Exam 3

Question 1

X Chromosome vs. Y Chromosome

Answer 1

X: 5 times bigger than Y, >1500 genes, acts homologous to Y
Y: 231 genes, a lot of palindromes which may destabilize DNA,

Question 2

Segments on Y

Answer 2

Pseudoautosomal Region (PAR): Connects with the X chromosome during fertilization, on the ends of both the X and Y, PAR1 on top or p arm and PAR2 on bottom or q arm
Male Specific Region (MSY): Everything in between, does not get crossed over, houses the SRY gene close to PAR1

Question 3

SRY Gene

Answer 3

Stimulates male development, on p arm, encodes for a transcription factor that controls the expression of other genes, developing testes secrete anti-Mullerian hormone that destroys female structures, testosterone and dihydrotestosterone are secreted and create male structures, turns on in the 5th week of development

Question 4

Y-Linked Traits

Answer 4

No known conditions, if we had them they would only occur in males, this would likely affect reproduction which is why we don’t see them

Question 5

X-Linked Traits

Answer 5

Criteria For Recessive: Always expressed in males, always expressed in a woman homozygote but rarely in a recessive heterozygote, a father would have to have the trait to pass it on to the female
Criteria For Dominant: Expressed in one female copy, much more severe effect in males, high rates of miscarriage due to the lethality in males, passed from male to all daughters

Question 6

X-Linked Diseases

Answer 6

Recessive:
Ichthyosis: Fish like scales, only affects males
Hemophilia: blood doesn’t clot properly, 12 different proteins are used to clot blood and in hemophilia A the 8 has a mutation, in hemophilia B the 9 has a mutation
Dominant:
Incontentia Pigmenti: Mutation in the NEMO gene which affects apoptosis, this causes apoptosis to occur to quickly and leads to rash and skin warts
Congenital generalized hypertrichosis: overactive hair growth (think greatest showman)

Question 7

X Inactivation Center (XIC)

Answer 7

Epigenetic phenomenon (affects gene expression without affecting gene sequence), when the XIC is active it causes the XIST gene to be active, the XIST gene produces RNA that coats the other X which inactivates it

Question 8

Genomic Imprinting

Answer 8

The phenotype of an individual differs depending on the gene’s parental origin, it is epigenetic, may be incomplete dominance, methyl binds to the DNA and suppresses gene expression in a pattern determine by the individual’s sex
The function is not fully understood but we believe that a gamete from a genetic male (placenta development) and a genetic female (embryo development) are required for a healthy embryo

Question 9

Genomic Imprinting Diseases

Answer 9

Prader-Willi Syndrome: baby doesn’t gain weight, when older it eats literally everything in sight, even non food items (hyperphagia), and have intellectual disability
caused by a deletion of the father’s copy of chromosome 15
Angelman Syndrome: small baby, poor growth, really bad seizures, and doesn’t develop the ability to speak
caused by a deletion of the mother’s copy of chromosome 15

Question 10

Empiric Risk, Incidence, and Prevalence

Answer 10

Empiric Risk: measures the likelihood that a trait will reoccur
Incidence: How many new cases are seen within a given amount of time
Prevalence: Total amount of cases seen within a given period of time

Question 11

3 Way Empiric Risk increases

Answer 11

1. Increases if family members have it
2. Increases if the disease is more severe
3. Increases if the family member is more related

Question 12

Heritability

Answer 12

Estimates the proportion of the phenotypic variation in a population to genetic differences
Genetic factors vs environmental factors
H values will be 0-1
H = 0 greater influence from environment
H = 1 greater influence from genes
Mathematical Aptitude is highly influenced by environment

Question 13

Coefficient of Relatedness

Answer 13

The proportion of genes shared between two related in a certain way. (Ex Brother is 1st degree, 50% shared genes)

Question 14

Twins and Concordance

Answer 14

Twin studies have largely replaced adoption methods
Concordance - measures the frequency of expression of a trait in both members of monozygotic or dizygotic twins
Twins who differ in a trait are said to be discordant for it
Twins who have the same trait or concordant
For a trait largely determined by genes, concordance is higher for MZ than DZ twins
DZ twins - shared environment and 50% of genes
MZ twins - identical genotype and shared environment
Twins raised apart - shared genotype but not environment
Adopted individuals shared environment but not genes

Question 15

Replication Fork

Answer 15

Place where DNA is actually replicated

Question 16

Enzymes involved in DNA replication

Answer 16

Helicase: Unwinds the DNA molecule
Binding Proteins: Keeps the unwinded DNA strands separate
Primase: an enzyme that places RNA primers at specific parts of the DNA, so DNA can be built
DNA Polymerase: Places nucleotides onto the DNA strand specifically the 3’ end of the RNA, checks for errors
Ligase: creates the phosphodiester bond in the newly placed DNA strand

Question 17

Activities at replication fork

Answer 17

1. Helicase binds to origin and separates strands
2. Binding proteins keep strands apart
3. Primase makes a short RNA primer to attach to the DNA template
4. DNA polymerase adds DNA nucleotides to the RNA primer
5. DNA polymerase proofreads activity checks and replaces incorrect bases
6. Continuous strand in a 5’ to 3’ direction (aka leading strand)
7. Discontinuous synthesis produces Okazaki fragments on the 5’ to 3’ template (aka lagging strand); the Okazaki fragments are around 20 nucleotides long
8. Enzymes Remove RNA primers, Ligase seals sugar-phosphate backbone

Question 18

3 Steps of PCR

Answer 18

Denaturation: Heat is used to separate the two DNA strands
Annealing: Two short DNA primers bind to the target DNA at a lower temperature
Extension/Elongation: Enzyme Taq1 DNA polymerase adds bases to the primers
Materials: Thermocycler, DNA primers, target DNA, DNA polymerase, nucleotides

Question 19

Genomic Library and DNA probes

Answer 19

Genomic Library: Collections of recombinant DNA that contain pieces of the genome, usually a set of bacteria
DNA is extracted from cells and digested with a restriction enzyme
DNA fragments are inserted into cloning vectors (usually plasmid, circular DNA)
Bacterial cells are transformed with vectors
DNA Probe: Radioactively (or fluorescently) labeled gene fragments, finds the gene you want by having a “tag”

Question 20

cDNA Library and Methods

Answer 20

cDNA library: Genomic library of protein encoding genes produced by extracting mRNA and using reverse transcriptase to make DNA (just has protein encoding genes)
We use a mature mRNA to make a mRNA-cDNA hybrid
It leaves a single-stranded cDNA
You add DNA polymerase and it becomes double stranded

Question 21

Creating Recombinant DNA Molecules

Answer 21

Manufacturing recombinant DNA requires restriction enzymes that cut donors and recipient DNA at the same sequence
These enzymes cut DNA at sites that are palindromic
The cutting action of many of these enzymes generate single-stranded extensions called “sticky ends”
Another “tool” used is a cloning vector
Carries DNA from the cells of one species into the cells of another
Commonly used vectors:
Plasmid (Bacterial)
Bacteriophages
Disabled retroviruses
Insulin in the lab was originally created by using this technology, but we originally harvested it from livestock which wasn’t as effective

Question 22

Applications of Recombinant DNA

Answer 22

Recombinant DNA is used to:
Study the biochemical properties of genetic pathways of that protein
Mass-produce proteins like insulin
Sometimes conventional methods are still the better choice because of economics
Textile industry can produce indigo dye in E. coli by genetically modifying genes of the glucose pathway and introducing genes from another bacterial species

Question 23

Monitoring Gene Function

Answer 23

Gene expression using DNA microarrays
Aka Gene Chips are devices that detect and display the mRNAs in a cell
A microarray is a piece of glass or plastic
Many small pieces of DNA of known sequence are attached to one surface, in a grid pattern
In many applications, a sample from an abnormal situation is compared to a normal control

Question 24

Genome Wide Association Studies

Answer 24

Older techniques search for known gene variants, typically in only a few people
Sequencing of the entire human genome and the HapMap project (which identifies SNPs) have led to a new tool
Genome-wide association studies seek correlations between SNP patterns and phenotypes in large groups of individuals

Question 25

Single Nucleotide Polymorphism

Answer 25

SNPs are sites in a genome where the DNA base varies in at least 1% of the population
In these studies SNPs span the genome, rather than define a single gene
A SNP can be anywhere among our roughly 3.2 billion base pair genome