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191 Cards in this Set

  • Front
  • Back
What are 4 characteristics of autosomal dominant pedigree patterns?
o Appears in every generation
o No gender differences
o Fathers can transmit to sons
o 50% of heterozygote will be affected
o Limitations: small families
What are 4 characteristics of autosomal recessive pedigree patterns?
o Does not appear in every generation
o No gender differences
o Increased frequency in consanguinity
o Can skip generations
o 25% of 2 heterozygotes should be affected
What are 3 characteristics of sex-linked dominant pedigree patterns?
o Does not skip generations
o No father-son transmission
o Females more likely to show trait (2x as likely)
What are 4 characteristics of sex-linked recessive pedigree patterns?
o Does not appear in every generation
o Males more likely to show trait (only 1 X)
o Can skip generations
o Females are often a carrier
o No father-son transmission (man cannot give an x to a son)
Define penetrance
o The degree to which a trait is expressed in a population
Define expressivity
o Different manifestations of the phenotype in an individual
• Could be genetic background
• Could be environment
What is an STS? What is it derived from?
A Sequence Tagged Site:

o Sequence is present once per haploid genome
o Can be amplified by PCR
o Defines a unique site
What is an EST? What is it derived from?
EST is an expressed sequence tagged site

o Derived from cDNA
How many different molecules of DNA do we have?
24. 22 autosomes, 2 sex chromosomes.
How may base pairs in the human genome?
3 billion
How much of the human genome is conserved sequences?
How many genes do we have?
How many different molecules of DNA do we have?
24. 22 autosomes, 2 sex chromosomes.
How much of the human genome is comprised of transposons?
o Centromeres
o Telomeres
o Scaffolding attachment sites

are examples of what?
Extragenic sequences
hsp70 is an example of what?

What makes it interesting?
A small gene. It has no introns.
Is gastrin small or large? Why is it interesting?
Small. It has a split exon arrangement.
Give an example of a modular gene, and descrive its structure.

It is a trimeric helix.

Every third helical structure connects with a glycine.
Name a procollagen-mutation derived pathology and describe it in terms of severity.
Osteogenesis imperfecta. A small missense mutation is very severe, and dominant negative.

A major mutation is less severe.
allelic heterogeneity involves
locus heterogeneity involves
many genes, same phenotype is known as
locus heterogeneity
many exons, same phenotype is known as
allelic heterogeneity
is osteogenesis imperfecta recessive or dominant?
Dominant. Looks recessive. Parents are often mosaics.
CFTR is an example of what? What makes it interesting?
A large gene. Lots of introns.
Cystic Fibrosis is a good example of a gene with what kind of heterogeneity?
Low locus heterogeneity
Loss-of-function mutations always follow a _________ inheritance pattern
Gain-of-function mutations always follow a _________ inheritance pattern
What does ∆F 508 mean ?
Change in phenylalanine at amino acid location 508.
What kinds of mutations could cause cystic fibrosis?
• Defective protein production (could be anything)
• Defective protein processing (post translational)
• Defective regulation (maybe ATP)
• Defective conduction (membrane spanning domains)
• Defective splicing
Dystrophin gene is on what chromosome? What kind of inheritance does it present with?
The X. X-linked recessive.
Who is muscular dystrophy seen mostly in?
Males. They only need one X.
What is the Dystrophin gene a good example of?
A large gene. 2.3 million base pairs.

Alternative splicing patterns.

5' end has 2 promoters, 3' has 1.
What does acrocentric mean?
Short P arm
which are the acrocentric genes?
13, 14, 15, 21, 22
What do the acrocentric genes have in common?
They all code for ribosomal RNA
Where do the acrocentric genes congregate?
Together. In the nucleolus.
How do the genes for ribosomal RNA maintain such stability?
Non-allelic recombination.
Commonly utilized way of looking at inheritance pattern
Hemizygous refers to
Is dominant/recessive more appropriate at the organismic or cellular level?
When did the human genome project begin? How long did it take?
1990. Took 13 years.
What were 3 goals of the Human Genome Project?
Sequence Genome

Build databases

Come up with new ways to analyze it
What were the first three genomes sequenced?
E. Coli, Drosophila, Mouse
What industry did the HGP start?
What does ELSI mean?
Ethical, Legal and Social concerns
What were three stages in the genome project?
Genetic map (recombination frequencies)

Physical map (Sequence Tagged Sites) non-repetitive DNA

Identify polymorphisms (SNPs, RFLPs)
On average, how many differences in nucleotides between people do we see?
500-1000 bp
What is an antimorph?
A mutant expressing some agent that antagonizes a normal gene product.

Poison product.
Loss-of-function generally shows a __________ inheritance pattern
Gain-of-function generally shows a __________ inheritance pattern
OI has _______ ________ heterogeneity and _______ _______ heterogeneity
high allelic, high locus
Examples of large genes are
CFTR (Cystic Fibrosis Transmembrane Regulator)

Dystrophin Gene
What domain of CFTR is completely encoded by a single exon?
R-domain (Regulatory)
What does a highly-salty sweat suggest?
Improper chloride ion transportation in CF ion channel.
Is CF a high or low allelic heterogeneity disease?
Low. But it has a high one across populations.
How long does the Dystrophin gene take to transcribe?
16-24 hours
What pattern does Muscular Dystrophy follow?
X-linked recessive
How many exons does the dystrophin gene have?
How many promoters does the dystrophin gene have?
What does the product of dystrophin gene do?
mediates growth and stability of muscles
How many base pairs in the dystrophin gene?
2.3 million
Deletions and duplications are associated with
Frameshift mutations
Gene families are clustered or distributed?
Why would we need multiple copies of a gene? (3 reasons)
Redundancy (backup)

A large amount is needed

It can acquire novel characteristics
Why are ribosomal RNA and histone genes so widely represented?
A large amount of gene product is needed at certain times.
What is a pseudogene?
It is a non-functional member of a gene family. They may be remnants of mutated genes.
Why are ribosomal RNA genes considered to be a family?
They are all on acrocentric chromosome.
What chromosomes code the ribosomal RNA genes
21, 22, 13, 14, 15
Acrocentric centromeres have the centromere ___________
close to one end
Metacentric centromeres have the centromere ___________
in the middle
Where are ribosomal RNA genes located in the nucleus?
They are collected in the nucleolus, which makes ribosomal RNA.
How do ribosomal RNAs maintain such similarity?
non-allelic recombination
How does the y chromosome stay so homogeneous?
Non-allelic recombination. Like Ribosomal RNA.
Are the photopigments all alike?
Normal color vision is called _______ vision
Trichromatic vision
Red and green opsins are coded for on the _________ chromosome
The most common color blindness is called ____________ color blindness
Deuteranopia means
Can't see green.
Protonopia means
Can't see red.
Red-green genes have __________
an extra exon.
Every human has how many red and green genes?
1 and at least 1.
The difference between red and green lies in
exon 5.
What happens when we have internal duplications in chromosomes?
Ectopic pairing, unequal crossing over
Red-green fusions result in
anomalous color detection, but not color-blindness
Old-world monkeys have how many color genes? New world?
3, 2.
What are 2 main categories of extragenic DNA?
Unique and highly-repetitive
What are some examples of tandem or clustered repeat DNA
Satellite, microsattelite
What are some extragenic DNA examples that are unique?
Gene fragments, pseudogenes
Where is satellite DNA found?
What is the size of repeat of satellite DNA
5-171 bp
Where is minisatellite DNA found?
At telomeres
What is the size of repeat of minisatellite DNA
9-64 bp
What is the size of repeat of microsatellite DNA?
12 bp.
Where is microsatellite DNA found?
All over.
How did we used to study DNA in the past?
Biochemical methods. Density tests (buoyant). This is where the moniker "satellite" comes from.
What is a VNTR?
Variable Number of Tandem Repeats. This is often used in DNA fingerprinting.
What is an SSR or STR?
Short Simple Repeat or Short Tandem Repeat. Name for microsatellites.
What is the difference between a SNP and RFLP?
More opportunities for polymorphisms in RFLPs.
Most transposons are
Retrotransposons (transpose via RNA)
What sort of transposons are ALUs?
Non-autonomous. SINES. Short Interspersed Elements.
What sort of transposons are LINES?
Viral. Long Interspersed Elements.
How does a retrovirus work?
RNA copies itself into DNA (Reverse transcription) that integrates into DNA genome.
SSR stands for
Short Simple Repeats
STR stands for
Short Tandem Repeats
SSRs and STRs are examples of
LINES ________________________
SINES ________________________
Encode Reverse Transcriptase
Do not encode Reverse Transcriptase (ALUs)
LINES stands for
Long INterspersed Elements
SINES stands for
Short INterspersed Elements
A retroviruslike element is...
A transposable element that uses reverse transcriptase to transpose, through an RNA intermediate.
Transposons are able to gain easier access to promoter elements, why?
Because they are more accessible to modification.
What are some features of the retroviral family of transposons?

Give an example:
Long terminal repeats

Reverse transcriptase

This is an RNA-dependent DNA polymerase

These are non-specific (location-wise)


THE1 family
Where does a poly-a tail manifest?
messenger RNA, LINES
Non-viral family has no
Reverse transcriptase
SINES have no
Reverse transcriptase
LINES have reverse transcriptase that acts in __________
_______ and ________ have a __________ tail
LINES and SINES have Poly-A tails
The name Alu comes from...
A restriction enzyme
The most common sequence in the human genome is the ______, with about _____________ copies.
Alu, 1,000,000
The Alu sequence is believed to be originated in
The Alu looks like an
Imperfect dimer, missing b and d on left.
FRAMs and FLAMs refer to
Free Left and Right Alu Monomer
Where does RT come from for Alus?
Probably LINES.
How does neurofibromatosis?
An inserted Alu element in an intron screws up splicing.
DNA Methylation, most basically, is
a form of transcriptional regulation
What kind of DNA is more heavily methylated?
Why might methylation be useful in terms of retrovirii?
It could limit the expression of the retrovirus.
Are most genes regulated by methylation?
Most repetitive DNA is associated with
How many genes are imprinted? What is a mechanism for repression?
Fewer than 100. Methylation.
Methylation is significant in what 2 areas?
X-inactivation, imprinting.
Most methylation is at what carbon?
The 5th.
What is the process (chemical) of methylation?
SAM to SAH (S-adenosyl-methionine to S-adenosyl homocysteine)

via the 5th carbon of cytosine.

Cytosine to 5-methylcytosine.
All methylcytosines that are present are in
CpG dinucleotides, with a guanine at 3' position.
What are enzymes involved in methylation?
DNMT1 (DNA Methyltransferase 1)

DNMT 3a, 3b (DNA Methyltransferase 3a, 3b)
DNMT1 (DNA Methyltransferase 1) is involved in
Maintenance methylation of hemimethylated DNA
DNMT3a, 3b (DNA Methyltransferase 3a, 3b) is involved in
De novo methylation
CpGs are often found in
CpGs are ______________ than we would expect
less frequently found
What is a transition? In terms of nucleotides?

What is a transversion?
Purine to purine, pyrimidine to pyrimidine.

The opposite.
What happens in normal cytosine deamination?
Uracil DNA glycosylase fixes it.
What happens in methylated cytosine deamination?
It gets converted to Thymine.
CpG regions are clustered in
5' regions
What is the activator exclusion model, and 2 subtypes?
Methylation inhibits binding of transcription factors.

This can be done directly or indirectly.
What is the intermediate in indirect activator exclusion?
Methyl-C binding proteins
MeCP and MBD stand for
MethylC binding Proteins

Methyl binding Domain Proteins
What are the core histones?
H2a, 2b, 3, 4.
What is MeCP2?
It is a Methyl Binding Protein
What are the 2 steps in Methylation-associated chromatin modification?
1. DNMTs (MeCP2) recruit HDAc; repression
2. MBDs draw HDAc

Or, just MECP2, HDAc, MBDP, HDAc
Epigenetic code is heritable: T/F
Epigentic modification is like _______ in text.
ICF syndrome is due to
A mutation in DNAMT3b
In ICF Syndrome, which chromosomes are not affected?
1, 9, 16
What is a HAT?
Histone Acetyl Tranferase
What is Rett’s Syndrome?
It is X-linked, usually fatal in males
How is Cancer regulated by methylation?
Hypermethylation removes regulation expression
What is an HDAc?
Histone De Acetylase
How did the sex chromosomes evolve?
From autosomes
What does the Y do?
It determines maleness
Klinefelters is
Male. XXY
Turners is
Female. XO
Do the X and Y pair?
Yes. During Meiosis 1.
What is the PAR?
The Pseudoautosomal region
Where are the PARs?
Telomeric regions of p and q
What is the big male gene?
What does SRY encode?
What is TDF?
Testis Determining Factor
Are XXX or XO normal?
No. Haploinsufficiency, PAR genes.
When is significant about Y-chromosome appearance?
To detach from environmental cues
What are the ancestral X regions called?
What was surprising in the Y-chromosome?
The ampliconic region; much like the rDNA regions.
What is the Xi sometimes called?
Barr body
What is a good example of an x-linked disease affected by X-inactivation?
Duchenne Muscular Dystrophy
Name 2 characteristics of an inactive X
Replicates later in S-phase

Extensively methylated
What is the XIC?
X inactivation center;
Initiation and propogation
What is XIST?
X Inactive Specific Transcript
Start and Spread
What is the XCE?
X Controlling Element
What is TSIX
Regulates XIST in an antisense fashion
What is XCITE?
X-Intergenic Transcription Elements
Does choice require transient pairing? How do we know?
Yes. If we ablate the XIC, pairing does not happen, no inactivation.
Unequal X-inactivation can be due to
Tissue selection
What are proposed as way-stations for XIST RNA
LINES. Twice as abundant on X-chromosome.
What does XIST RNA recruit?
Histone Methyltransferase, Histone Deacetylase
What is the 2-factor model for TSIX?
X+Autosome factor = Active
Geonomic imprinting is only found in mammals? T/F
Define genomic imprinting
The differential activation of an allele depending upon the parent from which it is inherited
How may traits are uni-allelic?
Less than 100
When is the imprint made?
During gametogenesis
Is imprinting reversible?
Yes. It is usually sex-specific.
Name 2 diseases based in imprinting
Prader-Willi, Angelman’s syndrome
How is Prader Willi imprinted?