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Genetics test 5 Flashcards

1
Q

functions of protein macro level

A

form structures - hair, scales, feathers
glow to act as a signal between organisms
Be used to kill - rattlesnake venom

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2
Q

Functions of protiens within and between cells

A

Machines - DNA polymerase, ATP synthase, Dynein
Signals - Insulin, Oxytocin, Leptin
Structures - microtubules, actin, membrane channels

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3
Q

acidic amino acids

A

Non essential
negative charge
hydrophilic
ionic and hydrogen bonds

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4
Q

basic amino acid

A

lysine
positive charge
hydrophilic
ionic and hydrogen bonds

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5
Q

neutral polar amino acids

A

threonine
no charges

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6
Q

nuetral nonpolar amino acids

A

tryptophan
phenylalanine
valine
isoleucine
leucine
methionine
hydrophobic

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7
Q

start codon

A

AUG

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8
Q

Stop codon

A

UAA
UAG
UGA

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9
Q

amino acids are linked together via

A

peptide bonds

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10
Q

Protien structure language

A

a chain of amino acids is a peptide or polypeptide
one oe more chains together may be a protien
protiens have structure: primary, secondary, tertiary, and quartenary

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11
Q

Primary structure of protiens

A

order of amino acids in polypetide chain

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12
Q

secondary structure of protiens

A

regular folding of a single chain
maintained by weak bonds (hydrogen pairing)
ALPHA helix or BETA sheet

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13
Q

Tertiary structure of protiens

A

three-dimensional structure of an entire polypeptide chain

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14
Q

Quartenary structure of protiens

A

arragement of multiple polypeptides into a single multi-subunit complex

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15
Q

Structure of tRNA

A

75-90 nt long - different sequences
cloverleaf configuration
loop 2 contains anticodon
each tRNA binds one amino acid

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16
Q

anticodon

A

tRNA anticodon pairs with its complementary codon on the mRNA molecule
appropriate amino acid is inserted into the polypeptide

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17
Q

charging of tRNA

A

one ATP required
aminoacyl tRNA synthetase enzyme catalyzes reaction
molecules are chemically linked to proper amino acids
amino acids converted to active form - reacts with ATP to create aminoacyladenylic acid

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18
Q

Bacterial/prokaryotes ribosomes

A

70S = 50S (large) + 30S (small)
50 has 23S and 5S rRNA
30 has 165 rRNA
unit arranged as 5’–16S–23S–5S–3’
transcibed as single pre-rRNA transcript, but bound by ribosomal protiens and cleaved by enzymes co-transcriptionally to produce ribosomal complex
bacteria only have one RNA polymerase, so it also transcibes this RNA

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19
Q

Eukaryotic ribosomes

A

80S = 60S (large) + 40S
Large subunits have 28S, 5.8S and 5S rRNA
Small subunits contain 18S rRNA
Unit arranged as 5’–18S–5.8S–28S–3’
pre-rRNA is enzymatically cleaved by RNA pol III, the massive transcription from the tandem copies leads to nucleolus formation
The 5S rRNA is transcribed from a separate locus - RNA Pol I

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20
Q

ribosome site A

A

aminoacyl site
where the incoming charged tRNA binds

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21
Q

ribosome site P

A

aminoacyl site
where a tRNA bound to the growing polypeptide chain sits

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22
Q

ribosome site E

A

exit site
where a free uncharged tRNA preparing to exit the ribosome sits

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23
Q

shine dalgarno

A

relationship between start AUG and shine-dalgarno sequence
shine dalgarno binds to a complementary sequence in the 16S rRNA
shine-dalgarno sequence is located in the 5’ UTR of mRNA about 8-12 nts before the AUG start codon

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24
Q

prokaryotic initiation of translation

A

1) load mRNA onto small subunit
2) load first tRNA
3) add large subunit, kick out IF’s, hydrolyze GTP

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25
Step 1 of prokaryotic initation of translation - load mRNA onto small subunit
Initiation factor-1 blocks A site IF-3 blocks 50S attachment helps mRNA binding to 30S shine-delgarno sequence complementary to 16S rRNA in 30S subunit
26
Step 2 of prokaryotic initation of translation - load first tRNA
since A site is blocked and E site doesn't exists, tRNA loads into P site IF-2 brings a special fMET tRNA for iniation in prokaryotes
27
how are eukaryotic initation of translation different
IF's = eIF's and there are many more than 3 Initiator Met is NOT modified no shine-dalgarno Best model is scanning model for identifying start
28
Key points in the scanning model
eIF-4e is "cap binding protien' (binds 5' cap on mRNA) the poly-a-tail loops around and is involved through association with eIF-4F and eIF-4G the 40S subunit, bound to Met-tRNA Met loads onto 5' end and slides along looking for an AUG that is not a Kozak sequence
29
elongation
Once 70S initiation complex is formed, fMet-tRNA fMEt is bound to AUG codon in the P site of the ribosome 1) Next charged tRNA loaded into the A site 2) peptide bond formation 3) translocation 4) repeat steps 1-3
30
elongation step 1
EF-Tu (elongation factor 2) TS and GTP/GDP are required to bring new tRNA's to the ribosome for elongation
31
elongation step 2
peptide bond forms between the two adjacent amino acids, catalyzed by peptidyl transferase The linked amino acids are attached to the tRNA in the A site, forming a peptidyl-tRNA
32
elongation step 3
the ribosome shifts doen one codon the empty tRNA is ejected from the E site the tRNA + growing chain shifts to P site, the A site is empty again
33
termination
1) stop codon is encountered 2) release factor (RF1) binds to stop codon 3) polypeptide chain is released 4) RF3-GDP binds causing RF1 relase. GTP replaces the GDP and GTP hydrolysis relases RF3 5) ribosome recycling factor (RRF) binds to A site 6) EF-G-GTP binds to ribosome. Hydrolsysis of GTP tp GDP causes translocation of the ribosome, putting RRF in the P site, and the tRNA in the E site 7) RRF relases the uncharged tRNA, EF-G then releases RRF, and the two ribosomal subunits dissociate from the mRNA
34
tetrapeptide
a polypeptide made up of four or more amino acids
35
N-terminus
Amino group
36
C-terminus
Carboxyl group
37
R-group
will differ based on the amino acid
38
a-carbon
carbon at the center of the amino acid
39
peptide bond
bond between amino acids
40
inducible enzymes
bacteria adapt to environment by producing inducible enzymes only when specific substrates are present
41
constitutive enzymes
enymes are continuously produced regardless of the chemical makeup of the environment
42
positive control
transcription occurs only when regulator molecule directly stimulates RNA production
43
negative control
genetic expression occurs unless shut off by regulator milecule
44
gene regulation - prokaryote
metabolic response to the environment
45
gene regulation - eukaryote
cell-type specific gene expression all cells have the same DNA but specific cells need to express specific genes depending on thier function expression under certain conditions
46
operons
genes coding for enzymes with similar functions organized in clusters with their regulatory sequences
47
cis-acting
regulatory region on same strand regulatory site determine if genes are transcribed into mRNA
48
trans-acting elements
binding at cis-acting site regulates cluster negatively (turning off transcription) or positively (turning on transcription)
49
Lac (lactose) operon
has three structural genes: lacZ, lacY, and lacA all three genes transcribed as single unit result in polycistronic mRNA
50
cistron
part of nucleotide sequence coding for single gene
51
In the presence of lactose
transciption occurs onyl when repressor fails to bind operator region repressor is allosteric - reversibly interacts with another molecule, causes conformational change in shape and chemical activity
52
Lac operon subject to negative control
repressor normally binds DNA sequence in operator region inhibits RNA polymerase represses transciption of strutual genes
53
catabolite-activating protien (CAP)
helps activate expression of lac operon able to inhibit expression in the presence of glucose inhibition called catabolite repression
54
cAMP: cyclic adenosine monophosphate
to bind to promoter, CAP must be bound to cyclic adenosine monophosphate glucose inhibits activity of adenylyl cyclase, which catalyzes conversion of ATP to cAMP prevents CAP from binding when glucose is present
55
closed chromatin
inhibitory conformation (closed chromatin) tight association of DNA with histones inhibits access to DNA protiens-affects transcription chromatin structure must become "open" prior to transcription initation
56
DNA methylation
type of chromatin modification plays role in gene regulation: represses gene expression methylation occurs most often: at 5 posistion cytosine
57
Enhancers
located on either side of gene, some distance from gene or even within gene increase rate of transcription confer time- and tissue- specific gene expression
58
silencers
repress the level of transcription initiation acts as negative regulator of transcription acts in tissue- or temporal- specific ways in gene expression
59
transcription factors
promoters, enhancers and silencers act as binding sites for transcription factors Activators repressors
60
activators
increase transcription iniation
61
repressors
reduce transcription initiation
62
coactivators
serve as bidge between activators and promoter-bound GTFs
63
enhanceosomes
Large complexes of activators and coactivators that direct transcription activation
64
repressor protiens
at silencer elements decrease rate of PIC assembly and RNA Pol II release
65
introns
areas within a gene that are going to be ignored
66
exons
areas within a gene that are going to be expressed
67
type of mutation that changes the entire sequence of DNA following the mistake
frameshift mutation
68
tRNA and mRNA are involved in
protien synthesis
69
a mutation can chanve the _____ and be replicated when forming new cells
Genetic code
70
DNA replication is
semiconservative
71
after transcription, mRNA leaves the nucleus and attaches itself to a
ribosome
72
________ carries amino acids to the site of protien synthesis
tRNA
73
the bases are often abbreviated to _, _, _, and _
ACGT
74
_____ joins the okazaki fragments
ligase
75
unwound DNA
chromatin
76
a mutation can be ______, beneficial, or harmful
neutral
77
DNA polymerase replicates one stran ______ and one not
continuously
78
A purine —> purine or pyrimidine —> pyrimidine mutation
transition
79
A(n) _____ is a sequence of three bases in a tRNA molecule
anticodon
80
Passed on from parents to offspring
trait
81
_____ connect the bases
hydrogen bonds
82
Part of a chromosome, passed on from parents to offspring
gene
83
_____ adds nucleotides and checks to make sure the new copy is correct
DNA polymerase
84
Ribosomes are located on the _____
Endoplasmic reticulum
85
Because it only makes 5'-3', DNA polymerase makes little sections for the other side called _____
okazaki fragments
86
One base is placed incorrectly
substiution
87
One base is added
insertion
88
_____ creates a primer on the DNA strand by adding RNA nucleotides
primase
89
DNA is shaped like a twisted ladder, or ____
double heliex
90
Mutations can be _____
inheritable
91
In DNA, adenine pairs with _____
thymine
92
One base is deleted
deletion
93
A purine —> pyrimidine or pyrimidine —> purine mutation
transversion
94
The message from the mRNA will be translated into an _____ sequence
amino acid
95
A(n) _____ is a sequence of three bases that codes for an amino acid
codon
96
The sides of DNA are made of _____ and phosphate.
deoxyribose
97
Transcription happens in the _____
nucleus
98
DNA replication does not happen when the cell _____
divides
99
DNA is _____
antipararallel
100
A change that takes place in DNA
mutation
101
A and G are both _____
purines
102
RNA has _____ instead of thymine
uracil
103
Translation occurs in the _____, specifically on the ribosomes
cytoplasm
104
_____ contain nitrogen
nitrogen bases
105
Transcription is the process of making _____
mRNA
106
T and C are _____
pyrimidines
107
_____ are made in the ribosomes
protiens
108
Helicase _____ DNA
unwinds

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