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Genetics > Exam 3 > Flashcards

Exam 3 Flashcards

Chapters 15-17

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1
Q

Amino Acids

A
  • Repeating unit of proteins

- Consists of amino group, carboxyl group, hydrogen atom, and variable R group

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2
Q

Peptide Bonds

A

-Chemical bond that connects amino acids in a protein

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3
Q

Polypeptide Chain

A
  • Chain of amino acids linked by peptide bonds

- Protein

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4
Q

One gene, one polypeptide hypothesis

A

-Each gene encodes a separate polypeptide chain

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5
Q

Sense Codons

A

-Codon that specifies an amino acid in a protein

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6
Q

Degenerate

A

-Refers to the fact that the genetic code contains more codons than are needed to specify all 20 AAs

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7
Q

Synonymous Codons

A

-Diff codons that specify the same codon

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8
Q

Isoaccepting tRNAs

A

-Diff tRNAs w/ diff anticodons that spcify the same AA

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9
Q

Nonoverlapping

A

-Each nucleotide is a part of only 1 codon and encodes only 1 AA in a protein

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10
Q

Reading frame

A
  • Particular way in which a nucleotide sequence is read in groups of 3 nucs (codon) in translation
  • Begins w start codon and ends w/ stop codon
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11
Q

Initiation/ start codon

A
  • Codon that specifies the 1st AA of protein
  • fMet in prok, Met in Euk
  • Most commonly AUG
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12
Q

Stop/Termination/Nonsense codons

A
  • Codon in mRNA that signals the end of translation

- UAA, UAG, UGA

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13
Q

Aminoacyl-tRNA sythetases

A
  • Enzyme that attaches an amino acid to tRNA

- Specific for a particular AA

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14
Q

tRNA charging

A

-Chemical rxn in which an aminoacyl-tRNA sythetase attaches an AA to its corresponding tRNA

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15
Q

IF3

A
  • Protein required for the initiation of translation in proks
  • Binds to the small subunit of the ribosome and prevents the large subunit from binding during initiation
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16
Q

IF1

A
  • Protein required for initiation of translation in proks

- Enhances disociation of the large and small subunits of the ribosome

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17
Q

IF2

A
  • Protein required for initiation of translation in proks

- Forms a complex w/ GTP and charged tRNA & delivers charged tRNA to initiator complex

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18
Q

30s initiator complex

A
  • Initial complex formed in the initiation of translayion in proks
  • Consists of small subunit of ribosome, mRNA, initiator tRNA charged w fMet, GTP, and IFs 1,2, and 3
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19
Q

70s initiator complex

A
  • Final complex formed in the initiation of translation in proks
  • Small and large ribosomal subunits, mRNA, and intiator tRNA charged w fMet
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20
Q

Cap binding complex

A
  • A group of proteins in euks
  • Binds to 5’ cap and initiates translation
  • Aids in exporting mRNA from nucleus to cytoplasm
  • Promotes initial/pioneer round of translation
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21
Q

Aminoacyl (A) site

A
  • One of 3 sites in a ribosome occupied by a tRNA during translation
  • All charged tRNAs w/ expection of initiator tRNAs first enter the A site
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22
Q

Peptidyl (P) site

A
  • One of 3 sites in a ribosome occupied by a tRNA during translation
  • In elongation stage, tRNAs move from A to P site
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23
Q

Exit (E) site

A
  • One of 3 sites in a ribosome occupied by a tRNA during translation
  • In elongation stage, tRNA moves from P to E site
  • –Exits the ribosome
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24
Q

Elongation Factor Tu (EF-Tu)

A
  • Protein taking part in the elongation stage of translation
  • Forms a complex w/ GTP and charged tRNA
  • Delivers charged tRNA to ribosome
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25
Q

Elongation Factor Ts (EF-Ts)

A

-Protein that regenerates EF-Tu in elongation stage of translation

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26
Q

Translocation

A

-Movement of a ribosome along mRNA in the course of translation

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27
Q

Elongation Factor G

A
  • EF-G

- Protein that combines w/ GTP and is required for movement of the ribosome along the mRNA during translation

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28
Q

Release Factors

A
  • Protein required for termination of translation
  • Binds to ribosome when a stop codon is reached and stimulates the release of the polypeptide chain, the tRNA, and the mRNA from the ribsome
  • Euk cell requires eRF-1 and eRF-2
  • Proks require RF-1, RF-2, and RF-3
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29
Q

Structural Genes

A

-DNA sequence that encodes a protein that fxns in metabolism or biosynthesis or that has a structural role in the cell

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30
Q

Constitutive

A

-A gene that is expressed continually w/o regulation

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31
Q

Regulatory elements

A

-DNA sequence that affects the transcription of other DNA sequences to which it is physically linked

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32
Q

Domian

A

-Functional part of protein

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33
Q

Operon

A

-Set of structural genes in a prok. cell, along with their common promoter and other sequences (operator) that control their transcription

34
Q

Regulator Gene

A
  • Gene associated w an operon in prok cells

- Encode a protein or RNA molecule that fxns in controlling the transcription of one or more structural genes

35
Q

Regulator Protein

A
  • Protein produced by a regulator gene

- Binds to another DNA sequence (operator) and controls the transcription of one or more structural genes

36
Q

Operator

A
  • DNA sequence in an operon of prok cells
  • A regulator protein beings to
  • Binding affects rate of transcription of structural genes
37
Q

Neg control

A
  • Gene reg in which the binding of a regulator protein to DNA inhibits transcription
  • Reg protein= repressor
38
Q

Positive control

A
  • Gene reguation in which binding of a reg protein to DNA stimulates transcription
  • reg protein= activator
39
Q

Inducible operons

A

-Operon in which transcription is normally turned off so that something must occur for transcription to be induced/turned on

40
Q

Repressible Operons

A

-Operon in which transcription is normally turned on, so that something must happen for transcriotion to be repressed/turned off

41
Q

Inducer

A
  • Substance that stimulates transcription in an inducible system of gene regulations
  • Usually a molecule that binds to a repressor protein, alters that repressor so that it cannot bind to DNA and inhibit transcription
42
Q

Allosteric Proteins

A

-Protein that changes confirmation upon binding w another molecule

43
Q

Corepressor

A
  • Substance that inhibits transcription in a repressible system of gene regulation
  • Molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription
44
Q

Coordinate Induction

A

-The simultaneous synthesis of several enzymes stimulated by a single environmental factor

45
Q

Partial Diploid

A
  • Prok cells that possess 2 copies of the same genes

- -One on chromosome, one on plasmid

46
Q

Catabolite Repression

A
  • System of gene control in prok. operons

- Glucose is used preferentially and the metabolism of other sugas is repressed in the presence of glucose

47
Q

Catabolite Activator Protein (CAP)

A
  • Proteins that fxn in catabolite repression

- When bound w cAMP, CAP binds to the promoter of certain operons and stimulates transcription

48
Q

cAMP

A
  • Modified nucleotide that fxns in catabolite repression
  • Low levels of glucose stimulate high levels of cAMP
  • –cAMP attaches to CAP, which binds to the promoters of certain operons and stimulates transcription
49
Q

Attenuation

A
  • Type of gene regulation in some prok operons

- Transcription is initiated but terminates prematurely b4 transcription of structural genes

50
Q

Attenuator

A
  • Secondary structure that forms in the 5’ untranslated region of some operons
  • Causes the premature termination of transcription
51
Q

Antiterminator

A

-Protein or DNA sequence that inhibits the termination of transcription

52
Q

Antisense RNA

A
  • Small RNA mol that bps w a complementary DNA or RNA sequence and affects its fxning
  • Control gene expression by binding to sequences on mRNA and inhibiting its translation
53
Q

Riboswitches

A
  • Regulatory sequence in an RNA molecule
  • When inducer binds to riboswitch, binding changes the configuration of the RNA molecule and alters the expression of RNA
  • -Usually by affecting the termination of transcription or translation
54
Q

Structural Genes on the Lac Operon

A
  • Lac Z–> gene that makes B galactosidase enzyme
  • Lac Y–> Permease
  • –Allows lactose into cell
  • Lac A–> Transacetylase
55
Q

Lac I

A

-Regulator gene, encode regulator protein
-Lac I- = nonfunctional repressor protein
-Lac I^s= superrepressor, allolactose cannot bind to it
-Trans
Lac I s> Lac I+ > Lac I-

56
Q

Lac O

A

-operator
-Cis
-LacO^C= Repressor cannot bind to operator region
Lac O c> Lac O+
*Can transcribe structural genes w or w/o lactose

57
Q

Lac Operon

A
  • Ex of negative inducible operon
  • When lactose levels= high, allolactose converted to lactose by B-galactose, binds to repressor protein
  • –Repressor cannot bind to operator, transcription occurs
  • Lactose levels= low, no allolactose, transcription is inhibited
  • –Repressor can bind to operator
58
Q

DNase I hypersensitivity sites

A

-Chromatin region that becomes sensitive to digestion by enzyme DNase I

59
Q

Chomatin remodeling complexes

A

-Complex of proteins that alters chromatin structure w/o acetylating histone proteins

60
Q

Histone code

A
  • Modifications in histone proteins

- Add. or removal of phosphate, methyl, or acetyl groups that encode info affecting how genes are expressed

61
Q

CpG islands

A
  • DNA region that contains many copies of a cytosine base followed by a guanine base
  • Often found near transcription start sites in euk DNA
  • Cytosine base in CpG commonly methylated when genes are inactive
  • –Demethylated b4 initiation of transcription
  • METHYLATED DNA=REPRESSED TRANSCRIPTION
62
Q

3 processes that affect gene regulation by altering chromatin structure

A
  • Chromatin remodeling
  • Modification of histone proteins
  • DNA methylation
63
Q

Methylation of histones

A
  • Histone methyltransferases= add CH3 to histones
  • Histone Demethylases= remove CH3
  • Activates or represses transcription
64
Q

Acetylation of Histones

A
  • Addition stimulates transcription
  • CH3CO
  • Add by acetyltransferase
  • Removed by deacetylases (represses transcription)
65
Q

Arabidopsis and Flowering

A
  • FLD stimulates flowering by deacetylating chromatin around FLC
  • FLC inhibits flowering, when acetyl groups removed it is inhibited
66
Q

Mediators

A

-Complex of proteins that is one of the components of the basal transcription apparatus

67
Q

Insulators

A
  • DNA sequences that blocks or insulates the effect of an enhancer
  • Must be located btwn promoter and enhancer to block activity
  • May also limit the spread of changes in chromatin structure
68
Q

Response Elements

A
  • DNA sequence shared by promoters or enhancers of several euk genes
  • Regulatory proteins can bind to stimulate the coordinate transcription of these genes
69
Q

Regulation of Galactose Metabolism Through Gal4

A
  • Gal4= transcriptional activator protein
  • galactose low= genes not transcribed
  • –High= genes r transcribed and galactose broken down
  • Gal4 binds to UASg–> activates transcription needed to metabolize galactose
  • Gal4 and Gal80 bind–> prevents transcription when gal=low
  • When galactose= present, Gal3 binds to Gal80 so it cant bind to Gal4–> transcription occurs and galactose is metabolized
70
Q

siRNAs scilence transcription by altering chromatin structure

A
  • siRNA combines w protein to create RITS
  • Binds to complementary sequence in DNA or RNA molecule in process of being transcribed, repressing transcription by attracting enzymes that methylate histones
71
Q

Bacterial Enhancers

A
  • Element that affects transcription but far from gene its affects
  • Binding site 4 proteins to increase rate of transcription
  • -Do this by causing DNA btwn enhancer and promoter to loop out and interact w one another
  • Position independent
72
Q

Trp Operon

A
  • Ex of neg repressible operon
  • 5’ UTR has 4 complementary regions
  • –1 comp to 2
  • –2 comp to 3
  • –3 comp to 4
  • —-Allows 5’ UTR to make 2 secondary structures
73
Q

Attenuation process of Trp Operon

A
  • High levels of tryptophan–> no stalling of ribsome cuz tRNAs are charged
  • –> Bping of 3 and 4, hairpin followed by Us–> attenuation
  • Ribosome partially covers 2 when RNA pol finishes 3, so cannot BP
  • –3 bps w 4 because it didn’t w 2
74
Q

Antiterminator process of Trp Operon

A
  • Low levels of tryptophan–> stalling of ribosome cuz tRNA arent charged
  • –> Bping of 2 and 3, hairpin not followed by Us–> No attenuation
  • Ribosome stalls at trp codons UGG
  • 2 and 3 bp because ribosome stuck at 1
75
Q

Combinatorial Control

A
  • Different combinations of activators and repressors determine transcription
  • -Stimulates interaction of multiple regulatory proteins (activators and repressors) binding to enhancers and scilencers in diff combos
76
Q

3 regions that euk regulatory proteins interact w

A
  1. Core promoter
    - -Upstream from gene regulating
  2. Proximal elements
    - -Found in reg. promoter, upstream of gene
  3. Enhancers and Scilencers
    - -Proximity-dependent, bind to activators or repressors
77
Q

SWI/SNF complex

A
  • Chromatin remodeling
  • Uses energy from hydrolysis of ATP
  • Slides or ejects nucleosomes, freeing promoters to bind to transcription factors and RNA pol 4 transcription
78
Q

What does RNA pol do when it encounters nucleosomes? How does this differ for genes of diff transcription levels?

A
  • Highly transcribed genes–> RNA pol ejects histones, nucleosomes reform on DNA behind RNA pol II
  • Lowly transcribed genes–> H2A/H2B dimer is ejected, RNA pol moves around histone hexamer, nucleosomes reform behind RNA pol II
79
Q

RNA interference

A
  • A noncoding RNA targets complementary mRNAs w/in a cell for scilencing or degradation
    1. miRNAs–> form small hairpins, mRNA unable to be translated
    2. siRNAs–> degrades mRNA
80
Q

Dicer

A

-Endonuclease that cuts the dsRNA into 21-25 bp fragments

81
Q

RISC

A
  • RNA-induced scilencing complex
  • Degrades 1 strand of RNA
  • Binds to target mRNA and..
  • —Cleaves and degrades
  • —Inhibits translation
  • —Attracts methylases and deacetylases, spreading heterochromatin
82
Q

Wobble

A
  • Occurs at 3rd position

- Multiple mRNA codons can be recognized by the same tRNA

Genetics (4 decks)

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