  • each has unique anticodon which pairs to codon on mRNA during translation
  • hydrogen bonds bwtn bases
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19
Q

flow of genetic info

A
  • DNA is transcribed into RNA (genetic info is copied into mRNA)
  • RNA is translated into protein (amino acids are polymerized into polypeptides which are then folded into proteins)
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20
Q

one gene, one-polypeptide hypothesis

A

-some proteins are composed of multiple polypeptides

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21
Q

proteins have variety of functions

A
  • fibroin (spider’s web)
  • luciferin (generates bioluminescence, firefly ex.)
  • ricin (natural poison in castor beans)
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22
Q

3 characteristic groups of all (20) amino acid

A
  • amino group (-NH2)
  • carboxyl group (-COOH/ -COO)
  • unique side chain (-R)
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23
Q

peptide bonds

A

-join amino acids to form polypeptide chains

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24
Q

polypeptides

A
  • polar
  • read from N-terminus to C-terminus
  • after formation it folds into 3D shape (determined by a.a. sequence)
  • once folded, polypeptide makes a protein
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25
Q

how is a proteins 3D shape determined

A

-protein’s amino acid sequence determines 3D structure and function

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26
Q

4 levels of protein structure

A
  • primary
  • secondary
  • tertiary
  • quaternary
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27
Q

primary level

A
  • linear amino acid sequence in polypeptide chain

- most important level

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28
Q

secondary level

A
  • hydrogen bonding btwn peptide bonds (backbone)
  • causes amino acid to fold in pattern on itself
  • forms 3D alpha helix fig, pleated flat sheet (or beta sheet), and randomized coil structures
  • interactions btwn NH and CO groups
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29
Q

tertiary level

A
  • folding of secondary structure back on itself again (side chain interactions)
  • forms 3D folded polypeptide chain pattern
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30
Q

quaternary level

A

-interactions between two or more polypeptide chains

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31
Q

the genetic code

A
  • info to encode a single a.a. is carried in sequence of 3 nucleotides
  • code is degenerate (several code words have same meaning)
  • multiple stop codons
  • one start codon (AUG)
32
Q

codon

A

-sequence of 3 nucleotides/ each triplet

33
Q

how many combos of nucleotides encode the 20 a.a.

A

-3 nucleotides gives 4^3 dif combos

34
Q

nucleic acid code in mature mRNA is _______ into amino acids to synthesize polypeptides

A

-translated

35
Q

3 sites in the ribosome

A
  • aminoacyl (A) site: site for the next aminoacyl tRNA, closest to 3’ end of mRNA
  • peptidyl (P ) site: site of growing polypeptide chain
  • exit (E) site: site where spent tRNA is expelled
36
Q

structure of tRNA

A
  • amino acid attaches to 3’ end (sticks out)

- anticodon loop: anticodons on this cul-de-sac attach and decode the mRNA

37
Q

4 stages of protein synthesis

A
  • tRNA charging
  • initiation
  • elongation/ translocation
  • termination
38
Q

tRNA charging

A

-requires amino acid, tRNA and energy (ATP)

39
Q

initiation of protein synthesis

A

-requires initiation factor proteins (IF’s) to assemble the small and large ribosomal subunits onto mRNA template

40
Q

elongation/ translocation of protein synthesis

A
  • building blocks occupy A site, P site, and E site
  • tRNA with amino acid attaches to mRNA
  • repeat these steps xMANY
  • everytime peptide blond forms, elongation is repeated
41
Q

termination of protein synthesis

A

-elongation ceases once a stop codon is reached (UAA, UAG or UGA)
-release factors bind the ribosome and complex falls off
[later: mRNA and tRNA then used again to make new polypeptide]

42
Q

the central dogma

A

-DNA is transcribed into RNA which is translated into a protein

43
Q

Alzheimer’s disease or genetic disorders cause

A

-mutations can cause protein misfolding which results in genetic disorders like Alzheimers

44
Q

cystic fibrosis (CF)

A
  • results from defective folding of CF transmembrane conductance regulator (CFTR) protein
  • delta 508 = misfolded protein that is identified as destructive, then destroyed before the protein can even leave the ER
45
Q

prion diseases

A

-protein refolding diseases

46
Q

prions

A

-proteins refolded into infectious conformation that then causes several disorders (ex. mad cow)

47
Q

Creutzfeldt- Jakob disease (vCJD)

A
  • human variant of mad cow disease (BSE)
  • prions cause normal proteins in body to refold into new, infectious 3D shapes
  • new infectious shapes kill cells in brain and nervous system
  • brain matter becomes sponge like with holes/ voids in brain (unable to communicate btwn brain and body)
48
Q

gene expression

A

-genes (in nucleus of eukaryotes) that are turned on and off in response to external stimuli

49
Q

gene regulation

A

-encompasses the mechanisms and systems that control the expression of genes

50
Q

central dogma fails to explain _____

A
  • the way the flow of information is regulated

- does connect genotype to phenotype tho

51
Q

e.coli biochemical flexibility

A
  • e.coli is able to have biochem flexibility (converts nourishment into what it needs) because of gene regulation
  • this optimizes energy efficiency bc it would be too hard for the e.coli to constantly produce all the enzymes for every Dif environment
52
Q

gene

A
  • any DNA sequence that is transcribed into an RNA molecule (which may or may not encode protein)
  • include DNA sequences for proteins, rRNA, tRNA, snRNA, and other types of RNA
  • may be expressed all the time or intermittently
53
Q

structural genes

A

-encode proteins used in metabolism, biosynthesis, or that play structural role in the cell

54
Q

regulatory genes

A

-encode proteins or RNAs that interact with other sequences affecting transcription or translation

55
Q

constitutive genes

A

-expressed all the time

56
Q

regulatory elements

A
  • DNA sequences that are not transcribed, but still play role in regulating other nucleotide sequences
  • ex. promoter, operator, etc.
57
Q

many levels of gene regulation/ control

A
  • alteration of structure
  • transcription
  • mRNA processing
  • RNA stability
  • translation
  • post-translational modification
58
Q

positive control gene expression

A
  • stimulate gene expression

- activator (regulatory protein that binds to DNA) involved

59
Q

negative control gene expression

A
  • inhibit gene expression

- repressor involved

60
Q

operon

A
  • group of bacterial structural genes that are transcribed together (into a polycistronic mRNA)
  • controlled by single promotor
61
Q

where does the operon regulate the expression of structural genes

A
  • transcriptional level

- most important level in bacteria

62
Q

inducer

A
  • a substance that stimulates transcription in an inducible system of gene expression
  • usually a small molecule that binds to a repressor so that it cannot bind to the DNA sequence so that transcription can occur
63
Q

repressor

A

-regulatory protein that binds to DNA sequence (on operator) to stop transcription

64
Q

inducible operon

A
  • transcription is normally off, can be turned on by inducer
  • inducer binds to activator on mRNA
  • activator attaches to mRNA at CAP site before RNA pol binding site
65
Q

repressible operon

A
  • transcription is normally on, can be turned off by repressor
  • corepressor can bind to repressor
  • binds to operator behind RNA pol
66
Q

negative inducible operon

A
  • transcription is off when active protein binded, but when inducer binds to protein transcription occurs
  • ex. lac operon
67
Q

negative repressible operon

A

-transcription is on but when corepressor binds to inactive repressor protein it binds to mRNA and stops transcription

68
Q

allosteric

A
  • shape change in repressor protein caused by corespressor

- enables repressor to bind with operator

69
Q

repressible operons usually control ____ that carry out _________ of molecules (amino acids)

A
  • control proteins

- carry out biosynthesis

70
Q

gene regulation in eukaryotic cells

A
  • genes not organized into operons so can’t transcribe in polycistronic mRNA (groups)
  • chromatin structure affects expression of genes
  • gene regulation can happen at RNA processing level
  • nuclear export of mRNAs regulates
  • RNA degradation regulates
71
Q

how does chromatin structure affect gene expression (eukaryotic)

A
  • DNA must partially unwind from histone proteins before transcription
  • HATs; DNA wraps around histones, but histone will loosen grip when acetyl group is transferred
72
Q

how does gene regulation happen at RNA processing (eukaryotic)

A
  • alternative splicing allows pre-mRNA to be spliced in many dif ways
  • may generate dif proteins in dif tissues or at dif times in development
73
Q

RNA degradation

A
  • form of gene regulation (eukaryotic)

- greater time lag transcription and translation allows mRNA stability to be manipulated in eukaryotes

74
Q

lac operon

A
  • ex. of initiation of transcription
  • ex. of negative inducable set of genes
  • without lactose: repressor protein binds to lacO operator not allowing transcription
  • lactose present:allolactose (present if lactose present) binds to repressor protein which does not allow it to bind to mRNA, this allows transcription to happen; transcription then produces more enzymes needed to break down glucose so it can transcribe more.
75
Q

allolactose

A
  • isomer of lactose (present if lactose is present)
  • acts as an inducer of transcription
  • if allolactose is bound to inducer then inducer does not bind, so RNApol can bind to transcribe

BIO 303 (4 decks)

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