Exam 1 Molecular Flashcards
(208 cards)
1
Q
Biology’s unifying principles
A
All organisms use genetic systems that have a number of features in common
2
Q
Central Dogma
A
DNA->transcription->RNA->translation->amino acids-> protein
3
Q
Molecular genetics focuses on
A
the level of the gene
4
Q
Divisions of genetics
A
Molecular genetics, transmission genetics, and population genetics
5
Q
Transmission genetics focuses on
A
heredity and how traits are passed from one generation to the next
6
Q
Population genetics focuses on
A
the collection of genes within populations
7
Q
Genome
A
complete set of genetic instructions for any organism
8
Q
all genomes are composed of
A
nucleic acid, DNA or RNA
9
Q
What makes a good genetic model
A
short generation time
large but manageable number of progeny
adaptability to laboratory environment
ability to be housed and propagated inexpensively
10
Q
Two basic cell types
A
prokaryotic
eukaryotic
11
Q
Prokaryotic cells
A
lack nuclear membrane, generally lack organelles
12
Q
eukaryotic cells
A
posses nucleus and organelles
13
Q
Fundamental unit of heredity
A
gene
14
Q
Alleles
A
multiple forms of a gene
15
Q
what determines the phenotype
A
genetics+environment
16
Q
Genetic information is carried in
A
nucleic acids
17
Q
Genes are located on
A
chromosomes
18
Q
Chromosomes separate through the processes of
A
mitosis and meiosis
19
Q
Mutations
A
permanent changes in genetic information that can be passed from cell to cell or from parent to offspring
20
Q
Traits are affected by
A
multiple factors
21
Q
Evolution is
A
genetic change
22
Q
What is needed for inheritance
A
information storage
information copying (replication)
Information retrieval (translation)
Ability to vary
23
Q
DNA was identified
A
before 1900 but it wasn’t until 1940s-1950s that we knew that DNA and not protein was the genetic material
24
Q
DNA is a molecule composed of
A
repeating subunits (nucleic acids)
25
Three parts of DNA/RNA
Pentose sugar
Base
Phosphate
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Pentose sugar is used as
an anchor
-DNA uses deoxyribose
-RNA uses ribose
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Nitrogenous Bases
Purines-Adenine and Guanine
Pyrimidines- Cytosine, Thymine, Uracil
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Purines
Adenine and Guanine
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Pyrimidines
Cytosine
Thymine- only in DNA
Uracil- only in RNA
30
Nucleosides
base linked to sugar by 1' carbon of pentose sugar
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Nucleotides
phosphate group attached to the 5' carbon
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Phosphodiester bonds
covalent bonds between a phosphate group of one nucleotide and the 3' carbon of the next nucleotide's sugar (5' to 3' linkage)
33
The two ends of the polynucleotide chain are
not the same
the 5' end has a phosphate group attached to the 5' carbon of the pentose sugar
the 3' end has a hydroxyl group attached to the sugar's 3' carbon
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A polynucleotide chain has
polarity
35
Base pairings
A-T
C-G
A-U RNA only
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A-T bonding
two H bonds
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C-G bonding
Three H bonds
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Which nucleotide bonding is the strongest?
C-G bonding
39
Watson and Crick investigated the structure of DNA by
using all available information about the chemistry of DNA not by collecting new data
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DNA is what type of structure
double helix
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DNA strands are
antiparallel
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What types of bonds are between the complimentary base pairs
hydrogen
43
The strands are arranged helically meaning
10 base pairs between each turn of the helix
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If 10 bp per turn= 3.4 nm what is the distance between each pair
0.34 nm
45
If a single chromosome is 2.058 bp how long is it in meters
200 million bases
46
Genetic material must contain
all of the information for the cell structure and function of an organism- storage
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1C Value
a single set of genes (or the number of unique DNA bases)
what we contribute to our offspring
48
Diploid
two copies of every base pair/gene
2C
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Haploid
sperm and egg cells have only 1 copy
1C
50
What does N stand for
the number of chromosome molecules in a cell
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DNA is _____ for compaction
supercoiled
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Supercoiling relies on
topoisomerases
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topoisomerases
enzymes that break the double helix
- rotate the ends then rejoin
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Eukaryotic chromosomes have additional levels of compaction-
multiple linear chromosomes
also supercoiled
proteins including histones compact further
55
Chromatin
DNA with a protein scaffold
56
Histones
a group of basic proteins found in chromatin
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Histones have
a net positive charge thus bind to negatively charged DNA
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Histone sequences across species
is very similar
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linker between nucleosomes
H1
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Histones have two copies of _____ thus an octamer
H2B, H4, H3, and H2A
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The fundamental repeating unit of chromatin
nucleosome
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what is the structure of chromatin
beads on a string
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Karyotype
a chart of chromosomes
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how many chromosomes do humans have
23 pairs
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Diploid eukaryotic cells have
two sets of chromosomes
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Types of chromatin
euchromatin
Heterochromatin
67
Euchromatin
stains slightly, uncoiled except during cell division
holds active genes
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Heterochromatin
stains darkly, more condensed
genetically inactive
found near centromeres, telomeres, and species-specific locations
69
Types of heterochromatin
Constitutive
facultative
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Constitutive heterochromatin
involved in maintaining chromosome structure
includes centromeres and telomeres
71
Facultative heterochromatin
has the potential to become condensed, e.g. X chromosome inactivation
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Centromeres
used by the cell during cell division to make sure that each daughter cell gets a copy of each chromosome
sites at which chromosomes attach to the mitotic and meiotic spindle
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Where do kinetochores form and spindle microtubules attach
centromeres
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Centromeres are responsible for
accurate segregation of the replicated chromosomes during meiosis and mitosis
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Telomeres are located
at the ends of the chromosomes
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Telomeres
short tandemly repeated sequences and other repeated sequences further in from the ends
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What is the job of telomeres
adds new copies of the repeat so the chromosome isn't destroyed by the loss of material after each round of synthesis
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Circular genome
a form of closed -loop DNA that has no end
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uniparental inherited
offspring inherit genotype from only one parent
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Replicative segregation can lead to
both heteroplasmic and homoplasmic cells
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Semiconservative
one strand of double helix is conserved, the other is new
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Dispersive
each strand is a mix of old and new DNA
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Conservative
one double helix is unchanged by the process, the other is completely new
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Three proposed models of DNA replication
Conservative
dispersive
semi-conservative
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DNA structure was discovered in
1953
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Why do we use heavy nitrogen (N) in the experiment that demonstrated that replication is semi-conservative
?
87
Raw materials of DNA synthesis
template
enzyme
substrates (raw materials)
Mg2+ ions
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What is the role of DNA polymerase in DNA synthesis
catalyzes the formation of phosphodiester bonds
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DNA polymerase joins the ______ group of the last base in the DNA chain to the incoming ______ of a dNTP
3'-OH
5' Phosphate
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Synthesis is
5' to 3'
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How is it decided which dNTP to use
selected by the DNA polymerase 1 using the opposing base on the template strand
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When new DNA is synthesized from deoxyribonucleoside triphosphates (dNTPs) the newly synthesized strand is
complementary and antiparallel to the template strand
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5 key elements of each replication fork
1. helicase to unwind the DNA
2. SSBP to protect ssDNA
3. Gyrase to remove stain ahead of fork
4. Primase to synthesize RNA primer
5. DNA polymerase
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Okazaki fragments
?
95
lagging strand
?
96
leading strand
?
97
Describe the process that happens at the DNA fork during DNA replication
?
98
key factors of DNA replication in Eukaryotes
occurs in the nucleus during S phase of the cell cycle
is initiated by RNA primers
occurs in the 5' to 3' direction
semiconservative
initiated at the same time at many points (origins of replication) along the chromosome
99
Packaging of newly replicated DNA
histones must first disassemble to allow DNA synthesis
synthesis of new histones is coordinated with DNA synthesis
Then must reassemble on two new chromosomes
100
Main polymerases have a _____ activity
Why?
3' to 5'
?
101
Once DNA replication is complete, how do we package one copy of the DNA into one daughter cell and the other into another daughter cell
Mitosis
102
5 phases of a cell life-cycle
G1
G0
S
G2
Mitosis
103
What happens in the G1 stage
chromosome morphology changes from condensed to dispersed due to a change in the coiling fibers
the cell also prepares for S by producing RNA and protein
Contains the checkpoint
104
Once a cell reaches the checkpoint in G1 can it go back?
no it must enter the S phase
105
What happens in G0
quiescent phase of neither growing nor progressing to S
Mature muscle cells and neurons go into this phase
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What happens in the S phase
DNA untwists and replicates
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What happens in the G2 phase
DNA condenses- generally a short phase
108
Mitosis is
the formation of two cells from one cell
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Mitosis has how many phases
5
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result of mitosis
2 daughter cells, each with a complete copy of the genome
111
Phases of mitosis
Interphase
Prophase
Metaphase
Anaphase
Telophase
112
What happens in interphase
the cell grows, replicates its chromosomes, and prepares for cell division
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What happens in Prophase
Chromosomes condense
Two sister chromatids become detectable
Mitotic spindle assembles outside the nucleus and the envelope begins to break down
114
At what stage in a cell's lifecycle is the DNA replicated
S phase
115
what happens during metaphase
chromosomes line up on the metaphase plate
centrosomes at opposite poles
microtubules from centrosomes to kinetochore
most condensed phase
116
the number of chromosomes per cell equals the number of
functional centromeres
117
What happens during anaphase
sister chromatids separate
chromosomes move towards opposite poles
118
The number of DNA molecules per cell equals the
number of chromosomes when the chromosomes are unreplicated and twice the number of chromosomes when sister chromatids are present
119
Product of meiosis
four daughter cells; each has half the genetic material of the parent cell (reduction)
120
Number of chromosomes in a diploid cell
2N
121
Number of chromosomes in a haploid cell
N
122
Parts of Meiosis
Meiosis I
- prophase I, Metaphase I, anaphase I, Telophase 1, cell division
Meiosis II
- prophase II, Metaphase II, anaphase II, telophase II, cell division
123
Meiosis includes how many cell divisions
two
124
the original cell is diploid with four chromosomes, after two meiotic division, each resulting cell is
haploid (1n) with two chromosomes
125
Why are brothers and sisters so different if they have the same parents
we don't get a complete copy of our mom's mom's chromosome or our mom's dad's chromosome
chromosomes cross-over during prophase I
126
Chromosome crossover
when chromosomes line up they can switch parts
127
Independent assortment
the random distribution of chromosomes in meiosis that produces genetic variation
128
when the cell starts meiosis II it already has
two daughter cells, each one with a replicated copy of each chromosome
129
In order for the cell to move past Metaphase II
fertilization has to take place
130
Regulatory promoter is located
upstream of core promoter
131
regulatory promoter
the binding site for transcription apparatus- RNA polymerase and it's cofactors
132
Transcription factors
bind at the regulatory promoter and affect the rate of transcription
133
Enhancers
distal location that can enhance transcription
134
Initiation
if the promoter (core and regulatory) and enhancers 'say so' a protein- coding gene is transcribed
135
Elongation
keep adding nucleotides
136
Termination
for RNA polymerase II there is no specific termination sequence
transcription can continue for 100s-1000s bp
137
What is a gene
the fundamental unit of heredity
138
Big picture of RNA processing
Start at a DNA template
RNA message- complimentary and antiparallel
Protein product
139
With colinearity
the number of nucleotides in the gene is proportional to the number of amino acids in the protein
140
Introns are found in
most eukaryote organisms
141
Introns
a non-coding region of DNA that doesn't code for a protein in between two regions that do
142
Exon
region of DNA that codes for a protein
143
In eukaryotes, intron size and number is related to
organism complexity
144
Some introns have
regulatory roles
145
introns tend to be _____ than exons
longer
146
in order to have collinearity,
introns are spliced out by snRNPs in a spliceosome
147
snRNPs
small nuclear nuclear ribonucleoproteins
148
All sequences in DNA are transcribed into
a single RNA molecule
149
mRNA
messenger RNA
150
role of mRNA
carries the instructions to make a protein
151
three primary regions of mature mRNA are the
5' untranslated region
protein-coding region
3' untranslated region
152
5' untranslated region
does not code for protein, ribosomes bind to 5' end of transcript
153
3' untranslated region
not translated
affects stability of mRNA
154
RNA transcribed in the
nucleus to produce primary transcript
155
post-transcriptional modifications that can be made
addition of 5' CAP
addition of Poly-A-Tail
introns spliced out
156
5' CAP
addition of extra guanine to 5' end of primary transcript
addition of methyl groups to G and sometimes other bases
157
5'CAP occurs
rapidly after transcription initiation
158
Function of 5' CAP
functions in initiation of translation
increases stability of transcript and influences splicing of introns
159
Poly-A-Tail
plays a role in transfer of mRNA into cytoplasm
functions to alter the half-life of transcript
160
RNA pol II does not have a
transcription sequence it keeps going
161
primary transcript is
cleaved based on consensus sequence (AAUAA) in 3' UTR, Polyadenylation signal
162
polyadenylation signal
the consensus sequence in 3' UTR that tells when to cleave the primary transcript
163
Splicing
removes the introns so the DNA and Proteins can be colinear
164
5' splice donor site
GU (GT in DNA)
165
3' splice donor site
AG
166
Splicesome
large, complex structure almost 300 proteins plus snRPS
removes introns from pre-RNA to generate mature RNA
167
Process of splicing
1. the mRNA is cut at the 5' splice site
2. the 5' end of the intron attached to the branch point
3. a cut is made at the 3' splice site
4. the intron is released as a lariat
5. and the two exons are spliced together
6. the bond holding the lariat is broken, and the linear intron is degraded
7. the spliced mRNA is exported to the cytoplasm and translated
168
Process of alternative splicing/ cleavage in thyroid cells versus brain cells
1. in thyroid cells, cleavage and polyadenylation take place at the end of exon 4
2. producing an mRNA that contains exons 1,2,3,4
3. translation produces the hormone calcitonin
Brain cells
1. in brain cells, 3' cleavage takes place at the end of exon 6
2. during the splicing, exon 4 is eliminated with the five introns
3. producing an mRNA that contains exons 1,2,3,4,5,6
4. translation yields calcitonin-gene-related peptide
169
where is the enhancer compared to an intron promotor
typically upstream
170
why is there extra nucleotides on the end of a gene
room for error
171
What are proteins
Functional molecules of the cell
172
Enzymes
proteins that act as biological catalyst
173
Structural proteins
membranes, filaments
174
transporter proteins
allow things to move
175
Regulatory proteins
transcription factors that bind to DNA
176
Like DNA and RNA, protein
has a linear sequence and an alphabet
repeats similar but not identical units
have directionality
177
Units that make up a protein
20 amino acids
178
Amino end of an amino acid
has a free amino group (NH3)
179
Carboxyl group of an amino acid
has a free carboxyl group (COO-)
180
R group
differs in each amino acid
181
Protein structures
Primary
secondary
tertiary
quaternary
182
primary protein structure
sequence of AA
183
secondary protein structure
interactions between AA (beta sheets, alpha helix)
184
tertiary protein structure
structures after folding
overall 3-D structure
185
quaternary
more than one polypeptide
186
Domains
groups of AA that form a discrete functional unit
187
Codon
three bases
188
degenerate
redundancy
more than one codon for each AA
189
First AA being translated
Met start codon
can occur internally as well
190
Wobble
typically the 3rd base of the codon can vary
191
synonymous
change in DNA sequence does not change AA
192
non-synonymous
change in DNA sequences changes AA
193
Nonsense
change in DNA introduces a stop codon
194
AUG
start codon
methionine
195
three stop codons
UAG
UAA
UGA
196
reading frame
a way of dividing the sequence of nucleotides in a nucleic acid molecule into a set of consecutive, non overlapping triplets
197
Each codon specifies the same AA in
almost all organisms, nearly universal
198
The genetic code provides the
logic
199
machinery that makes proteins
ribosomes
200
Four phases of protein synthesis
1. tRNA charging- binding tRNA to AA
2. Initiation- start of translation
3. elongation- synthesis of polypeptide chain
4. termination- ending synthesis
201
aminoacyl-tRNA synthetase
enzyme that attaches an amino avid to a tRNA
202
Each aminoacyl-tRNA is
specific for a particular amino acid
203
what forms the initiation complex recognizing the 5' CAP
ribosome small subunit
initiation factors
initiator RNA
204
When is the initiation complex added
just after transcription
205
What does the initiation complex do
scans the mRNA until it finds the start codon
206
translation stops when it encounters a __. Why?
stop codon
no incoming tRNA to match it to AA
207
three sites that a ribosome can occupy
Aminoacyl A site- where charged tRNA enter ribosome
Peptidyl (P) site- where peptide bond is formed
Exit (E) site
208
only codon to start in the P site
initiation codon met-tRNA
