Module 1: Intro & DNA Flashcards
1
Q
Organisms with complex cells containing a nucleus.
A
eukaryotes
2
Q
- Cells are relatively large
- Contain multiple linear DNA molecules complexed with histones
- Have a large amount of DNA
- Contain membrane bound organelles
A
the characteristics of eukaryotic cells
3
Q
Single-celled organisms without a nucleus.
A
prokaryotes
4
Q
- Cells are small
- Usually contain one circular DNA molecule
- Not complexed with histones in eubacteria
- Complexed with histones in archaea
- Have a small amount of DNA
- Do not contain membrane bound organelles
A
the characteristics of prokaryotic cells
5
Q
Non-cellular entities requiring a host to replicate.
A
viruses
6
Q
May contain DNA or RNA as nucleic acid.
A
What nucleic acids may viruses contain?
7
Q
DNA-transcription-> RNA-translation-> protein
A
the Central Dogma
8
Q
Basic unit of heredity encoding a protein.
A
gene
9
Q
Different forms of a gene affecting traits.
A
allele
10
Q
Outward expression of traits influenced by genotype.
A
phenotype
11
Q
Genetic makeup of an individual, including alleles.
A
genotype
12
Q
Study of inheritance patterns established by Mendel.
A
Mendelian Genetics
13
Q
Inheritance patterns not following Mendelian laws.
A
Non-Mendelian Genetics
14
Q
Study of genes at a molecular level.
- DNA structure
- Gene expression
- Mutation and Repair
A
Molecular Genetics
15
Q
Study of genetic variation within populations.
- Allelic frequencies
- Evolution
A
Population Genetics
16
Q
Study of how genes are passed to offspring; the inheritance patterns of alleles.
- Mendelian genetics
- Non-mendelian genetics
- Heredity
A
Transmission Genetics
17
Q
Species used for research to understand biological processes.
A
model organism
18
Q
Yeast
A
general model organism for eukaryotes
19
Q
Mice
A
model organism for mammals
20
Q
E.coli
A
model organism for simple genetic processes
21
Q
Nematode (round worm) and Drosophila (fruit fly)
A
general model organisms for animals
22
Q
Zebra fish
A
model organism for vertebrate development
23
Q
Thale-cress plant
A
model organism for plants
24
Q
The process by which information encoded in DNA directs the synthesis of proteins.
A
gene expression
25
Change in DNA sequence affecting genetic information.
a mutation
26
Process of copying DNA before cell division.
replication
27
Synthesis of RNA from a DNA template.
transcription
28
Process of synthesizing proteins from RNA.
translation
29
Molecules that hold genetic information.
nucleic acids
30
Basic unit of nucleic acids, composed of sugar, phosphate, base.
nucleotide
31
Isolated nuclei from white blood cells in pus and found that it contained an acidic (negatively charged) material high in phosphorus.
Johann Meischer
32
Discovered that nucleic acid is made up of four repeating, chemically similar components - nucleotides.
Phoebus Levene
33
He did not find any variability between these units 'A=G=T=C'.
What Phoebus Levene concluded about nucleotides
34
Demonstrated DNA as the transforming principle.
the Avery-MacLeod-McCarty experiment
35
If proteins are the transforming principle, then taking away the DNA (using DNAse) should result in no effect.
the hypothesis of the Avery-MacLeod-McCarty experiment
36
The DNase sample did not transform the nonvirulent strain to become virulent - strong evidence that DNA was the transforming principle.
the result of the Avery-MacLeod-McCarty experiment?
37
Discovered the transforming principle was heat stable.
Fred Griffith
38
Injected a mouse with live virulent streptococcus - the mouse died.
Fred Griffith's experiment
39
The transforming principle found in the virulent strain was heat stable.
the conclusion of Fred Griffith's experiment
40
1. Number of A nucleotides = T nucleotides and G nucleotides = C nucleotides (in DNA). 2. A+T does not equal G+C. 3. A+G = T+C; purines = pyrimidines.
Chargaff's Principles
41
Substance responsible for genetic transformation.
the transforming principle
42
Demonstrated that DNA is conclusively the transforming principle using T2 bacteriophage infection.
Alfred Hershey and Martha Chase
43
The 32P was transmitted to progeny phages so DNA, not protein, is the genetic material.
the result of the Hershey-Chase experiment
44
Double helix formed by two antiparallel strands.
structure of DNA
45
Specific pairing of nucleotides: A:T and G:C.
base pairing in DNA
46
Link between nucleotides in a nucleic acid strand.
phosphodiester bond
47
1'C - site of base attachment, 2'C - H (DNA) or OH (RNA), 3'C - always OH, 5'C - site of phosphate attachment.
the nucleotide carbons labeling
48
Scientists who proposed the double helix model of DNA.
Watson and Crick
49
Consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group.
a nucleoside
50
Single-stranded nucleic acid that can store genetic information.
RNA
51
Consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups.
a nucleotide
52
The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.
antiparallel (in DNA)
53
5' to 3'.
the direction of DNA synthesis
54
Process of copying DNA before cell division.
DNA replication
55
Each new DNA molecule contains one original strand.
semi-conservative replication
56
Weak bonds between base pairs in DNA.
hydrogen bonds in DNA
57
How many hydrogen bonds are between A and T
2
58
How many hydrogen bonds are between G and C
3
59
Purine and pyrimidine form different hydrogen bonds which can result in triple helix and other abnormal structures.
Hoogsteen base pairing
60
Adenine and Guanine, two types of nitrogenous bases with double ring shapes.
purines
61
Cytosine and Thymine, types of nitrogenous bases with single ring shapes.
pyrimidines
62
Compact form of DNA, less common than B-DNA.
A-DNA
63
Most common form of DNA, right-handed helix.
B-DNA
64
Left-handed DNA helix, forms under certain conditions.
Z-DNA
65
Discovered that RNA serves as the genetic material in some viruses.
Fraenkel-Conrat and Singer
66
Once RNA primer is cleaved, nucleotides cannot be added to replace it.
end replication problem
67
Protective caps at chromosome ends in eukaryotes.
telomeres
68
Enzyme that extends telomeres by replacing the RNA primer using RNA template.
telomerase
69
Y-shaped structure where DNA replication occurs.
replication fork
70
Enzyme that synthesizes new DNA strands from the 5' to the 3' end of the DNA.
DNA Polymerase III
71
Proofreading function of DNA polymerase for accuracy.
3' to 5' exonuclease activity
72
An enzyme that removes successive nucleotides from the end of a polynucleotide molecule.
an exonuclease
73
Starting point for DNA replication in DNA.
ORI (Origin of Replication)
74
DNA replication model in bacteria with circular DNA.
the theta model
75
Replication bubble - unit of replication, consisting of DNA from the origin of replication.
a replicon
76
DNA replication model in viruses and plasmids.
the rolling circle model
77
DNA replication model used by eukaryotes.
the linear replication model
78
Region where DNA strands are separated for replication.
replication bubble
79
Replication occurring in two directions from ORI.
bidirectional replication
80
Deoxynucleotide triphosphate, building blocks of DNA.
dNTP
81
Short DNA segments formed on the lagging strand.
Okazaki fragments
82
Proteins that unwind DNA at the ORI.
DnaA (Initiator Proteins)
83
Initiation, elongation, termination.
steps of DNA replication
84
Single ORI is bound by initiator proteins that unwind the DNA.
initiation in bacteria
85
Enzyme that unwinds and unzips DNA strands during replication.
helicase
86
Proteins that prevent reannealing of unwound DNA during replication.
single-stranded binding proteins (SSB)
87
Type II topoisomerase that prevents torsional strain on DNA during initiation.
gyrase
88
Enzyme that synthesizes short RNA segments (primers) to allow DNA pol III to synthesize.
primase
89
Removes and replaces RNA primers with DNA on lagging strand.
DNA Polymerase I
90
Enzyme that seals nicks between Okazaki fragments after DNA pol I replaces the primers.
DNA ligase
91
Prevents core enzyme dissociation from template; holds DNA to template strand.
DNA clamp
92
Complex that loads DNA polymerase onto the template.
clamp loader
93
Multiple ORI, multiple helicases, gyrases, and DNA polymerases for multiple ORI.
eukaryotic replication
94
Process generating recombinant chromosomes during reproduction.
homologous recombination
95
Cross-shaped structure that forms during the process of genetic recombination.
holiday junction
96
Homologous recombination involving single-strand breaks.
single-strand break recombination
97
Homologous recombination involving double-strand breaks.
double-strand break recombination
98
Complex of enzymes involved in DNA replication.
replisome
99
Short RNA strand required for DNA synthesis initiation.
primer
100
The first step in gene expression, generating an RNA molecule from a DNA template.
transcription
101
- If DNA is damaged, that change is permanent, but it is not with RNA (no replication).
- DNA is too large for translational machinery to access it.
- DNA contains info that does not need to be translated.
- RNA is small and single stranded, allowing for the translation of a single protein.
transcription important
102
A transcription unit; a stretch of DNA that encodes an RNA molecule (either mRNA or a functional RNA).
gene
103
- Promoter
- Coding region
- Terminator
sequences included in a gene
104
An RNA molecule that functions without being translated, carrying out a job in the cell as RNA.
functional RNA
105
- rRNA
- tRNA
- ncRNA
examples of functional RNA
106
The DNA strand that provides the template for ordering the sequence of nucleotides in RNA.
template strand
107
Read in the 3' to 5' direction so that new DNA is generated in the 5' to 3' direction.
How is the template strand read?
108
The strand of DNA that is not used for transcription.
coding strand
109
It is identical in sequence to mRNA, except it contains uracil instead of thymine.
How the coding strand compares to mRNA
110
Messenger RNA, carries genetic information for proteins.
mRNA
111
Ribosomal RNA, RNA component of ribosomes.
rRNA
112
Transfer RNA, links amino acids during translation.
tRNA
113
DNA sequence initiating the transcription process.
promoter
114
It will shift the transcription start site, because consensus sequences must always be at the -10 and -35 positions (bacteria).
What happens if the promoter region is shifted
115
DNA sequence signaling the end of transcription.
terminator
116
Protein aiding bacterial RNA polymerase initiation.
sigma factor
117
How is eukaryotic initiation different from bacterial initiation
It is more complex, involving 3 types of multisubunit RNA polymerase that recognizes the TATA box in the promoter.
118
Region of DNA that is closer to the 5' transcription start site or past it.
upstream in DNA
119
Region of DNA that is closer to the 3' transcription termination site.
downstream in DNA
120
Enzyme that synthesizes RNA from a DNA template.
RNA polymerase
121
- Large
- Always adds to 3' OH (built 5' - 3')
- Unwinds and rewinds DNA in the absence of helicase
- Initiates new strand synthesis (no need for primers)
- Weak proofreading ability
characteristics of RNA polymerase
122
One multisubunit RNA polymerase recognizes -10 and -35 consensus sequences in the promoter to orient the polymerase and begin transcription.
How bacterial transcription initiation occurs
123
1. Rho independent - GC rich loop by palindrome, then UUU rich sequence. mRNA pulling itself out.
2. Rho dependent - rho protein runs behind RNA polymerase. When there is a termination signal, a small loop forms and rho pushes the mRNA out.
two types of prokaryotic transcription termination
124
In prokaryotes (50%), termination of transcription by an interaction between RNA polymerase and the rho protein.
rho-dependent termination
125
In prokaryotes (50%), GC rich loop by palindrome, then UUU rich sequence. mRNA pulling itself away.
rho-independent termination
126
Building blocks of RNA, containing ribose.
ribonucleotides
127
Protein that controls the binding of RNA polymerase to the promoter in bacteria.
role of the sigma factor
128
Consensus sequences in prokaryotic promoters.
the -10 and -35 boxes
129
Short RNA synthesized with sigma factor before RNA polymerase moves on without it.
abortive initiation
130
Essential DNA sequence for initiating eukaryotic transcription - not sufficient alone.
core promoter
131
DNA sequence located immediately upstream of the eukaryotic core promoter; contains consensus sequences to which transcriptional regulator proteins bind.
regulatory promoter
132
Common core promoter element in eukaryotes.
TATA box
133
Proteins assembling on core promoter to recruit RNA polymerase II.
general transcription factors
134
9 different polypeptides (transcription factors) that must fully assemble before transcription can begin.
TFIID
135
Strain on DNA by TBP of TFIID causes DNA to open, allowing for RNA polymerase to begin adding nucleotides to synthesize RNA transcript.
the open complex
136
Proteins that bind to regulatory promoters of DNA to regulate transcription.
transcriptional factors
137
Process where transcription continues beyond the end of the gene - sequence in RNA causes nuclease to break pre-mRNA from the transcription machinery.
eukaryotic termination
138
Eukaryotic polymerase responsible for transcribing rRNA genes.
RNA polymerase I
139
Main polymerase of eukaryotic transcription - transcribes protein encoding genes as well as regulatory RNAs.
RNA polymerase II
140
The number of nucleotides in the gene should be proportional to the number of amino acids in the protein.
co-linearity
141
Coding regions of DNA that express proteins.
exons
142
Initial mRNA containing both introns and exons.
primary mRNA transcript
143
Processed mRNA containing only exons. In eukaryotes, only this mRNA can be exported from the nucleus.
mature mRNA
144
Removal of introns from pre-mRNA.
splicing
145
Involves small nuclear RNAs (snRNAs) and snRNPs (snurps), forming a 'lariat' structure.
mechanisms are involved in splicing
146
Genes with many introns can have differential splicing, resulting in different patterns of exons.
alternative splicing
147
Eukaryotes only, transcribes tRNA and other small RNAs.
RNA polymerase III
148
Modified guanine added to mRNA's 5' end.
the 5' cap
149
- Protects the mRNA from degradation.
- Regulates export.
- Aids in ribosomal binding; translation.
functions of the 5' cap
150
String of adenine nucleotides added to mRNA, making it more stable and protecting it from degradation.
poly A tail
151
Coding region in mRNA that translates to protein.
open reading frame (ORF)
152
Untranslated region aiding mRNA export and translation.
5' UTR
153
Untranslated region involved in stability (miRNA interaction) and translation.
3' UTR
154
Small nucleolar RNA involved in rRNA processing.
snoRNA
155
Small interfering RNA regulating gene expression.
siRNA
156
Micro RNA involved in post-transcriptional regulation.
miRNA
157
Piwi-interacting RNA targeting transposons.
piRNA
158
Bacterial micro RNA that is important for defense, now used as a bio-tool.
CRISPR
159
Long non-coding RNA, gene silencing (Xist in x-chromosome inactivation).
LncRNA
160
Transfer RNA - carries amino acids to ribosomes; each molecule is specific for a different amino acid.
tRNA
161
Three-nucleotide sequence coding for an amino acid.
codon
162
Codons are shared by almost all organisms.
universal code
163
Codons are read sequentially without overlap.
non-overlapping code
164
Multiple codons can encode the same amino acid, but each codon can only code for one amino acid.
degenerate/redundant code
165
AUG
start codon
166
UAA, UGA, UAG
stop codons
(u are annoying, u go away, u are gone)
167
The start codon (AUG), dictates codon grouping.
How an open reading frame is determined
168
tRNA sequence complementary to mRNA codon.
anticodon
169
Refers to flexibility in the pairing between the base at the 5' end of a tRNA anticodon and the base at the 3' end of an mRNA codon.
wobble pairing
170
tRNA loading with amino acid prior to use.
tRNA charging
171
Enzyme that charges tRNA with the correct amino acid.
aminoacyl-tRNA synthetase
172
Macromolecular complex that synthesizes proteins.
ribosome
173
Initiation factor 3 (IF-3) binds to small ribosomal subunit and allows it to read along the mRNA.
How initiation occurs in bacteria
174
N-terminus to C-terminus.
direction of protein synthesis
175
Elongation factors move ribosome along the mRNA to read a new codon, and the appropriate tRNA adds the corresponding amino acid.
What happens during elongation in bacteria
176
Assembly of ribosomal subunits and mRNA for initiation of translation.
initiation complex
177
Proteins assisting in the elongation phase of translation.
elongation factors
178
Ribosome encounters a stop codon, which does not have a tRNA to pair with it.
What happens during termination
179
Proteins that bind to the stop codon of mRNA and promote termination of translation.
release factors
180
- Start codon is regular met.
- Start sequence is the Kozak sequence.
- 5' cap, polyA tail, and UTRs play a role in translation.
- Different initiation factors (IF) and elongation factors (EF) are used, but have similar roles.
- Transcription and translation are not coupled.
characteristics of eukaryotic translation
181
Sequence that facilitates translation initiation in eukaryotes.
Kozak sequence
182
The sequence of initiation of translation in prokaryotes.
Shine-Dalgarno sequence
183
Proteins can be enzymes, transporters, structural, signaling, and storing.
functions of proteins
184
Covalent bonds linking amino acids in proteins.
peptide bonds
185
- Primary (linear sequence)
- Secondary (coiling or folding of a polypeptide due to H-bonding between amino acids)
- Tertiary (bending or coiling of secondary structure)
- Quaternary (association between two or more polypeptide chains within one protein)
levels of protein structure
