Chapter 6: Molecular Genetics [COMPLETE] Flashcards
(192 cards)
1
Q
what is the structure of a nucleotide?
A
ribose sugar, nitrogenous base, and phosphate group
2
Q
what is the structure of a nucleoside?
A
ribose sugar and nitrogenous base
3
Q
what is DNA - structure and polymer-wise?
A
polymer of nucleotides that have hydrogen on the ribose sugar’s 2’ carbon
4
Q
what is RNA - structure and polymer-wise?
A
polymer of nucleotides that have hydrogen on the ribose sugar’s 2’ carbon
5
Q
what is the full name of DNA?
A
deoxyribonucleic acid
6
Q
what is the full name of RNA?
A
ribonucleic acid
7
Q
what are purines and what falls under the category?
A
double-ringed nitrogenous bases; adenine and guanine
8
Q
what are pyrimidines and what falls under the category?
A
single-ringed nitrogenous bases; cytosine, thymine, and uracil
9
Q
pyrimidine mnemonic
A
CUT the PYE
C: cytosine
U: uracil
T: thymine
10
Q
in DNA, what bases bind with each other and how many hydrogen bonds exist between them?
A
A - T: 2 hydrogen bonds
G - C: 3 hydrogen bonds
11
Q
in RNA, what bases bind with each other and how many hydrogen bonds exist between them?
A
A - U: 2 hydrogen bonds
G - C: 3 hydrogen bonds
12
Q
why is a higher temperature needed to break DNA strands with a larger proportion of G-C bonds?
A
because G-C bonds have more hydrogen bonds
13
Q
what are nucleosomes?
A
complexes of DNA wrapped around histone proteins
14
Q
how many histones are there per nucleosome?
A
9 total
15
Q
what is the histone breakdown for each nucleosome; aka, what are the histones in the central core and on the outside?
A
central core:
(2) H2A
(2) H2B
(2) H3
(2) H4
outside:
(1) H1
16
Q
what is the function of the outside histone of a nucleosome?
A
holds the DNA in place
17
Q
what is chromatin?
A
refers to the overall packaging of DNA and histones
18
Q
what are the two types of chromatin?
A
euchromatin and heterochromatin
19
Q
in euchromatin, how are nucleosomes packed and what does this mean for DNA?
A
nucleosomes are “loosely packed”; so DNA is readily accessible for transcription
20
Q
in heterochromatin, how are nucleosomes packed and what does this mean for DNA?
A
nucleosomes are “tightly packed”; so DNA is mostly inactive
21
Q
what allows proper binding between DNA and histones?
A
the positive charge on DNA and the negative charge on histones
22
Q
what occurs when histones go through acetylation and how does it affect transcription?
A
removes its positive charges, relaxing DNA-histone attractions and allowing for more transcription to happen
23
Q
what occurs when histones go through deacetylation and how does it affect transcription?
A
increases its positive charges, tightening DNA-histone attractions and decreasing transcription
24
Q
what occurs when histones go through methylation and how does it affect transcription?
A
adds methyl groups, can either increase or decrease transcription
25
what is the flow of processes that DNA must go through to be translated into proteins?
mnemonic: Roast Turkey Later
replication --> transcription --> translation
26
what is the origin of replication, in DNA replication, and what is it required for?
it is where the DNA strands first separate, required to initiate DNA replication
27
how many origins of replication do organisms with circular DNA (bacteria) have?
single
28
how many origins of replication do organisms with linear DNA (humans) have?
multiple
29
what does it mean when DNA undergoes semiconservative replication?
each new double helix produced by replication will have one “new” strand and one “old” strand
30
DNA is antiparallel, what does this mean for the structure?
the 5’ end (terminal phosphate group) of one strand is always next to the 3’ end (terminal hydroxyl group) of the other strand and vice versa
31
what are the steps of DNA replication?
initiation, elongation, and termination
32
what occurs in the initiation stage of DNA replication?
origins of replication are created at A-T rich segments of DNA because they only have two hydrogen bonds and are easier to split apart
33
what occurs in the elongation stage of DNA replication?
new DNA strands are produced using different types of enzymes
34
[personal mnemonic] how many steps of elongation are there and what is the trigger word for each one?
ten
1. helicase
2. single-strand binding proteins
3. topoisomerase
4. primase
5. sliding clamp proteins
6. DNA polymerase
7. leading strand
8. lagging strand
9. different DNA polymerase
10. DNA ligase
35
what occurs in step 1 of elongation?
helicase unzips DNA by breaking hydrogen
bonds between strands, creating a replication fork. As this occurs, helicase leads to supercoiling (tension ahead of the replication fork)
36
what occurs in step 2 of elongation?
single-strand binding proteins bind to uncoiled DNA strands, preventing reattachment of the strands to each other
37
what occurs in step 3 of elongation?
topoisomerase nicks the DNA double helix ahead of helicase to relieve built-up tension and supercoiling
38
what occurs in step 4 of elongation?
primase places RNA primers at the origin of replication to create 3’ ends for nucleotide addition
39
what occurs in step 5 of elongation?
sliding clamp proteins hold DNA polymerase onto the template strand
40
what occurs in step 6 of elongation?
DNA polymerase adds free nucleoside triphosphates to 3’ ends. DNA polymerase can only add nucleotides onto a preexisting 3’ hydroxyl group provided by primase.
41
what occurs in step 7 of elongation?
the leading strand is produced continuously because it has a 3’ end that faces the replication fork
42
what occurs in step 8 of elongation?
the lagging strand is produced discontinuously because its 3’ end is facing away from the replication fork. Thus, many RNA primers are needed to produce short DNA fragments called Okazaki fragments
43
what occurs in step 9 of elongation?
a different DNA polymerase replaces RNA primers with DNA
44
what occurs in step 10 of elongation?
DNA ligase glues separated fragments of DNA together
45
what occurs in the termination stage of DNA replication?
replication fork cannot continue, ending DNA replication
46
what are telomeres?
noncoding, repeated nucleotide sequences at the ends of linear chromosome
47
why are telomeres necessary in eukaryotes?
because when the replication fork reaches the end of a chromosome, a small segment of DNA from the telomere is not replicated and lost (no RNA primer is present to help produce another Okazaki fragment)
48
what is telomerase?
an enzyme that extends telomeres to prevent DNA loss
49
what are the 8 DNA replicating proteins?
DNA helicase, single-stranded binding proteins, topoisomerase, primase, DNA polymerases, DNA sliding clamp, DNA ligase, telomerase
50
[DNA replicating protein] DNA helicase function:
separates complementary strands at the replication fork
51
[DNA replicating protein] single-stranded binding proteins function:
proteins that prevent the two strands from coming back together after separating
52
[DNA replicating protein] topoisomerase function:
relaxes the DNA double helix from the tension and supercoiling the opening helix is creating
53
[DNA replicating protein] primase function:
provides a 3’ hydroxyl group for DNA polymerase to attach new nucleotides to
54
[DNA replicating protein] DNA polymerases function:
the class of enzymes that extends DNA in the 5’ to the 3’ direction. several have proofreading capabilities that allow them to catch synthesis errors
55
[DNA replicating protein] DNA sliding clamp function:
helps to hold DNA polymerase to the template strand
56
[DNA replicating protein] DNA ligase function:
glues together separate pieces of DNA
57
[DNA replicating protein] telomerase function:
adds repetitive DNA to the ends of eukaryotic chromosomes, which prevents critical information from being lost
58
what role do genes play in DNA?
genes are instructions within DNA that code for protein
59
what must DNA go through before being translate into proteins?
be transcribed into RNA
60
what is the order sequence in a gene?
the promoter region, then the gene operator, then the gene
61
what does DNA specifically produce when it undergoes transcription?
single-stranded messenger RNA (mRNA)
62
in prokaryotes, where do transcription and translation occur simultaneously and why?
in the cytosol, because prokaryotes do not have membrane-closed nuclei
63
what are the steps of transcription?
initiation, elongation, and termination
64
what occurs in the initiation stage of transcription?
a promoter sequence (aka promoter) next to the gene attracts RNA polymerase to transcribe the gene
65
what occurs in the elongation stage of transcription?
transcription bubble forms and RNA polymerase travels in the 3’ → 5’ direction on the template strand, but it extends RNA in the 5’ → 3’ direction
66
what occurs in the termination stage of transcription?
a termination sequence (aka terminator) signals to RNA polymerase to stop transcribing the gene
67
what is the template strand used to transcribe the mRNA called?
the template/antisense/noncoding strand
68
what is the other strand called and why?
the coding/sense strand because it is almost equivalent to the transcribed mRNA
69
once DNA is transcribed to RNA, what is thymine (T) replaced with?
uracil (U)
70
in prokaryotes, when RNA polymerase opens up DNA, what does it form?
transcription bubble
71
before transcription can occur in prokaryotes, what does a sigma factor have to combine with and for what reason?
combines with 'prokaryotic core RNA polymerase' to form 'RNA polymerase holoenzyme'; gives it the ability to target specific DNA promoter regions
72
what are the two types of termination in bacteria?
rho independent termination and rho-dependent termination
73
what occurs in rho independent termination?
a termination sequence is reached and the RNA transcript folds into a hairpin loop → RNA polymerase falls off and transcription ends
74
what occurs in rho-dependent termination?
a rho protein binds to the RNA transcript, moving 5’ → 3’ to catch up and displace RNA polymerase, ending transcription
75
what is an operon?
a group of genes that function as a single unit that is controlled by one promoter
76
where is the operator region near?
near the operon’s promoter
77
to regulate the promoter, where do the repressors and activators bind, respectively?
repressors bind to the operator regions
activators bind to the promoter sites
78
what is a lac operon?
an inducible operon (it must be induced to become active)
79
what are the 3 genes contained within the lac operon and what are they used for?
lacZ, lacY, and lacA; they encode proteins required for lactose metabolism
80
under what circumstance will the lac operon be induced?
will only be induced when glucose is not available as an energy source, so lactose must be used
81
what is the first way/level that the lac operon is controlled/regulated?
by the lac repressor protein
82
how often is the lac repressor protein expressed?
constitutively expressed (always on)
83
to what, is the lac repressor protein always bound to and what does it do?
always bound to the operator; ends up blocking transcription
84
how does the presence of lactose end up unblocking transcription?
lactose is converted to allolactose, which binds directly to the repressor and removes it from the operator, allowing transcription to occur
85
what is the second way/level that the lac operon is controlled/regulated?
by cAMP levels and catabolite activator protein (CAP)
86
how are cAMP levels related to glucose levels?
inversely related: ↓ glucose ↑ cAMP
87
what happens when cAMP binds to catabolite activator protein (CAP) attaches near the lac operon promoter?
it helps attract RNA polymerase, which promotes transcription
88
what other operon do prokaryotes use and what is it responsible for?
trp operon; responsible for producing the amino acid tryptophan
89
what else is tryptophan known as and why?
known as a 'repressible operon'; it codes for tryptophan synthetase and is always active unless the presence of tryptophan in the environment represses the operon
90
what can cause the prevention of tryptophan production and what would this be considered as far as its regulation?
can be caused if tryptophan binds to the trp repressor protein, which then attaches to the operator on the trp operon; considered the 1st level of trp operon regulation
91
what will happen to the trp operon if tryptophan is not present in the environment, why?
the trp operon will undergo transcription because the trp repressor protein will be inactive
92
where does transcription occur in eukaryotes and what does it use?
nucleus; uses RNA polymerase II to transcribe most genes
93
what are transcription factors needed for in eukaryotes?
to help RNA polymerase bind to promoters
94
what is the TATA box?
sequence in many promoters that transcription factors can recognize and bind to
95
what are enhancers and how do they affect transcription?
DNA sites that activator proteins can bind to; help increase transcription of a gene
96
what are silencers and how do they affect transcription?
DNA sites that repressor proteins can bind to; they decrease transcription of a gene
97
since enhancers and silencers can be far upstream or downstream from the gene, what is the positioning of DNA from these sites?
DNA from these sites are thought to loop around to colocalize with RNA polymerase
98
where is the poly A signal located and what does it stimulate?
within the terminator; stimulates polyadenylation (addition of adenine nucleotides to the 3’ end of the mRNA)
99
what are exonucleases and what does its activity result in?
they are enzymes that cleave nucleotides from the polynucleotide chain at the ends of the chain; only results in sticky ends
100
what are endonucleases and what does its activity result in?
they are enzymes that cleave nucleotides from the polynucleotide chain from the inside of the polynucleotide chain; can result in either sticky or blunt ends
101
what does "post-transcriptional modification" describe?
the conversion of pre-mRNA into processed mRNA, which leaves the nucleus
102
what are the three main types of post-transcriptional modification?
5'capping, polyadenylation of the 3’ end, and splicing out introns
103
what occurs in 5'capping?
7-methylguanosine cap is added to the 5’ end of the mRNA during elongation, protecting the mRNA from degradation
104
what occurs in polyadenylation of the 3’ end?
poly A tail is added to the 3’ end to prevent degradation by exonucleases
105
what occurs in splicing out introns?
introns are removed from the pre-mRNA molecule, which causes the exons to join together
106
what are introns?
stretches of noncoding DNA that lie between regions of coding DNA (exons)
107
what does splicing refer to?
refers to removing introns from pre-mRNA using spliceosomes
108
what do 'splice signals' in introns, signal?
signal to spliceosome where to cut
109
how many protein coding genes does the human genome contain?
20,000
110
does the human genome contain more non-coding or coding DNA?
non-coding
111
what is alternative splicing and what does this mean for protein production?
describes a single pre-mRNA having multiple possible spliced mRNA products; means that the same pre-mRNA can produce many different proteins
112
what are miRNAs (micro RNA) and its function in post-transcriptional gene regulation?
small RNA molecules that silence mRNA expression as a method of post-transcriptional gene regulation by base-pairing with parts of sequences on the mRNA transcript that inhibits their translation
113
what are the functional parts of a spliceosome and what are they collectively referred as?
snRNAs (small nuclear RNA) and proteins; referred to as snRNPs (small nuclear RiboNucleic Proteins)
114
what is translation?
the process of converting mRNA into protein products
115
what are the 2 important players in translation?
ribosomes and tRNA (transfer RNA)
116
what are ribosomes made up of?
one small subunit and one large subunit
117
what are the small and large subunits of eukaryotes and what does it form?
small (40S) and large (60S);
subunits form a 80S ribosome
118
where are eukaryotic subunits made and assembled?
made in the nucleolus; assembled once exported to the cytosol
119
what are the small and large subunits of prokaryotes and what does it form?
small (30S) and large (50S);
subunits form a 70S ribosome
120
where are prokaryotic subunits assembled?
assembled in the nucleoid
121
what are all subunits composed of?
rRNA (ribosomal RNA) and proteins
122
what is a codon (found in mRNA) and what are its two functions?
a group of three mRNA bases (A, U, G,
or C); can either code for an amino acid or terminate translation
123
what are the total number of amino acids?
20
124
what are the total number of codon combinations?
64
125
what does degeneracy of codons mean?
multiple codons code for the same amino
acid
126
what is the start codon?
AUG (methionine)
127
what are the stop codons?
UAA, UAG, UGA (end translation, do not code for an amino acid)
128
what is the open reading frame?
the stretch of DNA between the start and stop codons
129
what is an anticodon (found in tRNA)?
group of three tRNA bases (A, U,
G, or C) that base pairs with a codon.
130
what does tRNA carry to be added to the growing protein?
amino acid
131
what is aminoacyl-tRNA?
refers to a tRNA bound to an
amino acid
132
what is aminoacyl-tRNA synthetase?
the enzyme that attaches an amino acid to a specific tRNA using the energy from ATP
133
what are the ribosomal binding sites for tRNA?
A site, P site, and E site
134
what is the A site?
the site where aminoacyl-tRNA first enters
135
what is the P site?
P for peptidyl-tRNA, which carries the
growing polypeptide; the polypeptide chain moves from P site to the tRNA on A site during peptide bond formation
136
what is the E site?
E for exit site; the tRNA from the P site
is sent here and released from the ribosome
137
what is the process of elongation in translation? (A-P-E site)
--> The ribosome catalyzes the formation of a peptide bond between the polypeptide in the P site and the newly added amino acid in the A site
--> Afterwards, the polypeptide is transferred to the A site’s tRNA and the ribosome shifts one codon
down the mRNA
--> The A site will now be empty and
ready to accept another aminoacyl-tRNA
--> The tRNA from the P site will be transferred to the E site and will leave the ribosome
138
what is the translocation process, during elongation?
when the tRNA molecule at the A site moves to the P site, and the tRNA at the P site moves to the E site (A → P → E)
139
what are chaperonins, where are they found, and what do they function in?
Specialized proteins; both eukaryotic and prokaryotic organisms; assist newly synthesized polypeptides to fold into their correct shape
140
what is a DNA mutation?
a change in the DNA nucleotide sequence
141
what does it mean when a DNA mutation occurs in a germ cell (the cells that give rise to gametes)?
that it can be inherited by offspring
142
what does it mean when a DNA mutation occurs in a somatic cell (all other cells)?
that it only affects the individual
143
what are the two main types of DNA mutations?
base substitutions (point mutations) and frame shift
144
what are base substitutions (point mutations)?
when one nucleotide is replaced by another
145
what are the 3 effects that base substitutions may have?
silent mutations, missense mutations, and nonsense mutations
146
describe silent mutations
no change in amino acid sequence
Due to “third base wobble”,mutations in the DNA sequence that affect the third base of a codon can still result in the same amino acid being added to the protein
Relies on the degeneracy (redundancy) of translation
147
describe missense mutations
single change in amino acid sequence
can be conservative (mutated amino acid similar to unmutated)
can be non-conservative (mutated amino acid different from unmutated)
148
describe nonsense mutations
single change in amino acid sequence that results in a stop codon
results in early termination of protein
149
what are frameshift DNA mutations?
mutations that result in a shift in the reading frame, changing the way the mRNA transcript is read
150
what are the two types of frameshift DNA mutations?
insertions and deletions
151
what do insertions do and how does it affect the frame?
add nucleotides into the DNA sequence; can shift the reading frame
152
what do deletions do and how does it affect the frame?
remove nucleotides from the DNA sequence; can shift the reading frame
153
what is another DNA mutation that could occur and what happens?
null mutation; a null (non-functional) allele is produced that lacks the function of the normal, wild-type allele
154
what are the 5 factors that contribute to DNA mutations?
1. DNA polymerase errors during replication
2. loss of DNA during meiosis crossing over
4. chemical damage from drugs
5. radiation
6. transposons
155
what are transposons (jumping genes) and what do they do?
DNA sequences in prokaryotes and eukaryotes that
can move and integrate into different places in
the genome and cause mutations
156
what are the 3 factors that help prevent DNA mutations?
DNA polymerase proofreading by DNA
polymerase
mismatch repair machinery that checks
uncaught errors
nucleotide excision repair that cuts out
damaged DNA and replaces it with correct
DNA using complementary base pairing
157
what do chromosomal mutations affect?
affect the entire chromosome rather than individual
nucleotides
158
what are the 4 types of chromosomal mutations?
duplication, translation, deletion, and inversion
159
what occurs in duplication and what does it result in?
a region of DNA is duplicated, resulting in a larger
chromosomal arm and an atypical banding pattern
160
what occurs in translocation?
a piece of one chromosome breaks off and attaches to another chromosome
161
what does translocation increase and what does it result in?
translocation increases chromosomal arm length and results in an abnormal banding pattern
162
what is the only mutation that affects both chromosomes?
translocation
163
what occurs in deletion?
a portion of the chromosome is deleted, resulting in a shorter chromosomal arm
164
what occurs in inversion and what does it result in?
a portion of the chromosome becomes inverted on the arm of the chromosome; results in an abnormal
banding pattern, but does not affect the length of the chromosome
165
why are viruses not living?
because they must infect living cells to multiply
166
what is a capsid?
a viral protein coat that is made of subunits called capsomeres
167
what else do viruses have that they pick up from the host cell membrane?
phospholipid envelope
168
in order for an infection to continue to spread,
why do viruses undergo viral replication?
to create new viruses that can further infect other cells/hosts
169
what is the bootcamp mnemonic for viral replication cycle?
APUSAR!!!! sounds like a sneeze form someone who has a viral infection
170
what are the 6 steps of the viral replication cycle?
1. attachment - binding of a virus to host cell
2. penetration - virus crosses through the host’s cell membrane
3. uncoating - viral capsid is removed and degraded by host enzymes
4. synthesis - components of viral capsid are manufactured
5. assembly - viral capsid components assemble to form the viral capsid
6. release - last step of viral replication, fully assembled viruses are released
171
what are the two viral life cycle types?
lysogenic cycle and lytic cycle
172
what happens to the virus in the lysogenic cycle?
virus is considered dormant because it inserts its own genome into the host’s genome and does not harm the host; each time the host genome undergoes replication, so does the viral genome
173
what happens to the virus in the lytic cycle?
virus takes over host to replicate and does cause harm to the host. The viral particles produced can lyse the host cell to find other hosts to infect
174
what are viruses able to do between the lysogenic and lytic cycles?
switch
175
how can favorable conditions affect the virus?
it can stimulate a virus in the lysogenic cycle to replicate and enter the lytic cycle
176
what do retroviruses have?
an RNA genome that infects host cells and an enzyme called reverse transcriptase
177
what does reverse transcriptase do to retroviruses?
converts their RNA into cDNA (complementary DNA), so that it can integrate into the host genome and enter the lysogenic cycle
178
what are bacteria and what do they divide by?
asexual, divide by binary fission
179
what occurs when bacteria divide by binary fission?
they only receive genes from one parent cell and do not increase genetic diversity through reproduction
180
what are prophages?
bacteriophage genomes that have been integrated into the host genome
181
what is horizontal gene transfer?
the transfer of genes between individual organisms
182
how can bacteria increase genetic diversity?
through horizontal gene transfer
183
what are the 3 methods of horizontal gene transfer?
conjugation, transformation, and transduction
184
what occurs in conjugation (horizontal gene transfer)?
bacteria use a cytoplasmic bridge called a pili to copy and transfer a special plasmid known as the F plasmid (fertility factor).
185
[conjugation] what is the fertility factor referred to as when a bacteria contains it? what if the bacteria does not contain fertility factor?
contains F plasmid: F+
does not contain F plasmid: F-
186
[conjugation] what are plasmids?
circular DNA pieces that are independent from a bacteria's single circular chromosome
187
what occurs in transformation (horizontal gene transfer)?
bacteria take up extracellular DNA; bacteria are considered competent if they can perform transformation
188
what is electroporation?
process of using electrical impulses to force bacteria to become competent
189
what occurs in transduction (horizontal gene transfer) and when does it occur?
viruses transfer bacterial DNA between different bacterial hosts; occurs when a bacteriophage enters the lysogenic cycle in its host and carries bacterial DNA along with its own genome upon re-entering the lytic cycle
190
what is quorum sensing?
the mechanism of communication by cells, regulating the release of signaling molecules that affect microbial metabolism and gene expression
191
what is quorum sensing dependent on?
cell density
192
bacteria also contain R-factors; what are R-factors?
extrachromosomal pieces of DNA in the form of a plasmid that contains antibiotic resistance genes
