Exam 5 - GENE 3200

Non-sister chromatids

Recombination occurs between _____________

Recombinant:

- 0.16/2= 0.08

Non-recombinant:

- 1- 0.16= 0.84... 0.84/2= 0.42

If 2 genes are known to be 16 cM apart, the proportion/frequency of each recombinant phenotype is what? Non-recombinant?

recombination

Genes linked together on the same chromosome usually assort together. Linked genes may become separated by ______________ (crossing over)

meiosis I

Recombination between linked genes occurs during ___________

Genetic locus

________________= any location in the genome that is defined by genetic or physical map or genome coordinates

Polymorphic locus

___________= locus with two or more alleles that are each present in >1% of a species' members

Molecular (DNA) markers and molecular genotyping

_____________ = characteristic of DNA that identifies different alleles of a locus

A= Point mutation, substitution

B= 1 bp

C= 3.5 x 10^6

D= Microsatellite

E= 1-6 bp

F= 1 x 10^5

Fill in the following blanks

- Identification of genotypes for disease risk, paternity testing, and experimental analysis.

- Genetic mapping of loci/genes that cause or are associated with heritable diseases and traits.

- Forensic genetics - human and animal.

- Epidemiology and food safety science.

- Human population history.

- History of domestication.

- Improvement of domesticated plants and animals.

- Indicators of key biological species in ecological environments.

- Evolutionary genetics.

- Population studies (humans, domesticated plants and animals, and wild populations).

- Conservation genetics.

What are some of the uses of DNA markers?

Variable number tandem repeats (VNTR) & microsatallite

What is another name for short tandem repeats?

one unit of repeat is small, up to 20nt in length

Short tandem repeat markers= _________________________

STR

Inheritance of ________ alleles is just like inheritance of a gene

DNA fingerprinting

_______________= identification of individuals through DNA analysis

Probability of two randomly selected people having the same allele at each of the 13 loci is less than 1 in 10 billion. Identical twins, who originate from the same fertilized egg, are an exception as they share the same DNA profile.

DNA finger printing aka CODIS is unlikely to show two identical profiles for anybody other than identical twins. Why is this?

Single nucleotide polymorphisms (SNPs)

____________ account for the vast majority of total sequence variation between human genomes

biallelic

Almost all SNP's are ____________

don't

Most SNPs ___________(do/don't) alter restriction sites.

Single base primer extensions (illumina)

What is a method that allows genome-wide genotyping? (determining the whole DNA sequence of an individual)

Eddard & Wylla

Answer the following question.. (Lyanna & Rhaegar OR Eddard & Wylla)

Look at the next slide

Show the results from crossing the heterozygous parents

ok

Answer to the previous slide

200 bp allele in each parent

Answer the following question

II-1: 200/400= Aa

II-2: 200/200= aa

II-3: 100/200= Aa

II-4: 100/400= AA

II-5: 200/400= Aa

II-6: 100/200= Aa

II-7: 200/200= aa

II-8: 100/400= AA

II-9: 200/200= aa

II-10: 100/200= Aa

II-11: 200/400= Aa

Answer the following question

1, 3, 5, 6, 10, 11

Answer the following question

Since it is autosomal dominant and we see that the dad who has the disorder along with the affected children with the disorder all have the 175 bp allele, it must be this

Answer the following question

Genetic and physical maps

What determine the order and distances of linked genes/loci?

recombination frequency (cM)

Genetic maps (aka linkage maps)= based on what?

DNA sequence (bp, Kb, Mb)

Physical maps= based on what?

Linkage mapping, association studies

Two approaches to genetic mapping:

- ______________= family-based, involves crosses in experimental organisms and pedigrees in humans.

- ____________= population-based, doesn't require crosses or pedigrees

Case-control studies

_______________= Large number of unrelated individuals with the trait vs. large number of unrelated individuals w/o the trait.

a trait and a molecular marker OR two molecular markers

STR (microsatellite) markers occur between...

STRs, SNPs

Linkage maps make use of _________.

Association studies make use of _________.

ok

Study this chart that shows the recombinant and non-recombinant alleles

ok

Look over the following pedigree and understand where the blood types come from and how the syndrome is passed on

LOD scores

______________ are used to determine if human genetic loci are linked

Logarithm of odds scores= What is the likelihood of obtaining the observed data if the two loci are linked compared to the likelihood of observing the same data purely by chance?

What does LOD scores stand for?

higher

High LOD scores means that the likelihood of linkage is ____________(higher/lower) than the likelihood of no linkage

A= Strong evidence for linkage (i.e. 1000:1 in favor of linkage)

B= Means that linkage can be rejected (exclusion mapping)

C= Inconclusive

Fill in the following blanks of the LOD chart

Far left

In the following genetic map, where is the genetic distance (in cM) between markers found?

In humans 1 cm= 1 Mb, in mice 1cm= 2 Mb.

What is the relationship between genetic and physical distances?

- A-B= Genetic distance is about what is expected based on physical distance.

- C-D= Genetic distance is smaller than expected because frequency of recombination in this interval is less than expected

- E-F= Genetic distance is larger than expected because frequency of recombination in this interval is more than expected

Look at the following maps and determine if the genetic distance is expected

recombination frequencies between loci

Genetic maps (or linkage maps) are based on ________________________ and provide information concerning the relative location of gene

directly analyzing DNA fragments

Physical maps are constructed by _______________ or DNA sequencing from a genome

Physical, genetic

___________ maps are more accurate than ____________ maps and provide higher resolution

Haplotype

_____________= a specific set of SNP variants that are closely linked and very rarely separated by recombination

Linkage disequilibrium (LD)

_______________ = frequency of alleles within a haplotype is higher than predicted by random association

Linkage equilibrium

__________________ = genotype frequencies at one locus are independent of genotype frequencies at the second locus

meiotic recombination

With each generation, ______________ swaps the alleles originally found at polymorphic loci on a chromosome where a mutation associated with a disease emerged, exchanging them for different alleles on the corresponding homologous chromosome

disease-associated haplotype.

Over many generations, the alleles that remain in coupling with the mutation are those at loci so close to the mutant locus that recombination between the loci is very rare. These alleles are in linkage disequilibrium (LD) with the mutation and form a ____________________.

case-control studies

GWAS are done by analyzing thousands of samples for DNA markers that span the entire genome, they are usually conducted through _______________

SNP microarrays

In GWAS, DNA samples from each person are hybridized to _____________.

Genome-wide association studies (GWAS)

______________= Systematic testing for association between millions of SNPs across the entire genome and disease phenotype

- Pedigrees are NOT needed.

- Large numbers of cases and controls (n> 1000) are needed.

- A SNP in association with a disease is not necessarily functionally involved in the disease.

- However, if a SNP is in linkage disequilibrium (LD) with the disease allele, then it is very likely to be closely-linked

What are characteristics of GWAS

- Statistical methods= contingency table or logistic regression.

- Significance levels= p< 0.05 for each marker.

In case-control studies for binary traits/diseases, what are the statistical methods and significance levels?

For each disease, −log10 of the trend test P value for each SNP is plotted against position on each chromosome. Chromosomes are shown in alternating colors, with P values > 10-5 in green (green dots= highly associated with the disease)

How would you interpret the following plot?

Some genes are expressed in all conditions, & some genes are expressed in only some conditions

Why does gene expression need to be regulated?

All= Constitutive expression of genes required for basic cellular functions.

Some= Inducible expression or repressible expression (response to environmental signals, nutritional signals, ect.)

What kind of expression is seen in all conditions? What kind of expression is seen in only some conditions?

Need to rapidly respond to environmental signals, & need to conserve energy

What are some examples of signals that affect gene expression in prokaryotes?

A= Transcriptional regulation,

B= Post transcriptional regulation

Fill in the blanks that match the following descriptions of different regulations

Structural genes

______________= encode proteins that function in metabolism, biosynthesis, or structural aspects of the cell

Regulatory genes

________________= encode regulatory RNAs or proteins that control expression of structural genes and/or their products

DNA-binding

Many transcriptional regulatory proteins have _________________ activity

Regulatory elements (regulatory sequences)

_________________= DNA sequences that are not transcribed but play a role in regulating other genes

Regulatory sequence

What are the DNA sequences that regulatory proteins or RNAs recognize and bind to?

Effectors

_______________= small molecules that bind to regulatory proteins and control their activity

trans-acting

Are effectors cis-acting or trans-acting?

C

Which of the following statements is TRUE of polymorphic microsatellite markers (also called simple tandem repeats, STRs)?

A) In the human genome, they occur much more frequently than single nucleotide polymorphisms (SNPs).

B) They have autosomal dominant inheritance.

C) For a particular microsatellite marker, the same pair of PCR primers are used to amplify different alleles of the marker.

D) All of these choice are true.

E) The vast majority have only two alleles.

True

True or False: Linkage disequilibrium (LD) is when the frequency of haplotypes in a population deviates from the frequency expected if there is random association of alleles at the different loci.

True

True or False: In mapping human genes, a LOD-score of 4 means that the probability of two genes being linked is 10000-times greater than the probability of them being unlinked.

Male 1

DNA fingerprints from four people (a mother, her child, and two men) involved in a paternity case are to the right. Note that thick bands indicate signals with twice the amount of DNA relative to thin bands. Based on these results, which man could be the biological father of this child?

III-6

Below is the pedigree for a family that carries an autosomal dominant disorder that has complete penetrance and invariable expressivity. The mutation causing this disorder is LINKED to a DNA marker locus with four alleles A, B, C, and D. The marker alleles present within each individual are indicate below the pedigree symbols. Which individual in generation III is likely to be recombinant?

IV-3

Below is the pedigree for a family that carries an autosomal dominant disorder that has complete penetrance and invariable expressivity. The mutation causing this disorder is LINKED to a DNA marker locus with four alleles A, B, C, and D. The marker alleles present within each individual are indicate below the pedigree symbols. Which individual in generation IV is likely to be recombinant?

Cis-acting elements

________________= Specific DNA sequences that are binding sites for regulatory proteins, can only influence expression of adjacent genes on the same DNA molecule.

Trans-acting elements

________________= DNA binding proteins, can diffuse through the cytoplasm and act at target sites on any DNA molecule in the cell.

DNA-binding proteins

________________ are often dimers and have highly specific interactions with specific base sequences.

nucleotides

In DNA binding proteins, domains of the polypeptide have amino acids that simultaneously make contacts with multiple _____________

hydrogen, nitrogen, and oxygen

In DNA-binding proteins, specificity is dictated by the unique patterns of ___________, __________, & _________ atoms of the nucleotides in the regulatory element

Regulatory elements (sequences)

_________________= often have inverted or direct repeats

DNA binding domains

________________= domain of a regulatory protein that binds to specific DNA sequences OR has general affinity for any DNA

Positive control & negative control

What are the two general modes for transcriptional regulation?

activator, stimulates

Positive control: regulatory protein is an __________ that __________ expression of target gene(s).

repressor, inhibits

Negative control: regulatory protein is a _____________ that ____________ expression of target gene(s).

Both modes occur in prokaryotes and eukaryotes

What mode for transcriptional regulation occurs in prokaryotes? Eukaryotes?

Effectors

____________ are proteins or small molecules that affect the function of regulatory proteins

Inducible

_____________ expression= transcription is OFF until it is activated

catabolic; lac operon

Inducible expression is often used to control transcription of genes that encode ____________ enzymes. Name one example.

Repressible

____________ expression= transcription is ON until it is repressed

anabolic; trp operon

Repressible expression is often used to control transcription of genes that encode ____________ enzymes; name one example.

Negative inducible regulation, positive inducible regulation, negative repressible regulation, & positive repressible regulation

What are the 4 types of regulatory systems? Memorize chart

Repressor binding to operator shuts of transcription (Left 2), No repressor binding to operon (Right 2)

Describe the 2 types of negative regulation

Inactive activator doesn't bind to promoter (Left 2), active activator binds to promoter (right 2)

Describe the 2 types of positive regulation

Operon

___________= set of functionally related structural genes transcribed from a single promoter

Operator

_____________= cis-acting regulatory sequence where trans-acting regulatory proteins bind and affect transcription

constitutively expressed

Regulatory gene is often ___________________, but binding of regulatory protein to the operator is dependent on effector (inducer or repressor) molecules

Glucose, glycolysis

___________ is the preferred energy source of E. coli and is metabolized through ____________

Lactose

______________ is one of many sugars that can serve as an alternate carbon source to glucose

galactose, glucose

Lactose must be actively transported into the cell and broken down into ____________ and ___________

- lacY, permease

- lacZ, β-galactosidase (β-gal)

Three structural genes are transcribed into a single mRNA:

- __________ encodes ___________, transports lactose into the cell

- _________ encodes _______________, breaks down lactose.

- lacA encodes transacetylase, poorly understood function

lac promoter (lacP), lac operator (lacO), Catabolite activator protein (CAP)

The lac regulatory region:

- _______________ binds RNA polymerase

- ______________ binds the lac repressor protein

- _______________ binding site

cAMP-CAP

_______________ is a POSITIVE regulator of lac transcription and glucose controls its binding to the CAP binding site