AP Bio Exam 4 Flashcards
1
Q
Who created the model of DNA?
A
James Watson and Francis Crick
2
Q
Chargaff’s Rule
A
The base composition of DNA varies from one species to another
For each species, the percentages of A and T bases are roughly equal, as are those of G and C bases.
3
Q
Rosalind Franklin
A
Took an X-ray diffraction image of DNA
The pattern implied that the helix was made up of two stands, contrary to the three strand model.
The diameter was the same every time
Concluded that the sugar-phosphate backbones were on the outside of the DNA molecule. (The phosphate groups negatively facing the aqueous surroundings, and the relatively hydrophobic nitrogenous bases were hidden in the interior)
4
Q
Watson and Crick
A
Built DNA model that proved the:
Double helix theory
Chargaff’s rules
antiparallel arrangement
Purine and pyrimidine arrangement
5
Q
Hershey and Chase
A
Used radioactive isotope of sulfur to tag protein in one batch of T2 and radioactive isotope of phosphorus to tag DNA in a second batch
The phages infected E. coli and the phosphorus stayed. The protein does not enter the cells.
CONCLUSION: DNA must hold the molecule carrying the genetic information that makes the cells produce more viral DNA and proteins.
6
Q
Why are nucleic acids unique?
A
Their ability to replicate themselves from monomers
7
Q
Transformation
A
A change in genotype and phenotype due to the assimilation of external DNA by a cell
8
Q
Evidence that DNA can transform bacteria
A
Frederick Griffith mixed cell remains of killed pathogenic bacteria with living nonpathogenic bacteria. Some living cells became pathogenic and all offspring of pathogenic bacteria were also pathogenic.
Some DNA of the dead pathogenic cells cause this heritable change
9
Q
Evidence that Viral DNA can program cells
A
Bacteriophage (viruses that infect bacteria) “T2” programs E. Coli into T2 making machines. Hershey and chase found that the DNA entered the bacteria but not the protein
10
Q
Virus
A
DNA in a protective coat, often a protein. Infects a cell and takes over the cell’s metabolic machinery
11
Q
Three components of a nucleotide monomer
A
- Nitrogenous base
- Phosphate Group
- A pentose sugar (deoxyribose)
12
Q
Four nucleotide bases
A
Adenine, thymine, guanine, cytosine
13
Q
Chargaff’s rules
A
- DNA base composition varies between species
- For each species, the percentage of A and T (and C and G) bases are roughly equal
14
Q
What are 5’ and 3’?
A
The carbon in the pentose that the phosphate group attaches to
15
Q
Double helix
A
Presence of two strands
16
Q
The sugar phosphate complex in nucleotides is the
A
“backbone” of the structure
17
Q
What charge is DNA
A
Overall negative (because of the negative phosphate groups)
18
Q
Antiparallel
A
Subunits of two sugar-phosphate backbones run in opposite directions
19
Q
Purine
A
Two organic rings
20
Q
Pyrimidine
A
One organic ring
21
Q
Which bases are purines and which are pyrimidines?
A
Purine: Adenine and Guanine
Pyrimidines: Cytosine and Thymine
22
Q
How many organic rings per nucleotide base pairs?
A
3
2 is too narrow and 4 is too wide in diameter of the helix
23
Q
How many hydrogen bonds in each pairing?
A
A - T: Two
C - G: Three
24
Q
Modern DNA sequencing techniques confirmed that
A
Nucleotide base pair ratios are exactly equal
25
Base principle of DNA replication
1. Parental molecule is paired
2. Pairs separate into two DNA strands
3. Daughter strands pair complementary to both parental strands
26
Conservative Model of Replication
Two parental strands reassociate after acting as templates for new strands, restoring into a parental double helix
27
Semiconservative Model
True model*
The two strands of parental molecule separate and each functions as a template for synthesis of a new complementary strand
28
Dispersive Model
Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA
29
When does DNA replication occur
S phase in Interphase
30
T/F, DNA replication is slow but accurate
F: it is quick and accurate
31
Origins of replication
Where replication begins; short stretches of DNA that have specific sequence of nucleotides
32
How is a parent DNA separated?
Protein locate the specific sequence of the origins of replication and form bubbles which expand as daughter strands are synthesized from both directions of the strand
33
Replication fork
A Y-shaped region where the parental strands of DNA are being unwound
34
Helicase
Enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands
35
Single-strand binding proteins
Bind to the unpaired DNA strands, keeping them from re-pairing (stabilizing)
36
Topoisomerase
Enzyme that helps relieve the strain of tighter twisting ahead of the replication fork. Done by breaking, swiveling and rejoining DNA strands
37
RNA
The initial nucleotide chain that is produced during DNA synthesis.
38
Primer
Initial RNA chain synthesized by a primase
39
Primase
Synthesizes an RNA primer at 5' end of leading strand and at 5' end of each Okazaki fragment of lagging strand
40
How many nucleotides does a primer cover at a time?
5-10
41
A new DNA strand will start from the ____ end of the RNA primer
3'
42
DNA polymerase
Catalyze the synthesis of new DNA by adding nucleotides to the 3' end of a preexisting chain
Attach incoming nucleotides and takes everything but pyrophosphate (two phosphates)
43
How many DNA polymerases are discovered so far?
11, (but I and III are most important)
44
DNA polymerase III
Adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides
45
DNA polymerase I
Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides added to 3' end of adjacent fragment
46
DNA polymerase can only add nucleotides to the free ____ end of a primer or growing DNA stand
3'
47
Leading strand
DNA pol III remains at the replication fork and continues to the end
48
Lagging strand
When DNA pol III must work along the other template strand in the direction away from the replication fork
49
Okazaki fragments
Series of fragments synthesized on the lagging strand
Okazaki fragments includes the primer until it is removed (by polymerase I) and replaced (by ligase) with DNA and brought together
50
DNA Ligase
Joins the backbones of all the Okazaki fragments into a continuous DNA strand
51
Are hydrogen bonds or covalent weaker
hydrogen
52
The overall negative charge of DNA means
It can only move in certain directions (and not across the membrane)
53
RNA vs. DNA
RNA:
- Single stranded
- Uracil - A
- Wide purpose: DNA replication, translation, and transcription
- Ribose
- ATP is used
DNA:
- Double stranded
- Thymine - A
- Genetic information and regulation
- Deoxyribose
- dATP is used
54
DNA replication quick facts
- 17-18 different enzymes
- Speedy and accurate
- More known how its done in bacteria than eukaryote
- Most of the process between prokaryotes and eukaryotes is similar
55
What happens when a DNA polymerase finds an error when comparing the nucleotide to the template?
It removes the nucleotide and then resumes synthesis
56
Mismatch pair
Evades the DNA polymerase proofread, and other enzymes remove and replace incorrect pair nucleotides resulted from replicatio errors
57
Describe how DNA damage after replication is fixed before they become mutation
They are corrected by about 170 DNA repair enzymes in humans
58
Nuclease
DNA cutting enzyme that cuts out damaged DNA
59
After a nuclease cuts out damaged DNA, what fills it back in?
DNA polymerase and DNA ligase
60
Nucleotide excision repair
Enzymes detect damaged DNA, nuclease cuts the segment out, DNA polymerase fills in the missing nucleotide, and DNA ligase seals the free end
61
Thymine dimers
After covalently linking thymine bases that are adjacent on a DNA strand, causing the DNA to bycle ajd interfere with replication
62
Mutation
A permanent change in the DNA
63
Why does linear DNA becomes shorter and shorter?
Usual replication cannot complete the 5' ends of daughter DNA strands. Most prokaryotes have circular DNA though
64
Telomeres
Do not contain genes and located on the ends of eukaryotics chromosomal DNA molecules. Prevent shortening of linear DNA. Hold a crap ton of short nucleotide sequences
65
Two functions of telomeres
1. Specific proteins in telomeric DNA prevent staggering ends of the daughter molecule from activating the cell's system for monitoring DNA damage
2. Acts as buffer zone that provides some protection against the organism's genes shortening.
They don't prevent erosion of genes at the ends, but postpone it
66
Shortening of telomeres contributes to
The aging of an organism overall and prevention of cancer
67
Telomerase
Catalyzes the lengthening of telomeres, restoring their original length.
68
In a bacterium, the DNA is “supercoiled” and found in a region of the cell called
the
nucleoid
69
Chromatin
A complex of DNA and protein, is found in the nucleus of eukaryotic
cells
70
Heterochromatin vs. Euchromatin
Heterochromatins dense nature makes it largely inaccessible
to the machinery responsible for transcribing genetic information
71
Heterochromatin
Irregular clumps of highly condensed chromatin
72
Euchromatin
Less compacted, more dispersed chromatin
73
Gene expression
The process by which DNA directs the synthesis of proteins
74
The one gene-one polypeptide rule is not entirely true. Why?
1. Alternative splicing
2. A few genes code for RNA molecules that have important functions in cells even though they are never translated into protein
75
Two stages of DNA expression
Transcription and Translation
76
Unique to RNA than DNA
Contains ribose instead of deoxyribose
Uracil instead of thymine
RNA molecule consists of a single strand
77
Transcription
The synthesis of RNA using information in the DNA
78
Molecules involved in transcription
messenger RNA
79
Messenger RNA (mRNA)
carries a genetic message from the DNA to the protein-synthesizing machinery of the cell.
80
Translation
The synthesis of a polypeptide using the information in the mRNA. mRNA nucleotide sequences are translated into amino acid sequences of a polypeptide
81
Molecules involved in Translation
Transfer RNA
82
Location of translation
Ribosomes (help orderly linking of amino acids into polypeptide chains)
83
Difference in bacterial and eukaryote transcription and translation
Bacteria do not have nuclei, so nuclear membranes do not separate bacterial DNA and mRNA from ribosomes and the other protein synthesizing equipment.
So what? Lack of compartmentalization allows for translation to occur even when transcription is happening
84
Transfer RNA
Translates a series of codons along an mRNA molecule
Transfer an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome
85
Transcription occurs in the
nucleus
86
mRNA must be transported from the ______ to the _______ for ______
nucleus, cytoplasm, translation
87
Pre-mRNA
The initial version of mRNA that contains the primary transcript
88
Central Dogma
cells are governed by a cellular
chain of command
DNA -> RNA -> Protein
89
How many nucleotide bases and amino acids are there?
4 bases, 20 amino acids
90
Why are enzymes translated from triplets of nucleotides?
It's the smallest unit of uniform length that can code for all amino acids (20)
1: only 4
2: only 16
3: 64
91
Triplet Code
The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three nucleotide words in mRNA, which is then translated into a chain of amino acids
92
Which strand does mRNA transcript?
Template strand. (3' -> 5')
it synthesizes an antiparellel strand
93
Transcribe the following template strand
3'ACCAAACCGAGT5'
5'UGGUUUGGCUCA3'
94
tRNA contains...
- an amino acid at one end and at the other end has a
nucleotide triplet that can base-pair with the complementary codon on
mRNA
-a single RNA strand that is only about 80
nucleotides long
- tRNA molecules can base-pair with themselves
95
Codons
mRNA nucleotide triplets
96
Anticodon
base pairs with an mRNA codon
97
Coding Strand
The nontemplate DNA strand
98
How many amino acids in a polypeptide will 300 nucleotide bases make?
100 amino acids
99
_____ of the 64 codons code amino acids
61
The other three are termination codons
100
Two functions of codon AUG
1. Codes the amino acid methionine (Met)
2. Functions as an initiation codon
101
Stop (nonsense) Codons
UAA, UAG, UGA
102
Polypeptide chains start with the _________ amino acid but _______
Methionine, but an enzyme may remove this starter amino acid later
103
RNA polymerase
Pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide
104
Promoter
The DNA sequence where RNA polymerase attaches and initiates transcription
105
Terminator
In bacteria, the sequence that signals the end of transcription
106
Direction of transcription
Downstream
107
The promoter sequence in DNA is said to be _______ from the terminator
Upstream
108
Transcription Unit
The stretch of DNA downstream from the promotor that is transcribed into an RNA molecule
109
Bacteria vs Eukaryote RNA polymerase
Bacteria:
One type
Synthesizes mRNA and other types of RNA for protein synthesis (ex. Ribosomal RNA)
Eukaryotes:
Three Types
RNA polymerase II: used for pre-mRNA synthesis
Other two transcribe RNA molecules that are not translated into a protein
110
Three stages of transcription and translation (both each)
Initiation, elongation, termination
111
Start point
The nucleotide where RNA polymerase actually begins synthesis of mRNA
112
Initiation
After RNA polymerase binds to the promoter, the DNA strands unwinds, and the polymerase initiates RNA synthesis at the start point on the template strand
113
Elongation
The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5'->3'
114
Termination
Eventually the RNA transcript is released and the polymerase detaches from the DNA
115
Transcription Factors
Mediate the binding of RNA polymerase and the initiation of transcription
116
Transcription Initiation Complex
Transcription factors and RNA polymerase II bound to the promoter
Assembles on the promoter sequence at the upstream end of the gene
117
TATA box
(TATAAA) A commonly included nucleotide sequence in eukaryotic promoters about 25 nucleotides upstream from the transcriptional starting point
118
Example of the importance of protein-protein interaction in controlling eukaryotic transcription
Interaction between eukaryotic RNA polymerase II and transcription factors
119
Transcription progresses at a rate of about 20 nucleotides per second in eukaryotes (TRUE or FALSE?)
FALSE; 40 nucleotides per second
120
How bacteria terminates transcription
Transcription proceeds through a terminator sequence in the DNA
121
How eukaryotes terminate transcription
RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence which specifies a signal AAUAA in the pre-mRNA. Once detected it binds with certain proteins in the nucleus. 10-35 nucleotides downstream these proteins cut the RNA transcript free, releasing the pre-mRNA
122
RNA processing
Both ends of the primary transcript are altered
5' end first receives a 5' cap x
3' end receives a poly-A tail
123
5' Cap
A modified form of a guanine nucleotide added onto the 5' end of pre-mRNA after transcription of the first 20-40 nucleotides
124
poly-A tail
50-250 adenine nucleotides added onto the 3' end of the pre-mRNA
125
Functions of 5' cap and poly-A tail
1. Facilitate the export of the mature mRNA from the nucleus
2. Protect the mRNA from degradation by hydrolytic enzymes
3. Help ribosomes attach to the 5' end of the mRNA once the mRNA reaches the cytoplasm
126
Untranslated Regions (UTR)
Parts of the mRNA that will not be translated into protein, but have other functions, such as ribosome binding
127
RNA splicing
Large portions of the pre-mRNA molecules are removed and the remaining portions are reconnected
128
Introns
"Intruder"
The noncoding segments of nucleic acid that lie between coding regions
129
Exons
"Expressed"
Translated into amino acid sequences
130
Spliceosome
Large complex made of proteins and small RNAs that removes introns
131
Ribozymes
RNA molecules that function as enzymes
ex. the RNA molecules in spliceosomes
132
Introns can catalyze their own splicing (True or false)
True
133
RNA splicing can occur without proteins, or even additional RNA
molecules (True or False)
True
134
Alternative RNA splicing
Many genes are known to give rise to two or more different polypeptides depending on which segments are treated as exons during RNA processing
135
Domains
Discrete structural and functional regions
136
Two steps of accurate translation
1. a correct match
between a tRNA and an
amino acid, done by the
enzyme aminoacyl-tRNA
synthetase
2. a correct match
between the tRNA anticodon
and an mRNA codon
137
Wobble
Flexible pairing at the third base
of a codon
- allows some tRNAs to bind to
more than one codon
138
The two parts of the ribosome
Small and Large subunit
139
rRNAs
Ribosomal RNAs
140
Parts of the Small and Large Subunit of the ribosome
Small: mRNA binding site
Large: A site, P site, E site
A and P are tRNA binding sites, E is the exit
141
Three stages of Translation
1. Ribosome Association and Initiation of Translation
2. Elongation of the Polypeptide Chain
3. Termination of Translation
142
Ribosome Association and Initiation of Translation
The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two
ribosomal subunits. A small ribosomal subunit binds with mRNA and a special initiator tRNA. Then the
small subunit moves along the mRNA until it reaches the start codon (AUG).
143
Elongation of the Polypeptide Chain
During elongation, amino acids are added one by one to the previous amino acid at the
C-terminus of the growing chain
144
Steps involving elongation factors
1. Codon recognition
2. Peptide bond formation
3. Translocation
145
Termination of translation
1. Ribosome reaches a stop codon on mRNA
2. Release factor promotes hydrolysis
3. Ribosomal subunits and other components disassociate
146
Two types of ribosomes in the cell and their function in producing proteins
1. Free ribosomes: mostly synthesize proteins that function in the cytosol
2. Bound ribosomes: make proteins of the endomembrane system and proteins that are
secreted from the cell
147
Polypeptide synthesis always begins in the
cytosol
148
Synthesis finishes in the cytosol unless
the polypeptide signals the ribosome to attach to the ER
149
signal peptide
Marking that indicates polypeptides destined for the ER or for secretion
150
Exon shuffling
Introns increase the probability of crossing over between the exons of alleles of a gene
151
The sequence of DNA nucleotides that codes for a eukaryotic polypeptide is usually not continuous but __________
split into segments
152
Two ways metabolic pathways can be controlled
1. adjust the activity of enzymes already present
2. Adjust the production level of certain enzymes
153
Operator
The on-off switch segment of DNA
Positioned within its promoter
Controls the access of RNA polymerase to the genes
154
Operon
The operator, promoter, and the genes they control
155
Trp operon
tryptophan (in e. coli)
156
Repressor
Bonds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes
157
What is a repressor protein encoded by?
A regulatory gene
158
Why are operons not switched off permanently when there are repressors?
1. The binding of repressors to operators is reversible
2. The repressor is an allosteric protein with two alternative shapes, active and inactive (it changes into active when it bonds)
159
Corepressor
A small molecule that cooperates with a repressor protein to switch an operon off.
160
Repressible operon
Transcription is usually on but can be inhibited
161
Example of repressible operon
trp operon
162
Inducible operon
Usually off but can be stimulated to be on when a specific small molecule interacts with a different regulatory protein
163
Example of an inducible operon
lac operon
164
Gene that catalyzes lactose metabolism
lacZ
165
lacl
Regulatory gene located outside the lac operon, and codes for an allosteric repressor protein that can switch off the lac operon by binding to the lac operator
166
Biggest difference between lac and trp operon
trp repressor protein is inactive by itself and requires tryptophan as a corepressor in order to bind to the operator
the lac repressor is active by itself, binding to the operator and switching the lac operon off
167
Inducer
A specific small molecule that inactivates the repressor
168
Inducer for lac operon
allolactose
169
Inducible enzymes
Generally function in catabolic pathways, where synthesis is induced by a chemical signal
170
Repressible enzymes
Generally function in anabolic pathways, which synthesize essential end products from raw materials
171
Negative control of genes
operons are switched off by the active form of their respective repressor protein
(both trp and lac)
172
Positive control of genes
A regulatory protein interacts directly with the genome to switch transcription on
173
When glucose and lactose are both present in its environment...
E. Coli prefers to use glucose
174
How does the E. Coli sense the glucose concentration and relay the information to the lac operon?
When cAMP binds to a cAMP receptor protein, the protein takes an active shape and can attach to the specific site at the upstream end of the lac promoter. Read the rest on page 367
175
cAMP receptor protein (CRP)
An activator: A protein that binds to to DNA and stimulates transcription of a gene
176
If the amount of glucose in the cell increases...
The cAMP concentration falls
177
A typical human cell might express about
20% of its protein coding genes at any given time
178
Differential gene expression
The expression of different genes by cells with the same genome
179
DNA methylation
(Occurs in most plants, animals, and fungi)
Enzymes methylate DNA on certain bases, where it is passed down to daughter cells, causing genomic imprinting
180
DNA methylation usually occurs on the base
Cytosine
181
Epigenetic Inheritance
Inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself
Changes in the cell can be passed down to subsequent generations
182
DNA methylation are permanent changes (True of False)
False, they are not changes to the DNA itself, but the chromatin
183
Control elements
Segments of noncoding DNA that serve as binding sites for the protein called transcription factors, which bind to the control elements and regulate transcription
184
Two types of transcription factors
General transcription factors, specific transcription factors
185
General Transcription Factors
Act at the promoter of all genes
186
Specific Transcription Factors
Bind to control elements that may be close to or farther away from the promoter
187
Proximal control elements
Located close to the promoter
188
Enhancers
Distal control elements
Thousands of nucleotides upstream or downstream of a gene or even within an intron
189
Two types of structural domains that are commonly found in a large number of activator proteins
1. DNA-binding domain
2. Activation domains
190
DNA binding proteins
A part of the protein's three dimensional structure that binds to DNA
191
Activation Domains
Bind other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in enhanced transcription of a given gene
192
Transcription produces
mRNA
193
Difference between eukaryote and Prokaryote gene expression
In eukaryotes, transcription is done in the nuclear envelope
194
Reading frame
Correct grouping of nucleotides in order for specified polypeptide production
195
RNA polymerases need a primer (true or false)
False
196
Point mutations
chemical changes in just one or a few nucleotide pairs of a gene (in the DNA!)
ex.
- Nucleotide-pair substitutions
- One or more nucleotide-pair insertions or deletions
197
nucleotide-pair substitution
replaces one nucleotide and its partner with another pair
of nucleotides
198
Silent mutations
have no effect on the amino acid produced by a codon because of
redundancy in the genetic code
199
Missense mutations
code for an amino acid, but not the correct amino acid
200
Nonsense mutations
change an amino acid codon into a stop codon, nearly always
leading to a nonfunctional protein
201
Mutagens
physical or chemical agents that can cause mutations
Spontaneous and induced
ex.
Spont: strand slippage
Induced: smoking
202
What brings unity and diversity in genetic code?
Unity: all living things have DNA with nucleotides
Diversity: The sequences (code for amino acids which fold into a polypeptide) are different
203
Main difference in eukaryote and prokaryote gene expression
Eukaryotes go through RNA processing
204
These three mutations cause the other three
Point Mutations (substitution, insertion, deletion) cause a nonsense, silent or missense mutation
205
Frame Shift Mutation
An insertion or deletion that alters the reading frame of the DNA
206
What will a frame shift mutation lead to?
A long chain of missense mutations
207
When glucose levels are scare
CAP (catabolite activator protein) acts as an activator of transcription
208
CAP is activated by
binding with cyclic AMP (cAMP)
209
Examples of noncoding RNAs
MicroRNAs
SiRNAs
Piwi-associated RNA
210
MicroRNAs
small single-stranded RNA molecules that
can bind to complementary mRNA sequences. These can degrade the
mRNA or block its translation
211
SiRNAs
Inhibits gene expression through a phenomenon called RNA interference
212
Piwi-associated RNAs
induce formation of
heterochromatin
213
How does recombinant DNA Technology work?
The plasmid of one bacterium is extracted, a gene of interest is extracted from a cell and put into the plasmid, and its all placed back into the bacterium
214
What is the biggest outcome of recombinant DNA?
You can get a bunch of copies of the gene and a bunch of copies of the proteins it makes
215
Plasmid technology
216
Restriction Enzymes
Don't really restrict, but cut DNA out at certain restriction sites. If the enzyme sees a palindrome, it will cut it to make "sticky ends". The safely cut places can have new DNA inserted into it!
217
Cloning Vector
DNA molecule that can carry foreign DNA into a host cell and replicate
218
Conjugation
When two viruses send genes to each other if one needs a copy. ex. for resilience
219
How do viruses infect?
Enters cell, injects DNA
DNA replicates
DNA, makes mRNA, makes protein coats
self assembly,
leaves cell
220
Genomic Library
A bunch of copies of a certain plasmid, or phage
221
cDNA
Reverse transcription
makes DNA out of mRNA
