L7 Flashcards
(168 cards)
1
Q
define genome
A
entire genetic component
2
Q
define genetics
A
study of inheritance/inheritable traits
3
Q
define gene
A
sequence that codes for a specific polypedtide or RNA
4
Q
What are nucleotides?
A
building blocks of nucleic acids
5
Q
What are base pairs, and how do they pair up?
A
(bp), the specific pairs of nitrogenous bases, G:C, A:T, A:U
6
Q
What is the 5’ end?
A
terminates in a phosphate group attached to the 5’ carbon
7
Q
What is the 3’ end?
A
terminates with a hydroxyl group bound to the 3’ carbon, strands run antiparallel (one runs 5’ to 3’, the other 3’ to 5’)
8
Q
define genotype
A
genetic makeup, potential properties
9
Q
What is the term for properties of appearance that is expressed genetically?
A
phenotypes
10
Q
define Central Dogma of Molecular Biology and who discovered/invented it
A
DNA > RNA > protein, by Francis
Crick in 1956
11
Q
localized region of bacterial chromosome
A
nucleoid
12
Q
organized molecule of DNA associated with proteins, typically circular in bacteria, usually 1-2 of them, cells are haploid, not back to back genes - there are non-coding STRs (short tandem repeats) occur in most repeating sequences of 2-5 bases
A
chromosomes
13
Q
small, circular DNA molecules that replicate independently of chromosomes
A
plasmids
14
Q
carry genes for enzymes or toxins to make the bacteria pathogenic
A
virulence plasmids
15
Q
carry genes for bacteriocins (toxins) to kill competitor bacteria, can kill same or similar species without the facter
A
bacteriocin plasmids
16
Q
double membrane surrounds genetic material
A
nuclear envelope
17
Q
10 nm beads of DNA wrapped around histones
A
nucleosomes
18
Q
nucleosomes clumped with proteins to form 30nm diameter fibers dispersed throughout nucleus
A
chromatin
19
Q
globular proteins used in packing DNA into chromosomes, DNA has a negative charge, histones have positive charge
A
histones
20
Q
Which genome is often diploid with more than 1 chromosome and linear?
A
eukaryotic genome
21
Q
This term describes the single leg of chromosome.
A
chromatid
22
Q
With semiconservative replication, the replicated DNA is composed of what two parts?
A
original daughter strand and one new strand
23
Q
Initial Process: begins at sequence called “__,” DNA __ unzip DNA and exposed nucleotides in __, DNA __ binds strand and adds nucleotides from __’ to __’
A
origin; helicases; polymerase; 3; 5
24
Q
Synthesis of lagging strand: synthesized in __ segments that are later __
A
short; joined
25
Synthesis of leading strand: synthesized __ as a single long chain of nucleotides from __' to __'
continuously; 5; 3
26
__ synthesis usually proceeds in both directions from its origin, involves sets of enzymes and replication forks
bidirectional synthesis
27
removes coils from unwinding by cutting, rotating, and rejoining ends
gyrase and topoisomerase
28
Replication of eukaryotic DNA uses different DNA polymerases, __ initiates and synthesizes primer, __ elongates leading strand, __ elongates lagging strand, __ replicates mitchondrial DNA
1st; 2nd; 3rd; 4th
29
Due to long, linear chromosome, how many origins of replication might you see eukaryotic DNA?
1000s
30
Approximately how many nucleotides long are Okazaki fragments in eukaryotic DNA?
100-400 nucleotides
31
sets of genes in genome of organism
genotype
32
physical features/traits of organism
phenotype
33
DNA > RNA, make an RNA copy of a gene from DNA
transcription
34
synthesis of polypeptide (proteins) from the RNA copy
translation
35
RNA molecules that act as enzymes
ribozymes
36
carry genetic information from chromosomes to ribsomes
mRNA
37
delivers amino acids to ribosomes
tRNA
38
used by DNA polymerase during DNA replication
RNA primer
39
combine with ribosomal polypeptides to form ribosomes
rRNA
40
interacts with DNA to control gene expression
regulatory RNA
41
(initiation) bacteria, unzips and unwinds DNA, binds promotor, sigma factor is necessary to recognize the promotor in
RNA polymerase
42
(initiation) near the beginning of the gene, initiates transcription, not all RNA polymerase binds to all promotos equally strong, affects amount/type of protein transcribed
promotor
43
(initiation) in bactera, this portion of RNA polymerase is needed for recognition
sigma factor
44
(initiation) protein used in eukaryotes to help bind RNA polymerase to primer
transcription factors
45
(elongation) Begins __ nucleotides away from promotor.
10
46
(elongation) Transcribes 1st __ ribonucleotides.
10
47
(elongation) RNA polymerase releases its __ to allow it to __ to the DNA tightly
sigma factor; adhere
48
(elongation) Many RNA polymerases can __ transcibe the same gene.
concurrently
49
(elongate) Links nucleotides in __ direction.
5' to 3' direction
50
self termination: RNA __ transcribes a terminator sequence rich in __ and __ bases followed by a region rich in __ and __
polymerase; G; C; A; U
51
(self-termination) It slows down in __ region, because of 3 __ bonds between them.
GC; H
52
(self-termination) Forms __ and __ structure to put __ on structure and then pulls off in __ rich area.
stem; loop; tension; adenine
53
(enzyme dependent termination) = __ dependent: depends on termination __ that binds to specific sequence near the __ of RNA __ moves towards __ end and forces RNA __ and DNA apart
Rho; protein; end; transcript; 3' end; polymerase
54
RNA unwinds DNA itself, DNA requires __.
helicase
55
RNA, regarding speed is __ compared to DNA.
slower
56
RNA incorporates __ instead of DNA's __.
ribonucleotides; deoxyribonucleotides
57
RNA uses "U" instead of DNA's __.
T
58
RNA is __ efficient proofreading compared to DNA, errors that occur every __ nucleotides.
less; 10,000
59
RNA polymerase copies only __ of the DNA strands
1
60
Transcription occurs in the __ of eukaryotics cell, and in the __ of a prokaryotic cell.
nucleus; cytoplasm
61
Transcription factors assist in binding __ to __.
RNA polymerase; promotor
62
Eukaryotes must process __ before translation.
mRNA
63
Name three events of eukaryotic DNA processing.
1) add 5' cap
2) add poly A tail
3) splicing to remove introns
64
introns
intervening sequences
65
exons
expressed/coding sequences
66
define translation
ribosomes read genetic info to synthesize polypeptide
67
What are the stop sequence codes?
UAA, UAG, UGA
68
What are the start codons in eukaryotes and prokaryotes?
AUG: methionine in eukaryotes; n-formyl methionine in prokaryotes
69
define genetic code
nearly universal with few exceptions, is redundant, more than 1 codon associated with each amino acid
70
Codons are triplets of mRNA nucleotides associated with what?
amino acids
71
What does mRNA carry?
AUG start
72
Prokaryotic ribosomes can start translation before transcription is done, T or F?
true
73
Eukaryotic mRNA contains __ called __.
noncoding regions; pre-RNA
74
Introns: __ removed to make a functional mRNA "__"
noncoding regions; intervening sequences
75
Exons: __, aka "__"
coding regions; expressed
76
Eukaryotic mRNA carry instructions for only __ polypeptide, where there may be more than __ in prokaryotes.
1; 1
77
Eukaryotic __ not __ until fully transcribed and move __ of nucleus.
mRNA; translated
78
enRPS: small nuclear __, remove __ and __ exons together, in some __ act as a __ to __ own __
ribonucleoproteins; introns; splice; introns; ribozyme; catalyze; removal
79
How many ribonucleotides long is tRNA? What structure does it form? Where are its receptor sites located, and what do they accept?
about 75; 3 main haripin loops; acceptor site for a specific amino acid at 3' end and anticodon in the bottom loop
80
Where are anticodons located? How many anticodons?
at the bottm of tRNA; 64
81
What benefit comes from most amino acids having signals from multiple alternative codons?
degeneracy
82
Ribosome: __ in prokaryotes, __ in eukaryotes, each has 2 subunits, the smaller subunit shaped to accomodate 3 __ a __ time
70s; 80s; codons; 1
83
the A site
accomodates tRNA delivering an amino acid
84
the P site
holds a tRNA and growing polypeptides
85
the E site
tRNA exits from this site
86
During initiation, what components form the initiation complex?
nRNA, 2 ribosomal subunits, tRNA, and several protein factors
87
During the first step of elongation the tRNA matching the next codon attaches to a __ site.
A
88
What happens in step 2 of elongation?
larger subunits ribozyme forms peptide bond between the terminal amino acid, the newly introduced amino acid, polypeptide attached to tRNA on A site
89
In step 3 of elongation, using GTP energy, the ribosome moves down 1 codon and transfers tRNA to what?
adjacent site
90
In step 4 of elongation, ribosomes release what?
"empty" tRNA from E site to be recharged
91
In step 5 of elongation, the cycle repeats, at about what rate of amino acid per second?
15 amino acids/second
92
after one ribosome exposes the start, additional ribosomes may attach behind the first one
polyribosome
93
release factor halt elongation, recognize stop codons and modify large subunit to activate ribosome to sever polypeptide from final tRNA and dissociates subunits
termination
94
about 75% of genes are expressed all of the time, others are regulated to polypeptides are only synthesized when needed
control of transcription
95
This type of transmission is similar to eukaryotes, but lacks ER.
archae translation
96
What components make up operon?
promotor, adjacent operator, and series of genes which code for enzymes and structures
97
Where does the repressor protein bond to stop transciption?
operator
98
This must be activated by inducers and its not usually transcribed.
inducible operon
99
What deactivates a repressible operon?
repressors
100
What controls a lactose operon?
regulator gene
101
What are two events that can activate a lac operon?
1) positive regulation by the CAP (catabolite activator protein)
2) deactivation of repressor
102
What does allolactose do to the lac operon?
induces lac operon by inactivating repressor so RNA polymerase can bind and translate lac genes
103
When tryptophan is not present, the operon is __.
tryptophan (operon)
104
There are used to regulate translation of polypeptides.
regulatory RNA molecules
105
small interfering RNAs, ds, may be complementary to mRNA, tRNA, or DNA, join RISC proteins to form siRISC, binds and cuts target nucleic acids to silence genes
siRNAs
106
RNA molecules that change shape in response to environmental conditions, some mRNAs can act as riboswitches to either favor or block translation depending on conditions and cells' needs
riboswitch
107
microRNAs, eukaryotic cells transcribe as miRNAs, not translated but join with regulatory proteins to form miRNA-induced silencing complex (miRISC), binds complementary mRNA and can cut mRNA to disable it or hide it from ribosomes to block translation, used to regulate embryogenesis, apoptosis, cell division, blood cell formation, and cancer among other things
miRNAs
108
How does epigenetic control turn genes off?
by methylating certain nucleotides
109
define mutations
a heritable change in the nucleotide base sequence of genome - particularly a gene
110
insert extra nucleotides
insertions
111
insert wrong nucleotides
substitutions
112
insertions or deletions
frameshift mutations
113
just 1 or a few nucleotide base pairs affected
point mutations
114
loss of a nucleotide
deletions
115
What causes frameshift mutation?
both insertions and deletions
116
What causes silent mutations?
when a substitution does not change the amino acid sequence
117
Which mutation has the worse consequences, missense mutation or nosense mutation?
nonsense
118
What is the term for physical/chemical agents that induce mutations?
mutagens
119
define spontaneous mutations
result from errors in replications and repair, in the absence of any mutation causing agents
120
define recombination mutation
relatively long stretches of DNA move along the chromosome (introduce frameshift)
121
This type of radiation can include z-rays and gamma rays. How does it affect DNA?
can cause mutations or break the DNA backbone and chromosomes
122
This type of radiation can include UV light. How does it affect DNA?
causes adjacent T bases to covalently bond to a make thymine (pyrimidine) dimmers --> prevent H bonding with A --> distorts sugar phosphate backbone
123
structurally similar to normal nucleotides, incorporate into DNA, inhibit polymerase/mismatch pairing, EX: 5 bromouracil, 5FU, antiviral and anticancer drugs
nucleotide/nucleoside analogs
124
alter structure of nucleotide: ex: nitrous acid removes amine off adenine and converts it to guanine analog, AT pair changed to GC pair, aflatoxin converts gaunine into T, so GC converted to TA base pair, aflatoxin can cause cancer
nucleotide altering chemicals
125
Give an example of a frameshift mutation. What do they do?
benopyrine in smoke, ethidium bromide used to stain DNA, acridine
insert or delete nucleotide base pairs, or slip between adjoining nucleotides
126
What is the mutation frequency?
seen in 1 out of 1 million genes, mutagens increase the rate 10-1000X, induce error in 1/1000 - 1/100,000 genes
127
What is the mutation rate?
probability that a gene will mutate when a cell divides, usually stated as a power of 10
128
What happens during Base-Excision repair?
enzymes cuts out erroneous base and DNA polymerase fills in gap
129
In prokaryotes, what activates DNA photolyase and what does it do?
activated by visible light; breaks bond between thymines
130
What happens in light repair?
enzyme photolyase activated by light, reverses mutation and restores original sequence
131
What happens in dark repair?
in prokaryotes, occurs in dark or light, cuts damaged section from DNA and is repaired by DNA polymerase ! and DNA ligase = nucleotide excision repair
132
What happens to old strands of DNA during mismatch repair?
they are methylated
133
What repair system is considered the last resort?
error-prone repair
134
What occurs when damage is too extreme to repair?
SOS repair = a new DNA polymerase capable of copying sequences with mistakes is used, introduces mutations but allows offspring to survive, involves novel DNA polymerase IV and V capable of copying less than perfect DNA
135
What are mutant cells?
cell that does not successfully repair its mutation and its descendants
136
What cells are found normally in nature?
wild type cells
137
What is positive selection?
selecting a mutation by eliminating wild type phenotypes
138
What is negative selection?
selects for auxotrophic mutants
139
What term describes organisms with different nutritional requirements than its wild-type phenotype?
auxotroph
140
What is the Ames test used for?
screens for mutants
141
What term describes something that causes cancer causing mutations?
carcinogenic/carcinogens
142
Genetic recombination: exchange between __ DNA molecules that are composed of __ sequences
2; homologous
143
Homologous sequences: DNA segments composed of __ sequences
identical/nearly identical
144
Crossing over: in __, homologous chromosomes __ while forming gametes
eukaryotes; recombine
145
Vertical gene transfer: passing copy of __ from 1 generation to the next
genome
146
Horizontal gene transfer: in less than __ % of population, in prokaryotes, can acquire genes from another microbe in the same generation
1
147
Donor cell: contributes part of __ to recipient
genome
148
Recipient cell: may be different __ or genus
species
149
Transformation: recipient cell takes up DNA from the __ such as dead organisms, cells have ability to take up __ are said to be "competent," results from __ in cell wall making it __ to large DNA molecules
environment; DNA; alterations; permeable
150
Transduction: transfer of DNA from 1 __ to another via __ viruses, both in pro and eukaryotes, __ method of horizontal gene transfer
cell; replicating; 2nd
151
Phage (bacteriophage): virus that infects __
bacteria
152
phage proteins incorporate bacteria DNA long with phage DNA when assembling new phase particles
transducing phage
153
generalized transduction: phage carriers __ DNA segment from donor and host cell to recipient, all __ equally likely to be packaged in a phage __ and transferred
random; genes; coat
154
specialized transduction: only certain host __ are transferred along with phage DNA
sequences
155
What happens in bacterial conjugation?
donor remains alive
156
define conjugation pili
(sex pili) protein rods extending from surface of cell to transfer genetic materials
157
What is F plasmid?
contains gene coding for sex pili, conjugative plasmid contains F factors
158
In Hfr, plasmid does not remain __ in but rather integrates into __.
cytosol; chromosome
159
dissimilation plasmids
code for enzyme that triggers catabolism of unusual sugars or hydrocarbons
160
transposons
segments of DNA 700-40,000 bp that can move from 1 location to another in DNA
161
transposition
action of transposon, acts like a frameshift insertion, in pro, eukary, and viruses
162
palinodrome
a sequence that reads the same forwards or backwards, usually on both ends of transposons, in genetics the region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complementary strand
163
IR = inverted repeat
sequence of nucleotides identical to inverted sequence in complementary strand
GAATTC
CTTAAG
164
transposase
recongizes own inverted repeat at a target site and cuts DNA at that location, and inserts transposon (or copy) into DNA at that site
165
insertion sequences
simplest transposons, consist of no more than 2 inverted repeats and a gene encoding transposas
166
complex transposons
contain 1 or more genes not connected with the transposition such as genes for AB resistance
167
R plasmids
often contain transposons
168
R factors
resistance factors, give resistance to heavy metals or toxins, many have 2 groups of genes, r-determinants have the resistance genes and the RTF (resistance transfer factor) includes genes for plasmid replications and conjugation
