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
|
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
|
|
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
|
|
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
|
Definition
|
|
Term
| the heterogametic sex will be ___ for all alleles on X |
|
Definition
|
|
Term
|
Definition
|
|
Term
| the rest of the chromosomes (that aren't sex chromosomes) are called ____. |
|
Definition
|
|
Term
|
Definition
|
|
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
|
|
Term
| how do you obtain information about the distance between genes on a chromosome? |
|
Definition
|
|
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
|
Definition
| 1 map unit = 1% recombination = 1cM (centiMorgan) |
|
|
Term
| as distance between 2 genetic loci increases, the likelihood of recombination increases/decreases |
|
Definition
|
|
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
|
|
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
|
|
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
|
|
Term
| The more/less crowded genetic markers are, the more accurate the genetic map will be. |
|
Definition
|
|
Term
| 3-point crosses are more reliable than 2-point crosses at longer/shorter distances |
|
Definition
|
|
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
|
|
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
|
|
Term
| in a _____, carriers exist and the affected individuals parents are unaffected by the condition because they are carriers |
|
Definition
|
|
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
|
|
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
|
|
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
|
|
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
|
|
Term
| ____ is the idea that linked genes show association in a population |
|
Definition
|
|
Term
| there are about (#) genes in the genome, and we know what about (#) of them do. |
|
Definition
|
|
Term
| ___ mapping allows us to locate genes for virtually any trait |
|
Definition
|
|
Term
| Watson and Crick used the principle of ____ to find out that A pairs with T and G pairs with C. |
|
Definition
|
|
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
|
|
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
|
|
Term
| enzyme that opens the double helix |
|
Definition
|
|
Term
| enzyme that relieves torsional strain |
|
Definition
|
|
Term
| The first prokaryotic DNA polymerase? |
|
Definition
|
|
Term
| ___ is the main DNA polymerase in E. coli used for DNA replication |
|
Definition
|
|
Term
| Which DNA polymerase is active on the lagging strand in RNA primer removal and replacement and thus involved in DNA repair? |
|
Definition
|
|
Term
| There are (#) human DNA polymerases |
|
Definition
|
|
Term
| Of the human DNA polymerases, only one is found in the ___. The rest are found in the ____. |
|
Definition
|
|
Term
| most human DNA Polymerases are involved in _____, not replication |
|
Definition
|
|
Term
| ___ are single-base changes involving just a few nucleotides |
|
Definition
|
|
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
|
|
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
|
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
|
|
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
|
|
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
|
|
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
|
|
Term
| mutagens that cause cancer |
|
Definition
|
|
Term
| normal rate of DNA mutations |
|
Definition
| 1000-1 million/day -- increases based on your activities (tanning = more mutations) |
|
|
Term
|
Definition
| Man-made chemicals, cigarette smoke, alcohol, man-made radiation (x-rays), Uv and other natural sources of radiation, Oxidative metabolism |
|
|
Term
|
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
|
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
|
|
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
|
|
Term
| heritable genetic diseases found in every cell of the offspring |
|
Definition
|
|
Term
| mutations resulting in cancerous tumor growth (tumorigenesis) |
|
Definition
|
|
Term
| T/F: Diseases can be due to single gene mutations |
|
Definition
|
|
Term
| what disease results in a recessive, chloride channel mutation |
|
Definition
|
|
Term
| what disease results from a genetic mutation in a recessive, lipid metabolism and accumulation of abnormal brain lipids |
|
Definition
|
|
Term
| what disease results from an X-linked recessive mutation in the clotting factor VIII |
|
Definition
|
|
Term
| complex relationship between genotype and phenotype (disease state) |
|
Definition
|
|
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
|
|
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
|
|
Term
| ____ are "accelerators" that over-stimulate cell growth and division caused by downstream signaling from receptors such as cyclins, etc |
|
Definition
|
|
Term
| ____ are genes that tend to be recessive and loss leads to malignant cells. |
|
Definition
|
|
Term
| ___ are the "brakes" that slow down the cell cycle. When they are damaged the cycle speeds up and produces tumor cells. |
|
Definition
|
|
Term
| RNA primers are always added 3'-->5' or 5'-->3'? |
|
Definition
|
|
Term
| enzyme that joins together the okazaki fragments |
|
Definition
|
|
Term
| enzyme that removes RNA primers and adds nucleotides |
|
Definition
|
|
Term
| ___ protein structure is the sequence of amino acids. |
|
Definition
|
|
Term
| amino acids in DNA are linked via __ bonds |
|
Definition
|
|
Term
| ___ structure of proteins is a characteristic folding of the peptide backbone |
|
Definition
|
|
Term
| 2 forms of secondary structure |
|
Definition
| alpha helix and beta sheets |
|
|
Term
| secondary structures are stabilized by __ bonds |
|
Definition
|
|
Term
| are R groups involved in the structure of a protein? |
|
Definition
|
|
Term
| ___ structure is the "shape" of the protein... the arrangement of the a-helices and beta sheets in space |
|
Definition
|
|
Term
| ___ is the final 3-D shape of a single peptide |
|
Definition
|
|
Term
| for proteins of only one peptide, the highest level of structure is ___. |
|
Definition
|
|
Term
| the 3-D arrangement in space of multiple polypeptides in a protein |
|
Definition
|
|
Term
| example of a protein with quaternary structure |
|
Definition
|
|
Term
| 1 protein with 4 polypeptides is called a |
|
Definition
|
|
Term
| 1 protein with 4 polypeptides is called a |
|
Definition
|
|
Term
| ___ are combinations of some elements of secondary structure seen in many polypeptides |
|
Definition
|
|
Term
| ___ are functional regions of a polypeptides |
|
Definition
|
|
Term
| ____ are repeated structural units found in different proteins |
|
Definition
|
|
Term
| ____ contain all of the components of the structures below it, ___ don't. |
|
Definition
| higher structures (quaternary, tertiary, etc).... motifs and domains |
|
|
Term
|
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
|
|
Term
| ___ is adding sugars to proteins |
|
Definition
|
|
Term
| ___ is the addition of a phosphate (PO4) to a protein |
|
Definition
|
|
Term
| ____ is addition of acetyl groups to a protein |
|
Definition
|
|
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
|
|
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
|
|
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
|
|
Term
| ___ is an alteration of independent assortment such that an excess of parental gametes are produced |
|
Definition
|
|
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
|
|
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
|
|
Term
| which kind of marker can be used to map genetic distances? |
|
Definition
|
|
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
|
|
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
|
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
|
|
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
|
|
Term
| DNA/RNA polymerases require a primer. DNA/RNA polymerases do not require a primer. |
|
Definition
|
|
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
|
Definition
| removes the RNA primer and replaces it with DNA 5'-3' |
|
|
Term
|
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
|
|
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
|
|
Term
|
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
|
|
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 |
|
|
