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BIOL 111 Test 2
N/A
178
Biology
Undergraduate 1
02/27/2010

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Term
What happens when genes are on the same chromosome (contrary to Mendel's principles that involve genes on separate chromosomes)?
Definition
the genes are LINKED - genes are inherited together because we inherit whole chromosomes - traits do not independently assort
Term
Testing for linkage
Definition
cross true breeding parents to make F1 :: Test cross F1 :: Look at parental v. recombinant genotypes :: Ind Assortment predicts equal numbers of parental and recombinant :: Linkage predicts only parental types in equal numbers
Term
___ genotypes are those not found in the parent generation
Definition
recombinant
Term
Meiosis with complete linkage results in ____ genotypes in the gametes... why?
Definition
all parental genotypes - because they are so close to each other on the chromosomes that they are inherited together and do not cross over
Term
If genes are far apart on a chromosomes, recombination can occur due to crossing over - results in mostly parental-type gametes and some recombinants... this is called?
Definition
partial linkage
Term
in Morgan's experiment with fruit flies, only males in the F2 generation had white eyes. Why is this?
Definition
Sex-linkage - Y chromosome is small and greatly reduced or inactive so males often only get one copy of some genes -- in drosophila, the Y chrom carries no gene for eye color, so the males got whatever was on their X chromosome, regardless of dominance.
Term
Heterogametic sex
Definition
Males - XY
Term
the heterogametic sex will be ___ for all alleles on X
Definition
hemizygous
Term
Homogametic sex
Definition
females - XX
Term
the rest of the chromosomes (that aren't sex chromosomes) are called ____.
Definition
autosomes
Term
Sex linkage is AKA
Definition
X linkage
Term
Recessive sex-linked traits are always expressed in males because ?
Definition
they have no second copy of the gene to dominate
Term
most linked genes are completely/partially linked
Definition
partially
Term
how do you obtain information about the distance between genes on a chromosome?
Definition
genetic mapping
Term
Recombination Frequency (RF)
Definition
Term
Recombination Frequency (RF)
Definition
used to calculate map distance - RF = recombinant progeny/total progeny -- convert to % for map distance
Term
units of map distance
Definition
1 map unit = 1% recombination = 1cM (centiMorgan)
Term
as distance between 2 genetic loci increases, the likelihood of recombination increases/decreases
Definition
increases
Term
relationship between genetic distance and % recombinations?
Definition
genetic distance = % recombinations
Term
what happens when 2 crossovers occur?
Definition
restores parental genotype, even though it is a recombinant individual
Term
As distance between genes increases and have multiple crossovers, what happens to RF?
Definition
becomes deflated
Term
With more crossovers, you begin to reach ___?
Definition
an even number of parental and recombinant phenotypes - begins to look like independent assortment
Term
When genes are on different arms of a chromosome or are very far apart on a single arm, genes will essentially be ____.
Definition
unlinked - independently assorting
Term
For long distances and frequent crossovers, an even number of crossovers results in ____ genotypes, and Odd numbers results in _____ genotypes.
Definition
Even: parental, Odd: recombinant
Term
an RF of ___ is the maximum
Definition
0.5
Term
Features of the 3-point cross
Definition
uses 3 loci instead of 2, allows us to order genes unambiguously and at longer distances, allows us to see multiple crossovers
Term
in a 3-point cross, the distances between multiple markers are ____
Definition
additive
Term
The more/less crowded genetic markers are, the more accurate the genetic map will be.
Definition
more
Term
3-point crosses are more reliable than 2-point crosses at longer/shorter distances
Definition
longer
Term
What are genetic markers in humans?
Definition
genetic diseases, clinical syndromes
Term
a ___ is a graphical method that summarizes family data over multiple generations and can suggest models of disease inheritance as well as can be used for genetic mapping
Definition
Pedigree analysis
Term
How do you do genetic analysis in humans?
Definition
use crosses that already exist (families) and do pedigree analysis
Term
in a ____, the dominant nature of the allele causing a disease is apparent because the trait appears in every generation.
Definition
dominant pedigree
Term
in a _____, carriers exist and the affected individuals parents are unaffected by the condition because they are carriers
Definition
recessive pedigrees
Term
6 characteristics of Anonymous markers
Definition
no phenotype :: highly variable (polymorphic) :: multiple alleles at detectable frequency :: high degree of heterozygosity :: DNA-based :: high density (common)
Term
Why are anonymous markers called "anonymous"?
Definition
they have no phenotype
Term
First kind of genetic marker discovered - cuts DNA at different places making fagments of DNA at different lengths
Definition
restriction fragment length polymorphism (RFLPs)
Term
in RFLPs, did the differences in DNA fragments translate into an obvious phenotype?
Definition
no
Term
___ are genetic markers that are sections of base pairs that repeat over and over.
Definition
Variable nucleotide tandem repeat (VNTR) ... AKA "microsatellites"
Term
which are more common RFLPs or VNTRs?
Definition
VNTR
Term
3 commonalities between VNTRs and RFLPs
Definition
both are usually without phenotypes, both are highly variable in populations, both have a high degree of heterozygosity
Term
Genetic maps consist of ___ markers. What do these markers have to do with disease?
Definition
VNTR - they don't case diseases but they are inherited with the disease so they signal disease
Term
____ are genetic markers in which there is just one base difference between individuals. There are (#) of them with a population frequency of __%.
Definition
Single Nucleotide Polymorphisms (SNPs) -- 7million with frequency of 5%
Term
SNPs allow for ___ studies, which are??
Definition
Association studies - associating a SNP with a gene that causes a disease or phenotype in humans
Term
There is a ___ (genetic marker) associated with every gene in the genome.
Definition
SNP
Term
____ is the idea that linked genes show association in a population
Definition
linkage disequilibrium
Term
there are about (#) genes in the genome, and we know what about (#) of them do.
Definition
30,000 ... 1,000
Term
___ mapping allows us to locate genes for virtually any trait
Definition
SNP
Term
Watson and Crick used the principle of ____ to find out that A pairs with T and G pairs with C.
Definition
complementarity
Term
semi-conservative model of DNA replication
Definition
one strand is conserved and one is replicated
Term
conservative model of DNA replication
Definition
both strands of DNA remain intact
Term
dispersive model of DNA replication
Definition
elements of the DNA double helix are dispersed throughout new molecule -- is a mix of the semiconservative and conservative model
Term
Outcome of Meselson and Stahl experiment
Definition
Tube of centrifuged DNA showed two bands - one lighter and one heavier. This proved the semi-conservative model because the dispersive model would just have one band of intermediate-weight DNA
Term
How does semiconservative replication happen?
Definition
each strand in a double helix serves as a template and produces a new, complementary strand
Term
base pairing depends on what kind of bonds?
Definition
hydrogen
Term
Basic mechanism of DNA replication
Definition
open up the helix and copy each strand... produces 2 new strands that are each hybrids of one new and one old strand
Term
3 possible models of DNA replication
Definition
conservative, semiconservative, dispersive
Term
5 requirements for DNA replication
Definition
Template (DNA to copy) :: Monomers (nucleotides) :: Enzymes (DNA polymerase, DNA primase) :: Open helix (by helicase):: Topoisomerase and gyrase to relieve torsional strain
Term
enzyme that winds and unwinds DNA
Definition
topoisomerase
Term
enzyme that opens the double helix
Definition
helicase
Term
enzyme that relieves torsional strain
Definition
gyrase
Term
The first prokaryotic DNA polymerase?
Definition
POL I - found in E. coli
Term
___ is the main DNA polymerase in E. coli used for DNA replication
Definition
POL III
Term
Which DNA polymerase is active on the lagging strand in RNA primer removal and replacement and thus involved in DNA repair?
Definition
POL II
Term
There are (#) human DNA polymerases
Definition
11
Term
Of the human DNA polymerases, only one is found in the ___. The rest are found in the ____.
Definition
mitochondria, nucleus.
Term
most human DNA Polymerases are involved in _____, not replication
Definition
DNA repair
Term
___ are single-base changes involving just a few nucleotides
Definition
point mutations
Term
2 types of point mutations
Definition
Deletion or insertion of single/couple bases :: Base substitutions
Term
2 types of base substitutions
Definition
transitions (purine to purine or pyrimidine to pyrimidine) :: Transversions (purine to pyrimidine or pyrimidine to purine)
Term
Which is a bigger deal, transitions or transversions?
Definition
transversions
Term
___ are insertions/deletions of somewhere around 4-100 nucleotides. Possible consequences of this?
Definition
Mutational indels :: consequences are frameshifts, whole segments of a gene missing, or additional amino acids introduced
Term
Frameshift mutations
Definition
deleting a nucelotide and then just shifting the rest of the nucleotides to fill the gap. :: Biology is my favorite class :: Biologi sm yf avoritec lass
Term
____ are larger genetic changes that cause large deletions, inversions, or duplications of DNA
Definition
Chromosomal rearrangments
Term
Inversions (chromosomal rearrangement)do what to the DNA
Definition
reverse the order
Term
___ is a type of genetic mutation that changes the copy number of all of the chromosomes (common in plants)
Definition
polyploidy - not a big deal because ALL of the chromosomes double
Term
___ changes the copy number of a single chromosome
Definition
aneuploidy
Term
___ is when there is an error in cell division that affects just one chromosome and is due to failure of cell cycle check points.
Definition
Nondisjunction
Term
consequences of nondisjunction
Definition
monosomy or trisomy - often leads to fatal or severly disabling diseases -- or miscarriage
Term
agents that cause a higher than normal rate of DNA mutations
Definition
mutagens
Term
mutagens that cause cancer
Definition
carcinogens
Term
normal rate of DNA mutations
Definition
1000-1 million/day -- increases based on your activities (tanning = more mutations)
Term
sources of mutagens
Definition
Man-made chemicals, cigarette smoke, alcohol, man-made radiation (x-rays), Uv and other natural sources of radiation, Oxidative metabolism
Term
DNA repair systems
Definition
specific (photorepair) - fixes the problem :: Non-specific (excision repair) - replaces the bad nucelotide :: error-free (if the damage is just to one strand of the double helix bc the other strand can serve as a template) :: can be imperfect (if both strands are damaged bc there is no template)
Term
photolyase
Definition
specific enzyme that fixes the thymines that result from sun damage to DNA
Term
What is Xeroderma Pigmentosa?
Definition
sun sensitivity disease caused by mutations in repair enzymes
Term
mutations in repair enzymes often happen when?
Definition
with age
Term
When one cell suffers DNA damage, what is the impact on its daughter cells.
Definition
all of them will have the mutation
Term
most alleles produced by mutations are ____.
Definition
deleterious
Term
heritable genetic diseases found in every cell of the offspring
Definition
germ line mutations
Term
mutations resulting in cancerous tumor growth (tumorigenesis)
Definition
somatic mutations
Term
T/F: Diseases can be due to single gene mutations
Definition
true
Term
what disease results in a recessive, chloride channel mutation
Definition
cystic fibrosis
Term
what disease results from a genetic mutation in a recessive, lipid metabolism and accumulation of abnormal brain lipids
Definition
tay sachs disease
Term
what disease results from an X-linked recessive mutation in the clotting factor VIII
Definition
hemophilia
Term
complex relationship between genotype and phenotype (disease state)
Definition
genetic diseases
Term
characteristics of genetic diseases
Definition
can be caused by multiple genes :: often only manifested in a particular environment :: diet, exercise and lifestyle are key contributors
Term
___ is caused by disruption or errors in the cell cycle control system
Definition
cancer
Term
2 kinds of "cancer genes"
Definition
oncogenes and tumor suppressor genes
Term
____ are usually dominant genes that, when present, lead to malignant cells
Definition
oncogenes
Term
____ are "accelerators" that over-stimulate cell growth and division caused by downstream signaling from receptors such as cyclins, etc
Definition
oncogenes
Term
____ are genes that tend to be recessive and loss leads to malignant cells.
Definition
tumor suppressor genes
Term
___ are the "brakes" that slow down the cell cycle. When they are damaged the cycle speeds up and produces tumor cells.
Definition
tumor suppressor genes
Term
RNA primers are always added 3'-->5' or 5'-->3'?
Definition
5'-->3'
Term
enzyme that joins together the okazaki fragments
Definition
ligase
Term
enzyme that removes RNA primers and adds nucleotides
Definition
POL I
Term
___ protein structure is the sequence of amino acids.
Definition
primary
Term
amino acids in DNA are linked via __ bonds
Definition
peptide
Term
___ structure of proteins is a characteristic folding of the peptide backbone
Definition
secondary
Term
2 forms of secondary structure
Definition
alpha helix and beta sheets
Term
secondary structures are stabilized by __ bonds
Definition
H
Term
are R groups involved in the structure of a protein?
Definition
no
Term
___ structure is the "shape" of the protein... the arrangement of the a-helices and beta sheets in space
Definition
tertiary
Term
___ is the final 3-D shape of a single peptide
Definition
tertiary structure
Term
for proteins of only one peptide, the highest level of structure is ___.
Definition
tertiary
Term
the 3-D arrangement in space of multiple polypeptides in a protein
Definition
quaternary tructure
Term
example of a protein with quaternary structure
Definition
hemoglobin
Term
1 protein with 4 polypeptides is called a
Definition
tetramer
Term
1 protein with 4 polypeptides is called a
Definition
tetramer
Term
___ are combinations of some elements of secondary structure seen in many polypeptides
Definition
motifs
Term
___ are functional regions of a polypeptides
Definition
domains
Term
____ are repeated structural units found in different proteins
Definition
domains
Term
____ contain all of the components of the structures below it, ___ don't.
Definition
higher structures (quaternary, tertiary, etc).... motifs and domains
Term
Hierarchy of structure
Definition
primary < secondary < motif < domain < tertiary < quaternary
Term
4 interactions that stabilize protein structure
Definition
H bonding in backbone and R groups :: electrostatic interactions (ionic bonds) called salt bridges (attraction of + and - charged R groups) :: Disulfide bonds (cysteine reacts to form covalent bonds) :: hydrophobic exclusion (bury hydrophobic R groups in interior)
Term
____ is one way to regulate protein activity by modifying them after synthesis
Definition
post-translational processing
Term
5 types of post-translational processing
Definition
proteolysis, glycosylation, phosphorylation, ubiquitination, acetylation
Term
___ is cleavage of proteins into smaller peptides
Definition
proteolysis
Term
___ is adding sugars to proteins
Definition
glycosylation
Term
___ is the addition of a phosphate (PO4) to a protein
Definition
phosphorylation
Term
____ is addition of acetyl groups to a protein
Definition
acetylation
Term
Effects of post-translational processing: cleavage
Definition
activates multiple enzymes (signal sequence cleaved), multiple hormones in single peptide
Term
effects of post-translational processing: glycosylation
Definition
many membrane proteins are glycoproteins, cell identity
Term
effects of post-translational processing: phosphorylation
Definition
activity conrolled by phosphorylation (cell cycle)
Term
Effects of post-translational processing: ubiquination
Definition
target for destruction in proteosome
Term
5 physical features of DNA
Definition
double stranded, polynucleotide chain, antiparallel, complimentary base pairs, polarity
Term
___ experiment provides the basis for understanding DNA replication
Definition
messelson-stahl
Term
Steps in meselson-stahl experiment
Definition
put cells in Heavy isotop (N15) medium and let them replicate once, put them in N14 medium and let them replicate again, centrifuge the cells and see where they settle
Term
What is sex-linkage and how can you recognize it
Definition
Sex-linkage is the alteration in patterns of inheritance based on the sex of the parents. This is seen for loci that are on the so-called sex chromosomes. These are chromosomes that differ between the sexes and these chromosomal differences lead to altered patterns of inheritance.
Term
the ____ sex will always show recessive traits
Definition
heterogametic
Term
The difference in ____ crosses is the hallmark of sex-linkage. In humans, it leads to males showing sex-linked traits more often (they are the heterogametic sex), and to inheriting these traits from their maternal grandfathers through their mothers
Definition
reciprocal
Term
___ is an alteration of independent assortment such that an excess of parental gametes are produced
Definition
linkage
Term
How does linkage relate to the behavior of chromosomes during meiosis?
Definition
alters Mendelian ratios significantly and in ways that cannot be viewed as a modified ratio the way some genetic interactions can. we can easily observe the excess of parental genotypes characteristic of linkage. This has a simple basis: two loci that are close together on the same chromosome would not be expected to segregate independently. If they are very close together, we should only see the parental combinations
Term
How can two genes on the same chromosome ever lead to recombinant gametes
Definition
partial linkage - The production of recombinant gametes from linked genes is due to the phenomenon of crossing over where chromosomes physically exchange material. This is also called genetic recombination as it does lead to recombinant genotypes
Term
Genetic markers in humans are ??
Definition
disease states
Term
___ markers are “polymorphic” and randomly scattered throughout the genome. They are molecular markers, that is, differences in DNA that do not cause phenotypic changes but can be seen using molecular techniques
Definition
anonymous
Term
which kind of marker can be used to map genetic distances?
Definition
anonymous
Term
how do you calculate map distance?
Definition
(# recombinant/total #) * 100
Term
What is the essential activity of DNA Polymerases and how is it done?
Definition
to synthesize DNA by the sequential addition of nucleotides to a growing nucleic acid polymer. This is done in the 5'-3' direction by adding nucleotides to the 3' end.
Term
What requirements are there for DNA POL to work?
Definition
a primer H-bonded to a template that can be extended
Term
a short 10-20 base polynucleotide of DNA or RNA H-bonded to the template.
Definition
primer
Term
What is an "extra" function of DNA polymerases?
Definition
exonuclease activity, an enzymatic activity that can remove bases from the end of a DNA strand
Term
2 kinds of exonucleases
Definition
5'-3': work with DNA POL I and works as a general repair mechanism, repairing damage after replication such as fixing sun damage. ::: 3'-5': works with DNA POL III - used to proofread the work of DNA POL III - happens as replication takes place by removing "wrong bases" when they are put in.
Term
What are the leading and lagging strands? How is synthesis different on these two strands?
Definition
We call the continuous strand the leading strand and the discontinuous strand the lagging strand. The discontinuous nature of the lagging strand requires both continual priming and continual removal of primers for this strand (because the primers are made of RNA see question 5), and the relatively short fragments produced must be stitched together. Thus a lot more enzymes are needed along the lagging strand and it is done in blocks.
Term
What kinds of enzymes are needed to prime synthesis of DNA from scratch?
Definition
The only enzymes to initiate synthesis of a nucleic acid de novo (from scratch) are RNA Polymerases, thus all primers are made by an RNA Polymerase.
Term
What kind of enzymes are needed to synthesize a new strand of DNA from a previously existing strand?
Definition
DNA Pol’s will only extend primers but will not initiate synthesis de novo.There are a variety of RNA polymerases that can function in this role in cells. The enzyme active during most of replication is a special replication-related enzyme called Primase
Term
What kinds of activities should we expect to be found at the fork?
Definition
helicase (open helix), DNA Pol III (to synthesize the DNA), Primase (priming on lagging strand), DNA Pol I (remove primers on lagging strand), and DNA Ligase to seal the nicks left after Pol I has removed primers.
Term
How are all of the enzymes involved in replication actually organized in the cell?
Definition
Replisome. This includes two Pol III molecules (each some 20 polypeptides), primase, helicase, some 20 other accessory proteins that together make up this replication organelle
Term
How do mutations arise? Is there any way the frequency of mutations can be increased?
Definition
Replication errors -- mutagens and carcinogens increase these errors
Term
What is the difference between a point mutation and a chromosomal mutation?
Definition
Point mutations affect a single site and chromosomal alterations affect large regions of chromosomes. Point mutations can be base substitutions, or small insertions or deletions. Chromosomal alterations can be larger deletions, inversions where the order of a region of a chromosome is reversed, duplications of a chromosomal region, or translocations where a portion of one chromosomes is moved to a different chromosome
Term
How are mutations related to cancer?
Definition
Point mutations affect a single site and chromosomal alterations affect large regions of chromosomes. Point mutations can be base substitutions, or small insertions or deletions. Chromosomal alterations can be larger deletions, inversions where the order of a region of a chromosome is reversed, duplications of a chromosomal region, or translocations where a portion of one chromosomes is moved to a different chromosome
Term
A ___ is a repeating unit of secondary structure that is used in many proteins. These appear to have been selected by evolution for particular functions, then reused over and over
Definition
motif
Term
A ___ is a functional substructure within the tertiary structure. Most proteins are composed of multiple of these that have different roles in the overall function of the protein
Definition
domains
Term
DNA/RNA polymerases require a primer. DNA/RNA polymerases do not require a primer.
Definition
DNA .. RNA
Term
What is the primer that is used for DNA replication
Definition
RNA polymerase... short sequence of RNA that is H bonded to the template
Term
DNA POL I
Definition
removes the RNA primer and replaces it with DNA 5'-3'
Term
DNA POL III
Definition
the main enzyme that builds new strands of DNA 5'-3' by adding nucleotides at the 3' end
Term
the action of synthesizing a new strand of DNA is catabolic or anabolic?
Definition
anabolic
Term
DNA is synthesized in which direction and read in which direction?
Definition
synthesized: 5'-3' ... read: 3'-5'
Term
Order of activities in the lagging strand
Definition
1. Primase (RNA POL) 2. DNA POL III 3. Ligase
Term
Polymerases make ___ bonds
Definition
phosphodiester
Term
nucleases do what?
Definition
cleave phosphodiester bonds
Term
3 checks on accuracy of base pairing
Definition
select the right base the first time, remove the incorrect base right away by 3'-5' exonuclease, repair of mismatched base by post-replication 5'-3' exonuclease
Term
What is the overall effect of multiple crossovers occurring between two genetic markers on the same chromosome?
Definition
The genetic distance between the two markers will be underestimated bc of excess parental phenotypes
Term
One particular feature of human pedigree analysis of dominant Mendelian traits is:
Definition
the trait appearing in every generation
Term
The 5' end of a DNA strand has a ___ attached to it, while the 3' end has a ___ attached to it.
Definition
phosphate, OH
Term
which are purines and which are pyrimidines?
Definition
purines: A and G ... Pyrimidines: T, C, and U
Term
If enzymes that have the 5’ --> 3’ exonuclease function are impaired, which function would be directly affected?
Definition
Removal of RNA primer segments
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