exam 3 Flashcards
1
Q
5 essential characteristics of hereditary molecules
1. genetic material localized to the _____
A
nucleus is a stable form in cells
2
Q
5 essential characteristics of hereditary molecules
2. genetic material must contain complex genetic info required to _______
A
direct the structure, development, function and reproduction of organisms
3
Q
5 essential characteristics of hereditary molecules
3. genetic material must replicate faithfully so that ___
A
daughter cells have the same information as parent cells
4
Q
5 essential characteristics of hereditary molecules
4. genetic material (the genotype) must encode the phenotype by expressing
A
rna and proteins
5
Q
5 essential characteristics of hereditary molecules
5. genetic material must have the capacity to undergo mutation at a low rate to introduce ______
A
genetic variation and serve as a foundation of evolutionary change
6
Q
dna structure
A
- double stranded
- deoxyribose sugar
- phosphate group
- nitrogenous base (ATGC)
7
Q
rna structure
A
- single stranded
- ribose sugar
- phosphate group
- nitrogenous base (GUAC)
8
Q
name the purines
how many rings?
A
- adenine , guanine
- 2 rings
9
Q
name the pyrimidines
how many rings?
A
- cytosine, thymine, uracil
- 1 ring
10
Q
phosphodiester backbone
A
- covalent bond, hydrophobic shell, formation releases phosphate
11
Q
base pairing
which one has 2 hydrogen bonds?
which one has 3 hydrogen bonds?
A
2: adenine - thymine
3: cytosine-guanine [more energy to break apart]
12
Q
dna has these 3 things
A
- phosphodiester backbone [hydrophobic]
- antiparallel strands
- bases facing inside connected by H bonds
13
Q
why are palindromes important?
A
- mark the beginning and end of a gene
- participate in control of a gene function
- identify break points in dna sequence
14
Q
dna replication is ______ and ________
A
semiconservative, bidirectional
15
Q
dna replication
A
- parental dna remain intact during replication
- each parental dna serves as a template to synthesize complementary antiparallel daughter strands
- produces 2 identical daughter duplexes
16
Q
semiconservative
A
2 molecules containing original and new dna
17
Q
conservative
A
one original strand and one daughter strand
18
Q
dispersive
A
2 molecules with old and new dna interspersed along each strand
19
Q
E. coli dna
A
- circular
- circle maintained during replication -> theta structure
- rep occurs bidirectionally from rep forks
20
Q
e coli rep rate
A
1,000 bp per second
21
Q
eukaryotic replication is slower, why?
A
more compact, dense
22
Q
topoisomerase
A
relaxes supercoiling
23
Q
dna helicase
A
unwinds dna at rep fork
24
Q
single strand binding protein
A
attaches to single strand dna and prevents secondary structure
25
rna primase
synthesizes short rna primer to provide a 3'OH group for the DNA attachment
26
dna pol III
elongates the new dna strand from the 5'-3' direction
exonuclease function allowing it to back up and fix mistakes
27
dna ligase
joins Okazaki fragments through the phosphodiester backbone
28
dna pol I
removes rna primers and replaces them with dna
29
telomeres
- hundreds of repeats of same short dna sequence
add to 3' end lagging strand
creates a free 3'-OH group that serves as a substrate for dna pol
30
Germline and stems cells telomarase is
active, elongated, continue to divide
31
somatic cells telomerase is
inactive, shorten, eventually stop dividing bc DS breaks
32
cancer cells can be stopped
if they can find how to inhibit telomerase by drugs as a part of cancer therapy
- because cancer cells avoid cell death by maintaining telomeres despite repeated divisions
33
long telomeres ____
short telomeres ____
good, bad
34
proofreading
DNAP recognizes mismatched pairs and removes incorrectly paired bases
35
mismatch repair
newly replicated DNA is scanned for mistakes by other proteins and can be corrected
36
xeroderma pigmentosum
rare autosomal recessive genodermatosis results to mutation
- sun sensitivity
37
trichothiodystrophy
rare autosomal recessive
cutaneous photosensitivity
38
pcr
multiply dna from small amount
oligonucleotides prime dna rep
- DENATURE, ANNEAL, EXTENSION
39
taq polymerase
polymerase from a bacteria found in the hot springs in Yellowstone
40
gene expression
the process by which a genes info is transferred to the RNA and the making of a protein
41
transcription
DNA sequence is copied to a complementary RNA sequence
DNA -> RNA
42
translation
RNA sequence is template for an amino acid sequence
RNA -> PROTEIN
43
mRNA
RNA molecule that is produced during transcription.
carries the gene code for a specific polypeptide to the ribosome
44
rRNA
part of ribosome, involved in catalyzing peptide bonds during translation
- made in nucleus in eukaryote cells
- made in nucleoid space in prokaryotic cells
45
tRNA
carries transfer amino acids from cytoplasm to ribosome
- adaptor molecule
standard cloverleaf structure :loop thats anticodon
46
telomerase RNA
provides a template for synthesizing repeating nucleotides at the telomere
47
small nuclear RNA (snRNA)
correct positioning of the spliceosome in RNA transcripts
48
micro RNA
21-23 NT
involved in RNA silencing and postranscriptional regulation of gene expression in plants and animals
49
small interfering RNA
DS RNA that degrades mRNA after transcription
50
transcription of prokaryotes
- includes 5' and 3' untranslated region
promoter: beginning of gene
-10 sequences 5'-tataat-3' box
-35 sequence 5'-ttgaca-3'
omega factor interacts with -10 and -35 position
51
bacterial RNA polymerase
holoenzyme = core enzyme + sigma factor
sigma factor recognizes start signal in sequence
without it, transcription is random, no direction
52
directionality - elongation
dna coding strand - 5'-3'
dna non coding [template] - 3'-5'
mRNA- 5'-3'
53
prokaryotes transcription steps
- RNAP holoenzyme binds to promoter and
- unwinds dna to form open-promoter complex
- sigma factor released after initiation
- enzyme continues transcription until it encounters termination sequences.
54
termination of transcription [prok]
intrinsic termination
rho-dependent termination
55
transcription in eukaryotes
promotes tell the enzyme where to start and which strand of dna to transcription
polymerase interacts with promoter indirectly through TFs
56
2 types of promotes euk
- TATA less [downstream promoter elements at +28]
- TATA box at -25
** TATA binding protein and TFs required to recruit polymerase
57
initiation
RNA pol binds to seq
sigma factors in prok
transcription factor in euk
58
elongation
- RNAP unwinds DNA 10 base pairs at a time, - - read in 3-5' direction, add in 5-3 direction
- transcript antiparallel to DNA
- rna DO NOT PROOFREAD
59
termination
specified by a specific DNA sequence
newly made pre-mRNA transcript and polymerase are released from the template
60
post transcription modification in euk
- mRNA travel nucleus -> cytoplasm for translation
- 5' end is capped by 7-methylguanosine
- A poly-A tail is added to the AAUAAA
- splicing: introns removed
61
pre-mRNA
the unprocessed transcript in eukaryotic cells that will undergo mRNA processing
62
spliceosome
a complex of small nuclear mRNAs and proteins to form a complex of small nuclear ribonucleoproteins
- responsible for removing introns and splicing exons to form mRNA
63
the genetic language is a simple vocabulary of ____ 3 letter words, ___ codons specify one of the ____ amino acids that make up proteins
___ codon signals the start and __ codons signal termination of translation
64, 61, 20 ; 1,3
64
for most amino acids, there is more than one codon
the genetic code is redundant
65
the genetic code is ____ ________ - each codon specifies only ___ ____
not ambiguous : one amino acid
66
the genetic code is nearly
universal: the codons are the same in all organisms
67
ribosomes are made of
protein (for stability) and ribosomal RNA (for catalytic activity)
- small subunit
- large subunit
68
large subunit binding sites
- A: tRNA charged with aa bind to mRNA codon
- P: tRNA adds the aa to the growing polypep chain
- E: where the recently discharged tRNA leaves the ribosome
69
small subunit
binds to the mature mRNA strand
70
amino-acyl synthetases
tRNA's specific enzyme that recognizes the tRNA and the amino acids that belongs on the tRNA
- coupling the correct aa to the correct tRNA
71
initiaton complex
what is it?
prokaryotes bind where?
eukaryotes bind where?
whats the start codon
charged tRNA and small ribosomal unit both bound to the mRNA
prokaryotes: rRNA binds to shine delgarnon sequence on mRNA
eukaryotes: bind to 5' cap
start codon: AUG
72
elongation
what is it?
another charged tRNA enters the site
P site is covalently attached via a peptide bond to the amino acid in the A site
73
termination
what is it?
ends when stop codon enters a site, they bind a protein release factor which hydrolyzes bond between the polypeptide and the tRNA in the p site.
74
several ribosomes can work together to translate the same mRNA -
producing multiple copies of the polypeptide
75
polysome or polyribosome
strand of mRNA with associated ribosome
76
mutations are important ingredient to the theory of natural selection -
as they increase the amount of genetic diversity in a population
77
mutation
any detectable and heritable change in the genetic material
78
mutant
an individual resulting from mutation
79
mutagens
agents that can cause mutation
chemical, uv, viruses
80
wild type
a strain, organism or gene of the type predominating in the wild population
81
mutation provides the _____ necessary for _____
variation ; evolution
82
transitions
a pyrimidine replaces a pyrimidine, or a purine replaces a purine
A <-> G
C <-> T
83
transversions
a purine and pyrimidine are interchanged AT, CG, AC, TG
A <---> T
C <----> G
A <-----> C
T <---->G
84
frameshift mutation
mutation that moves over the codons
85
promoter mutation
can reduce the amounts of transcripts and proteins
86
splicing mutation
dinucleotide sequences at the 3' end of the exon and the adjacent 5' end of the intron have a key role in splicing
- can result in splicing errors in which introns are removed from pre-mRNA
87
cryptic splicing site mutation
newly generated splicing sites are created by substitution mutations
-> alter original splicing patterns and create aberrant splicing, and thus mutated mRNAs and proteins
88
polyadenylation mutation
mutations in the poly adenylation sequences of a 5'AAUAAA3'
- can block and / or inhibit proper 3' poly-A modification
89
loss of function mutation
reduction or complete elimination of the protein's function
aka null mutations- they are recessive mutations
90
gain of function mutations
mutations create gene products with an enhanced or new function, dominant mutation, common in cancer
91
lethal mutation
affects a gene that is critical to the survival of the organism. it results in death or reduces longevity of organism
92
conditional mutation
wild type function and phenotype under certain environmental conditions. mutant phenotype develops under other conditions.
93
somatic mutations
passed on to the daughter cells during mitosis, but not passed on to sexually prod offspring
94
germ line mutation
a gamete with the mutation passes into its offspring
95
true reversion
DNA sequence reverts to encoding original message bc second mutation at the same site or within same codon
96
intragenic reversion
second mutation somewhere else in the gene
97
suppressor mutation
mutation in different gene
98
dna replication error
most common causes of spontaneous mutation
99
dna base damage
1. deamination: cytosine to uracil, gc pair converted to u-a pair
2. depuration: the loss of on of the nitrogenous bases in the intact DS DNA can cause mutation during replication
100
oxidative damage
reactive oxygen species and hydrogen peroxide can modify dna structure along with the loss of the base and a single strand break
101
intercalating agents
- cause frame shift mutations
- flat disc molecules like ethidium bromide
- distorts double helix
insert between bases
102
uv causes thymine dimers
- pol 3 reaches dimer and stalls
- inhibit dna rep
- may replicate as a single base -> frame shift
- potential factor causing skin cancer
103
the Ames test
bacterial assay used to evaluate a chemicals potential genotoxicity by measuring its ability to induce reverse mutations at selected loci
104
DNA REPAIR:
direct damage reverse;
photo reactivation repair
105
DNA REPAIR
excision of DNA damage
- mismatch repair
- nt excision repair
- base excision repair
- strand break repairing
106
photo reactivation repair
photolyase enzyme aka photo reactivation enzyme reverses the effect of UV radiation on the cells under the action of visible light esp blue light
- energy from light used to split bonds forming the cyclobutane ring
107
mismatch repair
distingues the newly synthesized strand from parental strand
- parental dna has methylation on the adenine nt in GATC seq
- gap filled by dnap and sealed by ligase
108
base excision repair
- what is it
- what is dna glycosylase
- what is ap endonuclease
- corrects small dna lesions, only damaged part
- u has been formed by deamination of cytosine
dna glycosylase- recognizes damaged bases and cleave bond between URACIL and deoxyribose
AP endonuclease- recognizes dna lesion and cuts phosphodiester bond
109
nucleotide excision pair
- cut and pased
- damaged dna is recognized and cleaved off both sides of DNA by 3' and 5' nucleases,
unwind by helices, filled by dnap, sealed by ligase
110
double strand breaks in euk
- homologous recombination repair
- nonhomolohous recombination repair
DS break repair- reattaches 2 broken dna strands
homologous- using info on intact sister chromatid or homo chromo or same, late s or g2 phase
nonhomologous- activated in g1, protein recognize and bind together
111
mutations are caused by
physical agent?
chemical mutagens?
spontaneous?
- X-ray and UV light
- nitrous acid
- unequal crossing over
112
euploid
cell follows normal meiosis and segregates a normal number of chromosomes
113
aneupleoid
missing chromosomes, or has an extra chromosome
114
disjunction
proper separation of chromosomes at anaphase
115
nondisjunction
failure to properly separate
- leads to loss or duplication of chromosome
116
TRISOMIC EQUATION
2N+1
117
MONOSOMIC EQUATION
2N-1
118
downs syndrome
trisomy 21
- link w maternal age
119
Edwards syndrome
trisomy 19
120
patau syndrome
trisomy 13
121
why is sex chromosome aneuploidy more common than autosomal aneuploidy?
Y chromo encodes few genes for nonsexual traits and X chromosome is active in diploid adult cells
122
genetic mosaicism
presence of two or more cell lineages with different genotypes arising from a single zygote in an individual
123
chromosomal breakages can be
consequences?
spontaneous or induced
- deletion, inversions, gene disruptions, eccentric fragments, dicentric bridges
124
deletion
heterozygous deletion?
- caused by breakage and rejoining of dna fragments
- pairing between a normal chromo and one with deletion ends with a loop-out structure
125
chromosomal deletion syndromes
- pleiotropic syndrome resulting from deletion of terminal end of chromosome 5;5p- (5p minutes)
126
heterozygosity for deletion - phenotypic consequence
- when heterozygote loses the dominant allele, the recessive allele is uncovered [expressed] because of the lack of the dominant allale
- deletions can act as recessive and cause pseudo dominance
127
pseudo dominance
- loss of function, remaining recessive allele will dictate phenotype
128
unequal crossing over results in
duplicated and deleted regions of chromosomes
129
inversion
chromosome broken in two places and put back together with a section flipped 180 degrees
130
paracentric or apocentric inversions
not along centromone
131
pericentric or concentric inversions
inversion at centromere
132
four strand pairing at meiosis 1 - paracentric
inversion heterozygote -> loop itself like a pretzel
133
translocations alter the locations of ______ _______ in the genome
genetic materials
134
balanced translocation [reciprocal translocation]
- genetic segments switch places between two nonhomologous chromosomes during chromosome breakage followed by reattachment
135
unbalanced translocations
normal chromosome breaks and reattaches to a nonhomologous chromosome in a one-way reciprocal event
136
robertsonian translocation
- unbalanced translocation
- lost at the very end of the short arm of one chromosome and the rest of the larger segments of the chromosome fuse together
137
pseudo linkage
- alleles that originally were on two separate chromosomes may appear to be linked to one another because of a translocation
