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Genetics Exam II
Pedigrees, Linked Genes, Transcription & Translation
161
Biology
Undergraduate 3
11/06/2008

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Term
What mutation causes Hutchinson-Gilford Progeria?
Definition
A mutation in the gene for Lamin A, a nuclear membrane scaffolding protein. Found on chromosome 1.
Term
What techniques are used to study heritable diseases?
Definition
Twin studies, adoption studies, pedigrees.
Term
Who was the holocaust doctor that used unethnical human experiments to learn about genetics?
Definition
Dr. Josef Mengele
Term
Why is the study of human genetics difficult?
Definition
Long generation time, controlled matings not possible, family size (n) is small.
Term
What is consanguinity?
Definition
Mating between related persons.
Term
Give an example of an autosomal dominant syndrome.
Definition
Waardenburg Syndrome, a type of deafness associated with a white forelock and vision problems.
Term
What are some characteristics of autosomal recessive traits?
Definition
  • Equal distribution
  • Tend to skip generations
  • Tend to appear in children of related parents

 

Term
What are some characteristics of autosomal dominant traits?
Definition
  • Equal distribution
  • Unaffected do not transmit trait
  • Affected have at least one affected parent
Term
What are some characteristics of X-linked recessive traits?
Definition
  • Appear frequently in males
  • Affected male does not pass trait to son
  • Can pass allele to daughter
Term
What is hemophilia?
Definition
An x-linked recessive trait, where there is an absence of protein required for clotting.
Term
Who created the first genetic map?
Definition
Alfred Sturtevant mapped the X chromosome of Drosophila.
Term
What is recombination?
Definition
The sorting of alleles into new combinations, happens by independent assortment of alleles.
Term
Who discovered the non-independent assortment of alleles?
Definition
Bateson, Saunders, and Punnett in 1905.
Term
What are the characteristics of linked genes?
Definition
  • Genes that are located close together on a chromosome
  • They belong to the same linkage group
  • Travel together during meiosis (same gamete)
  • Do NOT assort independently
  • Are inherited together
Term
What is an example of recombination?
Definition
Crossing over during meiosis
Term
How did Meselson and Stahl demonstrate that replication in E. coli occurs in a semiconservative manner?
Definition
They incorporated different isotypes of nitrogen into DNA and then weighed it to see how it mixed. Equilibrium density gradient centrifugation.
Term
What is the origen of replication in E.coli?
Definition
The oriC
Term
What is heteroduplex DNA?
Definition
DNA formed during a Holliday Junction, where the DNA molecule has 2 strands, one from each chromosome.
Term
What is one way that crossing over occurs?
Definition
Holliday junction model
Term
What did Creighton and McClintock use to discover intrachromosomal recombination?
Definition
The abnormal corn chromosome 9, which has a knob and an extra piece.
Term
What is amniocentesis?
Definition

Should take place during the 17th to 18th week of pregnancy, cells from the amniotic fluid are sampled to run genetic tests.

Term
What is chroionic villus sampling?
Definition
In the 10th to 12th week of pregnancy sampling of the blood from the villus containing fetal cells.
Term
What are characteristics of linked genes?
Definition
  • located close together on the chromosome
  • belong to same linkage group
  • travel to same gamete during meiosis
  • do NOT assort independently
  • inherited together
Term
What are the two ways that linked alleles can be arranged on homologous chromosome?
Definition
Coupled (cis) or repulsion (trans)
Term

What is the resulting cell called in somatic cell hybridization?

Definition
A heterokaryon
Term
What are some physical ways of gene mapping?
Definition
Deletion mapping, somatic cell hybridization, fluorescent molecular probes.
Term
Describe transcription initiation in a prokaryote.
Definition
  • Circular E. coli has 1 oriC
  • Iniator protein binds to oriC causing a short section of DNA to unwind
  • Allows helicase to attach to polynucleotide strand
Term
Describe unwinding in prokaryotic transcription. Is it different than in eukaryotic?
Definition

DNA helicase breaks H-bond between 2 strands
Moves along 5´--> 3 ´ direction (replication fork)

Term
How does DNA polymerase III work in prokaryotes?
Definition

Polymerase activity = adds nucleotides to the 3´
Exonuclease activity = removes nucleotides 3´5´ (corrects errors)

Term
How does DNA polymerase I work (prokaryotes)?
Definition

Polymerase and exonuclease activity similar to polyIII
Exonuclease activity 5´3´
Removes primers and replaces with DNA nucleotides 5´3´

Term
What are the steps of transcription in eukaryotes?
Definition

Licensing of DNA Replication
Replication licensing factor attaches to origin
Unwinding
Polymerization (polymerases)
Elongation
Nucleosome assembly (histones)
Termination

Term
What does does RNA polym. I transcribe?
Definition
Larger rRNAs
Term
What does RNA polym. II transcribe?
Definition
pre-mRNA, snRNA, snoRNA, some miRNA
Term
What does RNA polym. III transcribe?
Definition
tRNAs, small rRNAs, snRNAs, miRNAs
Term
What does RNA polym. IV transcribe?
Definition
Some siRNA in plants.
Term
What is a consensus sequence?
Definition
A consensus sequene consists of the most commonly encountered bases at each position in a group of related sequences
Term
In bacterial promoters, where are consensus sequences found?
Definition
Upstream of the start site, typically at -35 and -10
Term
How does eukaryotics promoter recognition occur?
Definition
By accessory proteins (transcription factors) that bind to the promoter and recruit specific RNA polymerases.
Term
What is the core promoter region?
Definition
  • located upstream of the gene
  • site where basal transcription apparatus binds
  • includes consensus TATA box
Term

Where are regulatory promoters found?

Definition
Upstream of the core promoter (TATA typically)
Term
What is the concept of colinearity?
Definition
That each gene encodes for one protein.
Term
Who discovered the validity of the one gene one enzyme theory?
Definition
1958 Beadle and Tatum used neurospora to prove this theory.
Term
What is tRNA charging?
Definition
Binding of tRNA to AA
Term
What is a somatic mutation?
Definition
A mutation in cells not producing gametes, passed on to daughter cells in mitosis, normal cells compensate.
Term
What are germ-line mutations?
Definition
Passed to future generations because they occur in cells producing gametes, offspring will carry mutations in all somatic and germ-line cells.
Term
What is a gene mutation?
Definition
A small DNA lesion that affects a single single.
Term
What is chromosomal mutation?
Definition
A large-scale genetic mutation affecting chromosome structure and function and therefore multiple genes.
Term
What is base substitution?
Definition
A type of gene mutation where a single nucleotide is altered.
Term
What is transition?
Definition
When a purine is replaced by a purine in base substitution, or a pyrimidine with a pyrimidine.
Term
What are the purines, and what are the pyrimidines?
Definition
Purines are A and G, Pyrimidine are C and T.
Term
What are insertions and deletions?
Definition
Types of gene mutations where one or more nucleotide pairs are inserted or deleted, leading to a shift in the reading frame.
Term
What are expanding trinucleotide repeats?
Definition
Gene mutations in which the number of copies of a set of three nucleotides (trinucleotide) is increased in number. # of repeats correlates with the severity of the disease.
Term
What is an example of a disease where trinucleotide repeats occurs?
Definition
In 1991 they observed that the FMR-1 gene causes fragile X, severe form of mental retardation. The tip of the X chromosome is attached by only a slender thread.
Term
What is anticipation?
Definition
The severity of the disease gets more severe with each generation.
Term
What is a forward mutation?
Definition
Alters the wild type phenotype to a mutant phenotype.
Term
What is a reverse mutation?
Definition
Alters a mutant phenotype back to a wild type phenotype.
Term
What is a suppressor mutation?
Definition
A genetic mutation that hides or suppresses the effect of another mutation (double mutant). Occurs at a site that is distinct from the site of the original mutation, thus they are a double mutant.
Term
Base substitutions can cause what three effects?
Definition
Missense, nonsense, and silent mutations.
Term
What does a missense mutation do?
Definition
The new codon encodes for a different amino acid, leading to a change in AA sequence.
Term
What does a nonsense mutation do?
Definition
The new codon is a stop codon, there is premature termination of translation.
Term
What does a silent mutation do?
Definition
The new codon encodes for the same amino acid as the original codon, there is no change in AA sequence.
Term
What is a loss of function mutation?
Definition
Complete or partial absense of normal protein function, alters structure of the protein, no longer functional, can occur at the level of transcription, translation, or splicing of the protein.
Term
What is a gain of function mutation?
Definition
Produces an entirely new trait, appearing in inappropriate tissue or in the wrong time of development, can affect receptors for growth factors and stimulate growth in the absense of GF - i.e. cancer
Term
What factors affect mutation rates?
Definition
  1. How often in the DNA
  2. Will it be repaired (effective or faulty repair)
  3. Will it be recognized and recorded
Term
What is achondroplasia?
Definition
A dominant dwarfism mutation occuring in 4 out of every 10,000 people.
Term
What is a spontaneous mutation?
Definition
A natural change in the DNA structure, includes tautomeric (H changing position), and mispairing due to wobble base pairing, as well as insertions and deletions
Term
How do insertions and deletions occur?
Definition
Strand slippage, where strand forms small loops, or unequal crossing over (duplicated copies of sequence)
Term
How does strand slippage occur?
Definition
If the new strand slips and forms a bubble, an insertion will occur to compensate, if it occurs on the template strand a deletion will occur.
Term
What is an example of early research on chemically induced mutations?
Definition
Charlotte Aeurbach's research in the mid 1900's on Mustard gas and fruit flies, which reduces the viability of gametes. It was used during WWI.
Term
What are four types of chemically induced mutation?
Definition
Alkylation (O beomes alkyl group), deamination (amine group becomes O), hydroxylation (group becomes hydroxyl group), oxidative (reactive oxygen damages DNA causing mispairing by adding O to nucleotide)
Term
What type of chemical mutagenesis is used in chemotherapy for cancer?
Definition
Alkylation is used to damage the DNA of cancer cells, using a line of drugs known as alkylating antineoplastic agents.
Term
What does radiation do?
Definition
X-rays and cosmic rays provide high energy, penetrate the tissues and damage DNA by dislodging e- (free radicals), and repair fail = death. Can form thymine dimers this way.
Term
What test is used to identify whether a compound can cause cancer?
Definition
The Ames test, shows whether number of colonies on a plate is increased due to the presense of chemical in question.
Term
What are the four types of DNA repair mechanisms?
Definition
Mismatch, direct, base excision, and nucleotide extension.
Term
What is the mismatch repair system?
Definition
Repairs replication errors, including mispaired bases and strand slippage.
Term
What is the direct repair system?
Definition
Repairs pyrimidine dimer, other specific types of alterations.
Term
What is the base excision repair system?
Definition
Repairs abnormal bases, modified bases, and pyrimidine dimers.
Term
What is the nucleotide excision repair system?
Definition
Repairs DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers.
Term
What is an example of a disease that results from defects in DNA repair?
Definition
Xeroderma pigmentosum, freckle-like spots on the skin and predisposition to cancer.
Term
Cancer is ...
Definition
A series of mutations, genetics, but not often hereditary.
Term
What are the characteristics of abnormal cell growth leading to cancer?
Definition
Inability to respond to normal cell signals, uncontrolled proliferation, and loss of cell integrity where normal cells are crowded out.
Term
What are three types of cancer cells?
Definition
Benign (localized tumor), malignant (invades nearby tissues), and matastic (travel and establish secondary tumors).
Term
What is pancreatic cancer?
Definition
Cancer of the pancreas is inherited as an autosomal dominant trait in a family that possesses a mutant palladin gene, an identical mutation on exon 2.
Term
What is the palladin gene?
Definition
Important in pancreatic cancer, palladin encodes for an essential component of the cell's cytoskeleton, when mutated it contributes to the spread of the cancer.
Term
What are some early observations that indicated cancer was a genetic disease and was inherited?
Definition
They result from genetic chance, they are associated w/ chromosomal abnormalities, and they seem to run in families i.e. are inherited.
Term
What later observations disproved that cancer is usually inheritable?
Definition
If inherited, every cell should receive the gene, tumors only appear in specific tissue, and many cancers don't run in families.
Term
Who proposed the multistep model of cancer?
Definition
Alfred Knudson in 1971, using retinoblastoma - two different mutations were necessary for cancer to occur.
Term
What is clonal evolution of tumors?
Definition
Tumor cells acquire multiple mutations as they divide, allowing them to become increasingly aggressive and proliferate, eventually the cell becomes malignant and divides uncontrollably, invading other tissues.
Term
What contributes to the frequency of clonal evolution?
Definition
How often mutations arise, the integrity of DNA repair mechanisms, and what genes are mutated, i.e. ones affecting chromosomal segregation (aneuploid)
Term
What are the types of signals that regulate cell division?
Definition
Molecules that stimulate division, and those that inhibit.
Term
What type of cell signaling occurs in normal cells?
Definition
Stimulatory and inhibitory molecules are present at the same time, causing proper speed.
Term
What are the two types of signaling genes in cell division?
Definition
Oncogenes stimulate cancer, tumor-suppresor genes inhibit cancer.
Term
Stimulatory genes are usually ...
Definition
dominant.
Term
Inhibitory genes are usually ...
Definition
recessive.
Term
Who and how was the first discovery of oncogenes proposed?
Definition
In 1909 physician Peyton Rouse injected tumor into one hen from another, tumor was transmitted by a virus (Rous sarcoma), assumed that the virus carried a cancer causing gene, SRC (1970).
Term
What did Michael Bishop & Harold Varmus do in 1975?
Definition
Used probes for viral oncogenes in normal cells, genome of normal DNA had same sequence as viral oncogene = proto-oncogenes.
Term
When a virus infects a cell, what occurs?
Definition
A proto-oncogene may incorporate (recombination), within the viral genome, proto-oncogene can mutate into an oncogene, and can then insert back into the cell, causing rapid proliferation.
Term
What type of viruses typically cause cancer?
Definition
Retroviruses
Term
How do retroviruses cause cancer?
Definition
They can mutate and rearrange proto-oncogenes into oncogenes, and they can also insert strong promoters near proto-oncogenes.
Term
What are some mutations of oncogenes as the result of viruses?
Definition
The sequence of the proto-oncogene can be altered or truncated, it can be incorporated next to a viral promoter or enhancer leading to over expression, or the function of the gene may be altered when the proto-oncogene is inserted into viral DNA.
Term
Tumor suppressor genes are more or less difficult to identify than oncogenes? Why?
Definition
More difficult because 2 alleles must mutate (they are recessive), because they FAIL to function harder to indentify, insert back to cell causes rapid proliferation.
Term
How does a tumor supressor gene cause cancer?
Definition
When the inactivation or loss of a functional allele occurs (loss of heterozygosity) this leads to cancer.
Term
What is haploinsufficiency with respect to tumor suppressor genes?
Definition
The appearance of a trait in an individual cell or organism that is heterozygous for a recessive trait, dosage effects occur because normal product is produced to suppress, but not enough is present.
Term
What is significant about heterozygosity for a tumor suppressor gene?
Definition
These people are predisposed to cancer because only one mutation, such as chromosomal deletion, can cause cancer by loss of the wild type allele and thus loss of suppressor activity.
Term
What is p53, and where is it found?
Definition
p53 is a tumor suppressor gene found in the nucleus, it acts as a transcription factor, and regulates apoptosis.
Term
Cell cycle progression is governed primarily by what?
Definition
Cyclins, CDK's, which function by phosphorylating proteins and thus activating or de-activating them.
Term
How do cyclins work?
Definition
They specificy which proteins CDK will phosphorylate, each cyclin appears at specific points in the cell cycle, its synthesis and destruction are regulated by other cyclins.
Term
What is the RB protein and how does it function?
Definition
The retinoblastoma protein helps control the progression through the G1/S checkpoint by binding transcription factor E2F.
Term
What is the G1/S checkpoint?
Definition
In G1, just before the cell enters S phase and replicates its own DNA.
Term
How does the RB/E2F complex function?
Definition
RB binds to E2F and keeps it inactive, increasing concentrations of cyclin-D-CDK and E-CDK phosphorylate RB which activates RB and RB releases E2F. E2F then binds to DNA and stimulates the transcription of genes required for replication - i.e. the cell moves into S phase.
Term
What is the G2/M checkpoint controlled by and how does it work?
Definition
Progression through the G2/M checkpoint is regulated by cyclin B. MPF, mitosis-promoting factor, is formed from cyclin B combining with CDK. During G1 cyclin B levels are low, so amount of MPF is low. As more cyclin B is produced to combine with CDK, MPF increases. Near the end of G2 the amount of MPF reaches a critical level and commits the cell to divide. MPF rises until it reaches its peak in mitosis.
Term
What does MPF do?
Definition
Mitosis promoting factor, when activated, phosphorylates other proteins - MPF is a KINASE. It induces nuclear-membrane breakdown, spindle formation, and chromosome condensation that occur during prophase.
Term
What happens when high or low levels of MPF are present?
Definition
When high levels are present mitosis is stimulated, when low, return to interphase conditions.
Term
What occurs when a mutation in the RB gene arises?
Definition
The cell is not held in G1, proceeds to division.
Term
What happens when the over-expression of genes encoding cyclin D occurs?
Definition
Stimulates the passage through the G1/S checkpoint
Term
What does a mutation of the p53 gene cause?
Definition
No regulation of CDK and no intitiation of apoptosis.
Term
What does a mutation in the signal transduction pathway cause?
Definition
External signals that trigger a cascade of intracellular reactions to produce a response.
Term
How does angiogenesis occur?
Definition
Stimulated by growth factors, highly regulated. In cancer the angiogenesis genes are over expressed, metastasis occurs. Genes contribute to metastasis, they encode components of the extracellular matrix and cytoskeleton, as well as adhesion proteins that hold cells together.
Term
What types of chromosomal arrangement may occur in cancer?
Definition
Deletion, inversion, translocation.
Term
What is deletion with respect to chromosomes in cancer?
Definition
The loss of tumor supressor genes.
Term
What is inversion with respect to chromosome rearrangement and cancer?
Definition
Segments of the chromosome are inverted end to end, may happen in a tumor supressor gene, causing inactivation.
Term
What happens in translocation, with respect to chromosome rearrangement in cancer?
Definition
Sequences from 2 different chromosomes are brought together, and generate a fused protein that stimulates cancer processes.
Term
What is an example of chromosomal translocation?
Definition
Chronic myelogenous leukemia, caused by translocation in chromosomes 9 and 22. Affects bone marrow cells, stimulates unregulated cell division.
Term
What is another example of chromosomal translocation?
Definition
Burkitt lymphoma (b cell), translocation between chromosomes 8 and 14 cause the lymphoma, which is cancer of the b cells. C-MYC is the cancer causing gene, comes under control of regulatory sequences that activate Ig.
Term
What is an example of spindle mutations?
Definition
Advanced colon cancer, the cells possess chromosomal abnormalities, including extras, missing, and rearrangements.
Term
What are the technical names of a benign tumor and a malignant tumor?
Definition
Adenomas and carcinomas
Term
What are restriction enzymes?
Definition
Restriction endonucleases cut DNA at specific point known as restriction sites, they were discovered in the 1960's as bacteria's natural defense against viruses.
Term
How does bacteria protect itself from it's own restriction enzymes?
Definition
By methylating its DNA.
Term
What are the 3 classes of RE, and which is most commonly used?
Definition
Types I and III cut at sites outside of the recognition sequence (4-6 bp palindrome), type II are more commonly used, cut at sites within the recognition sequence.
Term
What enzyme connects sticky ends?
Definition
Ligase.
Term
How can the fragments of gel electrophoresis be viewed?
Definition
Stained with dye (ethidium bromide), or a radioactive label (32P).
Term
What does an idealized cloning vector have?
Definition
An origen, selectable markers, unique resstriction sites.
Term
Describe a typical plasmid vector.
Definition
Circular DNA naturally occurring in bacteria, insert gene of interest and then introduce into bacteria via transformation, stable w/ DNA <15kb, pUC19 contains the lacZ and ampicillin resistance markers.
Term
How can a foreign piece of DNA be inserted into a vector?
Definition
Using restriction enzymes and ligase.
Term
What is an expression vector?
Definition
Instead of inserting the foreign gene into the selectable marker, the gene may be inserted into an expression vector, which contain operon sequence that allow inserted DNA to be transcribed and translated.
Term
What are the required reagents for PCR?
Definition
Template DNA, DNA polymerase, dNTPS, primers, magnesium ions, salts, thermocycler
Term
What are the limitations of PCR?
Definition
Must know the DNA sequence, contamination occurs easily, Taq doesn't proofread, only small pieces of DNA can be amplified.
Term
What are microsatelites and STR'S?
Definition
Very short DNA sequences repated in tandem and found widely within the genome. Can identify relationships, etc.
Term
How can siRNA's be produced?
Definition
By cloning DNA sequences corresponding to the siRNAs between two strong promoters. When cloned into an expression vector, both DNA strands will be transcribed and the complementary RNA molecules will anneal to form double stranded RNA that will be processed into siRNA by dicer.
Term
The theory of preformationism states that humans come from a preformed structure containing a mini human?
Definition
Homunculus.
Term
What purpose does the nucleosome serve and what is it?
Definition
Complex of DNA and histone proteins that forms chromatin, enables DNA to fit within the nucleus, limits access to DNA by proteins.
Term
What are the typical DNA compartmentalization schemes by prokaryotes and eukaryotes respectively?
Definition
Prokaryotes do not have have histones, have a circular molecule of DNA, Eukaryotes do have histones, and have multiple, linear DNA.
Term
What are the parts of a duplicated chromosome?
Definition
Sister chromatids, joined at the centromere by the kinetochore where the spindle microtubules attach.
Term
Which phases of meiosis contribute to genetic variation?
Definition
Prophase I and anaphase I and II.
Term
What is the law of equal segregation?
Definition
During meiosis alleles of a single gene segregate equally into gametes, 50% of the gametes carry one allele, 50% carry the other.
Term
What is the principle of independent assortment?
Definition
That alleles at different loci separate independently of one another.
Term
What is the binomial expansion?
Definition
Predicts probability of an event occurring

  (p + q)^n

  p = probability of child affected

  q = probability of child normal

  n = number of subjects (children)
Term
What is Turner Syndrome?
Definition
A lack of the Y chromosome, short, low hairline, broadchest, folds of skin neck, normal intelligence.
Term
What is Klinefelter Syndrome?
Definition
XXY, causes small testes, sterile, less facial and pubic hair, normal intelligence.
Term
What is the male determining gene?
Definition
SRY, located on the short arm of the Y chromosome.
Term
Color blindness is ...
Definition
An x-linked recessive trait.
Term
What is a Barr body?
Definition
An inactive x chromosome, shut off for dosage compensation, equalizes the amount of protein produced by x-linked genes in the two sexes.
Term
What is an example of codominance in humans?
Definition
The AB blood type.
Term
What is expressivity?
Definition
The degree to which a character is expressed.
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