Flashcards in Exam 2 Deck (216):
The further apart two genes are, the greater the probability of
What are synthetic genes?
genes located on the same chromosome
When genes on the same chromosome are completely linked, the test cross results in only two possible genotypes in progeny, and these are
__ __ leads to separation of linked genes
Departure from 1:1:1:1 ratio of F1 gametes in dihybrid cross indicates
__ __ always most numerous or equal to recombinant
__ __ are never >50% of total F2 progeny
Crossing over is a random event that will only result in ___ if genes are independently assorting
equivalent parental and recombinant phenotype ratios
Recombinant gametes are __ __ than parental gametes when genes are linked
What is recombination?
the reciprocal exchange as a result of crossing-over during meiosis
What is terminalization?
movement of chiamata
What happens during anaphase?
chromosome separation occurs after chiasmata reach the telomeres
What are the products of anaphase?
two recombinant and two parental gametes
Dihybrid test cross of independently assorting genes produces a ___ progeny ratio
Dihybrid test cross of completely linked genes produces a __ progeny ratio
Dihybrid test cross of genes on same chromosome that are sometimes but not always separated by crossing over in meiosis produce
intermediate progeny ratios
1 percent recombination =
1 RF (recombination frequency) = 1 map unit (m.u.) = 1 centiMorgan (cM)
In linked genes, parents __ recombinants
In unlinked genes (exhibit independent assortment), parents __ recombinants
Linked genes must be __ and __ so that they do not assort independently
syntenic; sufficiently close together or on the same chromosome
Independent assortment (unlinked genes) occurs wither when genes are on __ or when they are __
different chromosomes; sufficiently far apart on the same chromosome
We can use recombination frequencies from __ for pairs of genes to establish relative gene position
Genes chained together by linkage relationships form a
Linkage group =
chromosome = 1 DNA molecule
Order of genes revealed by genetic mapping corresponds to
the actual order of genes along the chromosome
Recombination frequency becomes a less precise estimator of genetic distance at
large physical distances
What limits the correspondence between map and physical distance?
-double, triple, and more crossovers
-50% limit on observable recombination frequency
-non-uniform recombination frequency across chromosomes
-mapping functions compensate some inaccuracies
-recombination rates differ between species and across genome (recombination hotspots)
Genes close together on the same chromosome are __ and __
linked; do not assort independently, they segregate together
Linked genes lead to a __ number of parental class progeny than expected in independent assortment
The mechanism of recombination is
__ are the visible signs of crossing over
The further away genes are the __ the opportunity for chiasmata to form between them
Recombination frequencies reflect
physical distance between genes
Recombination frequencies between two genes vary from
0% to 50%
Deviations from 1:1:1:1 ratios can represent
chance events or linkage
Chi squared tests evaluate
deviation from expected values and the probability that the data fit the expected outcome
What does the null hypothesis state?
observed values are no different from expected values
For chi square tests, low p values show __ and high p values show __
little deviation from expected; significant deviation from expected
Can a chi-square test prove linkage?
no, only provides a quantitative measure of the likelihood that the data can be explained by a hypothesis
All of the genetics functions of DNA depend on
specialized proteins that "read" the info in DNA sequence
DNA is localized almost exclusively within
DNA contains four kinds of __ linked in a long chain
What are phosphodiester bonds?
covalent bonds joining adjacent nucleotides
What is a polymer?
linked chain of subunits
DNA is made of only __ different subunits
Protein is made of __ different subunits
DNA is a __ structure with __ diameter
helical; 20 A
Spacing between repeating units in DNA is
The DNA helix undergoes a complete turn every
What are the 4 nitrogenous bases of DNA
adenine, guanine, cytosine, thymine
What are the ratios of nitrogenous bases?
A:T ratio is 1:1, G:C ratio is 1:1
What are DNA's chemical constituents?
deoxyribose, phosphate, 4 nitrogenous bases
What are the purines?
adenine and guanine
What are the pyrimidines?
thymine and cytosine
The attachment of base to a sugar makes a
The addition of phosphate to a nucleoside makes a
Nucleotides are linked together in a __ chain in the DNA molecule
Phosphodiester bonds always form covalent link between
3' carbon of one nucleotide and 5' carbon of the next nucleotide
Base pairs consist of __ bonds between a purine and a pyrimidine (G with C, A with T)
Each base pair has the same
shape (can fit together without disrupting shape of chain)
The strands of DNA are
antiparallel (one is 5'-3' going up-to-down, while other is 3'-5' going up-to-down)
In a double helix of DNA, sugar phosphate backbones are
on the outside
In a double helix of DNA, base pairs are
in the middle
The double helix of DNA is two chains held together by
hydrogen bonds between A-T and G-C base pairs
How does DNA carry information?
base sequence of A,T,C, and G's
How is the information DNA carries coped for transmission to future generations?
What mechanisms allow genetic information to change?
How does DNA-encoded info govern the expression of phenotype?
Most genetic info is "read" from
e.g. synthesis of DNA or RNA
Some genetic info is accessible within
e.g. DNA- binding proteins that regulate gene expression can access chemical info from "grooves" of DNA helix
What are the 3 possible models of DNA replication?
-semiconservative (Watson-Crick model)
What is the conservative model of DNA replication?
parental double helix remains intact, both strands of daughter helices are newly synthesized
What is the dispersive model of DNA replication?
both strands of both daughter helices contain original and newly synthesized DNA
What does the model of DNA replication postulated by Watson and Crick state?
-unwinding of double helix exposes bases on each strand
-each strand can as a template for synthesis of new strands
-new strand forms by insertion of complementary base pair
-single double helix becomes two identical daughter double helices
-replication is semiconservative: each new molecule contains 1 parent strand and one newly synthesized strand
Energy for DNA synthesis comes from
high-energy phosphate bonds associated with dNTPs (deoxynucleotide triphosphates (dATP; dGTP; dTTP; dCTP))
__ __ catalyzes new phosphodiester bonds
What happens during initiation of DNA replication?
proteins open up the double helix and prepare it for complementary base pairing
What happens during elongation of DNA replication?
proteins connect the correct sequence of nucleotides on newly formed DNA strands
What are the 3 strict requirements for DNA polymerase action?
-4 dNTPs (for incorporation into chain and energy)
-primer with exposed 3' hydroxyl***
-single-stranded template DNA (may be unwound by other proteins)
DNA synthesis ALWAYS proceeds in the __ direction
5' to 3'
Template and newly synthesized strands are
Initiation begins at the
origin (Ori) of replication
What happens in the process of initiation?
-initiator protein binds to Ori (origin of replication)
-helicase unwinds the helix
-two replication forks are formed: replication proceeds in both directions
-single-strand binding proteins keep the DNA helix open
-primase synthesizes RNA primer (RNA uses U instead of T)
-primers are complementary and antiparallel to each template strand
What happens in the process of elongation in DNA replication?
-the correct nucleotide sequence is copied from template strand to newly synthesized strand of DNA
-DNA polymerase III catalyzes phosphodiester bond formation between adjacent nucleotides (polymerization)
Leading strand of DNA synthesis has __ synthesis
Lagging strand of DNA synthesis has __ synthesis
What is an Okazaki fragment?
short DNA fragment on lagging strand
DNA polymerase moves along the template in the __ direction
What does DNA polymerase I do?
replaces RNA primer with DNA sequence
What does DNA ligase do?
covalently joins successive Okazaki fragments together
There are __ replication forks for each origin of replication
DNA can be __ or __; __ or __-stranded
linear, circular; double, single
In replication of a circular bacterial chromosome, replication proceeds in __ direction(s) from a single Ori
In replication of a circular bacterial chromosome, unwinding of DNA creates __ __ ahead of replication fork
In replication of a circular bacterial chromosome, DNA topoisomerases
relax supercoils by cutting the sugar phosphate backbone bond strands of DNA
In replication of a circular bacterial chromosome, unwound broken strands are sealed by
In replication of a circular bacterial chromosome, synthesis continues bidirectionally until
replication forks meet
What do telomeres do?
protect the ends of eukaryotic chromosomes that require special mechanisms for replication because DNA polymerase can't replicate some of the sequences at the 5' end of DNA
Telomeres consist of __ and don't contain __
specific repetitive sequences; genes
Telomeres are species-specific sequences and in humans that sequence us
Telomeres prevent __ and maintain __
chromosome fusions; integrity of chromosomal ends
Cells must preserve telomeres to maintain
normal genetic complement
Telomerase RNA is complementary to
telomere repeat sequences
Telomerase RNA serves as template for
addition of new DNA repeat sequences of telomere
Additional rounds of telomere elongation occur after telomeres
translocate to newly-synthesized end
After telomere extension, new RNA primer is synthesized and DNA is able to
be synthesized in 5'-3' direction at 3' end of template
Most somatic cells have low expression of telomerase. Why?
-telomeres shorten slightly at each cell division
-senescence after <50 generations in culture
Germ cells, stem cells, and tumor cells have high expression of telomerase. Why?
at each generation, telomere length is maintained
What do initiator proteins do?
bind to and open up origin of replication
What does DNA polymerase III do?
catalyzes polymerization of new strands of complementary DNA
What does DNA polymerase I do?
fills in gaps between Okazaki segments
What does DNA helicase do?
unwinds double helix
What do single-stranded binding proteins do?
keep helix open
What does primase do?
creates RNA primers to initiate synthesis
What does ligase do?
welds together Okazaki fragments
What does topoisomerase do?
relaxes supercoils by nicking strands
What does telomerase do?
What are 3 ways to ensure fidelity of DNA info?
1. REDUNDANCY: either strand of the double helix can specify the sequence of the other strand
2. PRECISION of cellular replication machinery: DNA polymerase I and III have proofreading ability
3. DNA repair enzymes
What are mutations?
heritable changes in DNA base sequences
Mutations can be caused by
errors in DNA replication or environmental factors
What is a forward mutation?
mutation that changes wild-type allele to a different allele
ex: A+ --> a or b+ --> B
What is a reverse mutation (reversion)?
mutation that changes a mutant allele back into wild type
ex: a --> A+ or B --> b+
Forward mutation rate is usually __ than reversion rate
What is a substitution?
replacement of a base by another base
What is a transition?
purine replaced by another purine, or pyrimidine replaced by another pyrimidine
What is a transversion?
purine replaces by a pyrimidine, or pyrimidine replaced by a purine
What are deletions?
when a block of 1 or more base pairs are lost from DNA
What are insertions?
when a block of 1 or more base pairs are added to DNA
What is an inversion?
180 degree rotation of a segment of DNA
What happens in reciprocal translocation?
parts of two non homologous chromosomes change places
Mutation rates are <10^-9 to >10^-3 per gene per
Average mutation rate in gamete-producing eukaryotes is __ than that of prokaryotes
Germ line mutations occur in __ and are __
gametes or in gamete precursor cells; transmitted to next generation
Somatic mutations occur in __ and are __
non-germ cells; not transmitted to next generation of individuals, but are heritable across generations of cell-division
Germ line mutations provide
raw material for natural selection
Somatic mutations can affect __ and can lead to __
survival of an individual; cancer
Base changes are often corrected by
Incorporation of incorrect bases by DNA polymerase is rare because mispaired bases are recognized and excised by __ portion of DNA polymerase
3' to 5' exonuclease
Complementation testing reveals
whether two mutations are in a single gene or in different genes
Complementation testing can only be used with __ phenotypes
A complementation group is a group of mutations that __ complement each other
Proteins are chains of amino acids linked by
Polypeptides have an __ and a __
N terminus; C terminus
Types of amino acids determine protein
shape, interactions, and function
Primary structure of a polypeptide is the
amino acid sequence
Secondary structure of a polypeptide is the
characteristic geometry of localized regions
The tertiary structure of a polypeptide is the
complete 3D arrangement of a polypeptide (natural folding of polypeptide under normal conditions)
The quaternary structure of a polypeptide are the
complexes of polypeptide subunits
Mutations alter __, which can alter __, and thus modify __
nucleotide sequence; amino acid sequence; protein structure and function
Protein recognition of DNA
1. particular structure
2. specific DNA shapes
3. specific nucleotide sequences
RNA polymerase transcribes DNA to
produce an RNA transcript
Ribosomes translate mRNA sequences to
What is the central dogma?
DNA --> RNA --> protein
__ is the key to the transfer of info from DNA to RNA and from RNA to protein
pairing of complementary bases
Polarities of DNA, RNA, and polypeptides help guide the
mechanisms of gene expressions
Gene expressions requires __ and __
input of energy; participation of specific proteins and macromolecular assemblies
Template strand of DNA is complementary to __ and to the __
mRNA; RNA-like strand of DNA
5' to 3' in the mRNA corresponds to __ in the polypeptide
What are the 3 major chemical differences between RNA and DNA?
-ribose sugar instead of deoxyribose
-U instead of T
-most RNAs are single stranded
Transcription generates a __ using DNA as a template
5'-to-3' polarity RNA chain
RNA polymerase catalyzes
Promoters are DNA sequences that
provide the signal to RNA polymerase for starting transcription
Terminators are RNA sequences that
provide the signal to RNA polymerase for stopping transcription
What are the 3 steps of RNA transcription?
initiation, elongation, termination
What happens during initiation of transcription in RNA?
-RNA polymerase binds to promoter sequence located near beginning of gene
-sigma factor binds to RNA polymerase (reduces affinity of RNA polymerase for binding DNA, but inc. affinity for tight binding to promoter region)
-region of DNA is unwound to form open promoter complex
-phosphodiester bonds formed between first two nucleotides
What happens during elongation of transcription in RNA?
-sigma factor separates from RNA polymerase (--> core enzyme)
-core RNA polymerase loses affinity for promoter and then moves in 3'-to-5' direction on template strand
-within transcription bubble, NTPs added to 3' end of nascent mRNA
What are the two kinds of terminators in bacteria?
-extrinsic: require rho factor
-intrinsic: don't require additional factors
Terminators usually form
The sense strand of RNA has the same sequence as the
The antisense strand of RNA is used as
the template for transcription
Most promoters are __ to the transcription start point
RNA splicing removes
What are exons?
sequences found in a gene's DNA and mature mRNA (Expressed regions)
What are introns?
sequences found in DNA but not in mRNA (intervening regions) (INTrons INTerrupt the exons)
RNA processing splices out __ and joins adjacent __
Splicing is catalyzed by the
Alternative splicing can produce
two different mRNAs from the same gene
What are the 3 stop codons?
UGA, UAA, UAG
Genetic code has __ codons
T or F? Codons are nonoverlapping
T or F? Genetic code is degenerate
Reading frame is established from a fixed starting point
codon for translation initiation is AUG
mRNAs and polypeptides have corresponding
What are the 3 ways that mutations can be created?
frameshift, missense, and nonsense
Codons must contain __ nucleotide
Each point mutation affects only one
What is the start codon?
What are missense mutations?
mutations that replace one amino acid with another
What are conservative missense mutations?
missesnse mutation in which the chemical properties of mutant amino acid are similar to the original amino acid
What are nonconservative missense mutations?
missense mutations in which the chemical properties of the mutant amino acid are different from original amino acid
What are nonsense mutations?
mutations that change a codon that encodes an amino acid into a stop codon
Frameshift mutations result from
insertion of deletion of nucleotides with the coding regions (no frameshift if multiples of three are inserted or deleted in frame)
do not alter the amino acid sequence
Frameshift mutations alter the reading frame of codons AFTER
the point of insertion or deletion
Ribosomes are the sites of
How do ribosomes facilitate polypeptide synthesis?
-recognizing mRNA features signaling start of translation
-ensure accurate interpretation of code by stabilizing interaction between tRNA and mRNA
-supply enzymatic activity to link aa's
-move 5'-to-3' along mRNA molecule, exposing mRNA molecule, exposing mRNA molecules in sequence and ensure linear addition of aa's
-help terminate polypeptide synthesis by dissociating mRNA and the polypeptide
During the initiation stage of translation in RNA,
start codon is AUG at 5' end of mRNA
During the elongation stage of translation in RNA,
amino acids are added to growing polypeptide
During the termination stage of translation in RNA,
polypeptide synthesis stops at the 3' end of the reading frame
Small subunit of a ribosome
binds to mRNA
Large subunit of a ribosome has __ activity
What are the 3 tRNA binding areas of a ribosome?
A, P, and E sites
In prokaryotes, the ribosome binding site consists of a
Shine-Dalgarno sequence (AGGAGG in 5' UTR before first AUG)
The 3 sequential steps of the initiation phase in PROKARYOTES are
1. small ribosomal subunit binds
2. fMet-tRNA (3' UAC 5' anticodon) position in P site
3. large subunit binds
The initiation phase in EUKARYOTES consists of
-small ribosomal subunit binds to 5' cap (no S-D sequence), then scans the mRNA for the first AUG codon
-initiator tRNA carries Met (not fMet)
What happens during the elongation phase of translation of mRNAs on ribosomes?
-ribosome moves along mRNA in 5' to 3' direction
-addition of amino acids to C-terminus of polypeptide
-charged tRNAs ushered into A site by elongation factors
Polyribosomes consist of several ribosomes
translating the same mRNA
What happens during the termination phase of translation of mRNAs on ribosomes?
-no normal tRNAs carry anticodons for the stop codons
-release factors bind to the stop codons
-release of ribosomal subunits, mRNA, and polypeptide
Loss of function mutations result in
reduced or abolished protein activity
Loss of function mutations are usually
Null (amorphic) mutations
completely block function of a gene product
In hypomoprhic mutations,
gene product has weak, but detectable, activity
Gain of function mutations
enhance a function or confer a new activity
Gain of function mutations are usually
generate more gene product or the same amount of a more efficient gene product