Exam 1 Flashcards
(141 cards)
1
Q
First part of the chemical composition and structure of DNA and RNA
A
Pentose Sugar (anchor)
DNA uses deoxyribose and RNA uses ribose
2
Q
What is needed for inheritance?
A
Information storage, information copying (replication), Information retrieval (translation), and ability to vary
3
Q
What makes a good genetic model?
A
Short generation time, large but manageable number of progeny, adaptability to laboratory evironment, ability to be housed and progagated inexpensively
4
Q
Genome
A
Complete set of genetic instructions for any organism
5
Q
Nucleosides
A
Base linked to sugar by 1’ ccarbon of pentose sugar
6
Q
Third part of chemical structure of DNA and RNA
A
Phosphate group attached to the 5’ carbon
nucleotides
7
Q
Phosphodiester bonds
A
Covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar (a 5’-3’ linkage)
\
8
Q
Second part of the chemical structure of DNA and RNA
A
Nitrogenous Base (data)
Purines (A&G) and Pyrimidines (C,T,&U)
9
Q
All organisms use genetic systems that have a number of features in common
A
True
10
Q
What does the 5’ end have attached to it
A
Phosphate group
11
Q
What does the 3’ end have attached to it
A
Hydroxyl group (OH)
12
Q
The chain has polarity
A
True
13
Q
How did Watson and Crick discover the structure of DNA
A
Not by collecting new data but by using all available information about the chemistry of DNA
14
Q
What did Watson and Crick discover about DNA
A
Double helix, antiparallel, and base complementarity
15
Q
Where do hydrogen bonds form
A
between complementary base pairs
16
Q
How many base pairs are between each helix turn
A
10 base pairs
17
Q
Storage
A
Genetic material must contain all the information for the cell structure and function of an organism
18
Q
Copying
A
Genetic materal must also replicate accurately so the progeny cells have the same genetic information as the parent cell
19
Q
Genetic material varies
A
True
20
Q
What does n equal
A
Number of chrosmosomes in a molecule
21
Q
haploid (1c)
A
A single set of genes (or the number of unique DNA bases)
Humans have 1c = 3.2X10^9 unique base pairs
22
Q
Diploid
A
Two copies of every base pair/gene (2c)
23
Q
DNA is supercoiled for compaction
A
True
24
Q
What does supercoiling rely on
A
Topoisomerases
25
Chromatin
DNA with protein "scaffold"
26
Histones
5 types, have a net positive charge that binds to a negatively charged DNA, sequences are very similar in all species
27
Nucleosomes
The fundamental repeating unit of chromatin
28
Karyotype
The laid out picture of chromosomes
29
Euchromatin
Strains lightly uncoiled except during cell division and holds active gene
30
Heterochromatin
Stains darkly, more condensed, and is genetically inactive
31
Constitutive heterochromatin
Having the power to establish or give organized existence to something, Involved in maintaining chromosomes structure, Includes centromeres and telomeres
32
Faculative heterochromatin
Capable of but not restricted to a particular function or mode of life and has the potential to becomes condensed
33
How are centromeres used
during cell division to make sure that each daughter cell gets a copy of each chromosome
34
Centromere
A constricted region of the chromosome where the kinetochores form and the spindle microtubules attach
35
Where are telomeres located
At the end of the chromosome
36
Telomerase
Adds new copies of the repeat so that the chromosome isn't destroyed by the loss of material after each round of synthesis
37
Mitochondria
has circular genome and uniparental inherited usually
38
Replicative segregation can lead to what
Heteroplasmic and homoplasmic cells
39
How does DNA replication occur
A semiconservative mechanism
40
Conservative
One double helix is unchanged by the process, the other is completely new
41
Dispersive
Each strand is a mix of old and new DNA
42
Semi conservative
One strand of double helix is conserved, the other is new
43
Raw materials of DNA synthesis
Template, enzymes, raw materials
44
What does DNA polymerase do
Catalyzes the formation of phosphodiester bonds
45
Where does the 3' OH group join
At the last base in the DNA chain to the incoming 5' phosphate of a dNTP
46
What direction is replication
Always 5'-3'
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5 key elements of each replication fork
Helicase to unwind the DNA, SSBP to protect ssDNA, Gyrase to remove strain ahead of fork, primase to synthesize RNA primer, DNA polymerase
48
Why does Gyrase ds break
To relieve torsional strain
49
What does Helicase break
H bonds between bases
50
What do SSB proteins do
They protect free DNA and prevent secondary structures
51
Key features of DNA replication in Eukaryotes
Is initiated by RNA primers, occurs in the 5' to 3' direction, semiconservative, origins of replication
52
Origins of replication
Initiated at the same time at many points along the chromosome
53
Packaging of newly replicated DNA
Histones must first disassemble to allow DNA synthesis, sythesis of new histones is coordinated with DNA synthesis, Then must reassemble on two new chromosomes
54
Main polymerases have what
3' to >5' exonuclease
55
G1 contains the checkpoint
True
56
What happens in the S cycle
The DNA untwists and replicates
57
Mitosis
Formation of two cells from one cell, requires successful replication of each chromosome, 5 phases, result is daughter cells each with complete copy of the genome
58
5 stages of Mitosis
Interphase, Prophase, Metaphase, Anaphase, Telophase
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Prophase
Chromosome condense and two sister chromatids become detactable
60
Metaphase
Chromosomes arranged on metaphase plate, centrosomes at opposite poles, and microtubules from centrosomes to kinetochore
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Chromosomes per cell equals
The number of functional centromeres
62
Anaphase
Sister chromatids separate and chromosomes move toward opposite poles
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Telophase
Sister chromatids arrive at opposite poles (now called chromosomes), nuclear membranes form, and chromosomes relax and lengthen
64
What happens during Prophase 1
Chromosomes cross over (recombination)
65
Recombination
Produces new combinations of alleles
66
There is independent assortment between chromosomes
true
67
Stages of Meiosis 1
Prophase 1, metaphase 1, anaphase 1, telophase 1, cell division
68
First step of making protein
Transfer of genetic information from DNA to mRNA
69
messenger RNA (mRNA)
Instructions to make a protein
Each protein has a unique mRNA
70
transfer RNA (tRNA)
Translates instructions into protein, the translator molecule, and has a stem/loop structure
71
ribosomal RNA (rRNA)
Machine that builds a protein, makes the ribosome, and has a large and a small subunit
72
Key components needed for transcription
DNA template, Raw materials (ribonucleotide triphosphates) needed to build a new RNA molecule, and the transcription apparatus, consisting of the proteins necessary for catalying the synthesis of RNA
73
RNA Pol 1
transcribes ribosomal rRNA
74
RNA Pol 2
Transcribes pre messenger mRNA
75
RNA Pol 3
Transcribes transfer tRNA
76
Chromatin needs to be remodeled in order to open up the DNA for transcription
True
77
Promotor
Sequence that transcription machinery recognizes and binds
78
Coding region
The sequence that is copied from DNA to RNA
79
Terminator
Specific sequences that indicate transcription should stop generally is transcribed
80
Core Promoter
required for any transcription, site where basal transcription machinery binds, TATA box (nearby regulation), transcription factors and regulatory factors can bind
81
Regulatory Promoter
Upstream of core promoter, variety of consensus sequences, transcription factors and regulatory factors can bind here, can be mixed and matched combinations, directly or indirectly make contact with basal transcription machinery, affect the rate of transcription
82
Enhancers
Distal locations can also enhance transcription
83
Initiation
If the promoter and enhancers "say so" a protein coding gene is transcribed
84
Enlongation
Keep adding nucleotides
TF and regulatory proteins dissociate and can be reused for another polymerase to bind and start another transcript
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Termination
For RNA Pol 2 there is no specific termination sequence
86
Units of proteins
Units are the 20 AA joined by peptide bonds
87
DNA, RNA, and proteins have directionality
True
88
What does the amino end of a protein have
a free amino group (NH3+)
89
What does the carboxyl end of a proten have
A free carboxl group (COO-)
90
R group differs in each amino acid
True
91
Primary
sequence of AA
92
Secondary
Interactions between AA
93
Tertiary
Structures after folding overall 3D shape
94
Quaternary
>1 polypeptides
95
Domains
Group of AA that form a discrete functional unit
96
Codon
A code that has 3 bases
97
How is a code degenerate
due to being 3 bases there are 64 possible AA (4^3)
98
Degenerate
More than one codon for each AA
99
Wobble
Typically the 3rd base of the codon can vary
100
Synonymous
Change in DNA seq does not change AA
101
Non synonymous
change in DNA seq changes AA
102
Nonsense
Change in DNA introdues a stop codon
103
AUG
start codon/methionine
104
Three stop codons
UAG, UAA, UGA
105
Reading frame
a way of dividing the sequence of nucleotides in a nucleic acid
106
How are codons nearly universal
Each codon specifies the same AA in almost all organisms
107
4 phases of protein synthesis
tRNA charging: binding tRNA to AA
Initiation: start of translation
Elongation: Synthesis of polypeptide chain
Termination: Ending synthesis
108
Aminoacyl tRNA synthetase
Enzyme that attaches an AA to a tRNA specific for a particular AA
109
Initiation
Ribosome small subunit initiation factors, initatior tRNA form initation complex recognizing the 5'Cap, the initiation complex scans the mRNA unit it finds the start codon
110
Elongation and Termination
Formation of peptide bond releases AA in P site from the tRNA, translocation of ribosome down the mRNA 5' to 3', translation stops when the ribosome encounters a stop codon, release factors bind to a site and promote cleavage of polypeptide
111
Aminoacyl site
Where charged tRNA enter ribosome
112
Peptidyl site
Where peptide bond is formed
113
Mutation
Inherited change in genetic information, the descendants that inherit the change may be cells or organisms
114
Somatic Mutations:
Happens during development, only effects the individual
115
Germ line mutation
Happens in the gamete and gets passed on
116
Base Substitutions
Alteration of a single nucleotide
117
Transition
Substitiution of a purine for a purine
118
Transversions
Substitution of a purine for pyrimidine
119
Neutral
Missense mutaiton that changes one AA for another chemically similar AA
120
Loss of Function
Results in complete or partial absence of a normally functioning protein
121
Lethal
Result is so drastic that the organism cannot survive
122
Indels
Insertion/deletion of one or more bases can cause frameshift
123
Replicative
The wrong base gets incorporated during DNA replication
124
Strand slippage
denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases.
125
Depurination
Loss of a purine base from a nucleotide generally replaced w/ an A
126
Deamination
Loss of an amino (NH2) group from a base spontaneous and chemically induced
127
Mutagen
Any environmental agent that significantly increases the rate of mutation above the spontaneous mutation rate
128
Environmental
Radiation UV light produces thymine dimers which block replication
129
What do repair mechanisms use
A common 4 step pathway; detection, excision, polymerization, ligation
130
Detection
The damaged section of teh DNA is recognized
131
Excision
Endonucleases nick the sugar-phosphate backbone on one or both sides of the DNA damage, and one or more nucleotides are removed
132
Polymerization
DNA polymerase adds nucleotides to the newly exposed 3' OH group by using the other strand as a template and replacing damaged nucleotides
133
Ligation
DNA ligase seals the nicks in the sugar phosphate backbone
134
Mismatch Repair
Incorrectly paired bases are detected and corrected by mismatch repair enzymes
135
Direct repair
Does not replace altered nucleotides, restores their original structures, thymine dimers
136
Base Excision Repair
DNA repair that first excises modified bases and then replaces the entrie nulceotide, set of enzymes called DNA glycosylases recognizes and removes a specific type of modified base @ 1' carbon, another enzyme recognizes the missing base and cuts phoshodiester backbone, another enzyme removes the sugar molecule, DNA polymerase adds the correct base to free 3' OH, Ligase seals the nick
137
Nucleotide Excision Repair
Removes bulky DNA lesions and other types of DNA damage
138
Double strand breaks
Very bad, stalls replication, can cause deletions, duplications, inversions, translocations
139
Homologous recombination
Using the identical or nearly identical genetic information contained in another DNA molecule usually a sister chromatid, same process as used in recombination
140
Nonhomologous end joining
Uses proteins that recognize the broken ends of DNA bind to the ends and then join them together
141
central dogma
DNA to RNA to protein
