Genome Guided Medicine

• What is the size of the human genome? How many chromosomes, genes, and percentage that code
for proteins?
3.1 billion, 2 sets of 23 chromosomes one from each parent, 1.5%
• How do we explain that we only have about 25,000 genes, but 100,000 different proteins?
1. Epigenetic control: methylation and histone modification
2. Promotors
3. Alternative splicing
4. Post-translational modifications
• How many copies of the mitochondrial DNA are found in sperm vs oocytes
More mitochondrial DNA in oocytes
• How is the mitochondrial genome inherited?
Maternal inheritance
• What feature in the genome indicates a protein coding sequence?
Presence of open reading frame
• How much genetic code is shared between two unrelated humans (on average)?
99.9% ( only 0.1 =% difference)
• What are the two broad categories of SNPs?
Tolerated and deleterious
• What kind of technology is usually applied for SNP analysis?
Gene chip
• What is the difference between high prevalence/low penetrance and low prevalence/high
penetrance genetic disorders?
1. Common in the population but not expressed
2. Uncommon in the population but expressed
• How can linkage or family studies be used to find disease-causing genes?
By comparing the genome of related individuals and see if the mutation was passed down.
• What sorts of variations can happen in the human genome?
1. Single nucleotide polymorphism (SNP)
2. Indels (insertion and deletion)
3. Copy number variants
4. Chromosomal variants
• What is a genome-wide association study? What is the role of cases and controls?
1. The discovery of association between certain variations in our genetic code and a certain disease
phenotype by looking at the SNPs .
2. Comparing between the cases and the controls, if a certain SNP is more frequent in the cases, that
might mean its associated with the disease.
• What is pharmacogenomics? How can genomics be helpful in selecting cancer treatments?
• It is the study of how genes affect drug response then tailoring the patient’s meds according to
their genes.
• If we know our patient’s genome, we prevent prescribing them meds that might be toxic or show
no effect due to their genetic compositions.
Single Gene Inheritance
• For each of the following, list the meaning, and the expected characteristics on a pedigree chart:
o Autosomal recessive
Two alleles are needed to show a phenotype
- Equal presence in male and female
- Skip generations
o Autosomal dominant
One allele is enough to show a phenotype
- No skipping of generations
 - Equal presence in male to female ratio
o X-linked recessive
- Male> female
- Skip generation
- No male to male transmission
o X-linked dominant
- Female>male
- No skipping in generation
- No male to male transmission
- Affected male= all affect female offsprings
• Why are persons with autosomal dominant disease almost always heterozygotes?
1. If it was homozygous it won’t be compatible with life
2. Rarity of the disease (1/10,000)
• In a case of autosomal recessive disease, what is the probability that an unaffected child of
heterozygous parents will be a carrier of the disease?2/3
• What is the coefficient of relationship between 2nd degree cousins? 1/32
• What is the difference between a X-linked trait and a sex-limited trait?
Sex-linked= gene is located on a sex chromosome, sex-limited= gene present on autosomal
chromosome but express a phenotype in one sex.
Non-Classical Inheritance
• What is the difference between allelic and locus heterogeneity?
Different abnormalities on the same loci cause the same phenotype, Locus heterogeneity: Different
abnormalities on different loci cause the same phenotype
• What is pleiotropy? Give an example.
Pleiotropy is when a mutation affects multiple organ, ex. Marfan disease
• What is the distinction between variable penetrance and variable expressivity?
1. Variable penetrance, is different level of phenotypical expression [An individual with an abnormal
genotype doesn’t always expresses the disease phenotype]
Variable expression, which is when a genotype is present but no phenotype is expressed
• What are incomplete dominance and codominance?
Incomplete dominance is when both phenotypes are expressed and mixed together. Codominance,
is when both phenotypes are EQUALLY expressed
• What is germline mosaicism?
Is when mutation is present in a sperm or ova but not in somatic cells
• What is somatic mosaicism?
Mutation is present in somatic cells [A mutation in the somatic cells that show affect at different part
of the body. Cant be passed down.]
• Why might a given X-linked disease only be seen in females?
It might be fatal in men if expressed
• Non-classical inheritance
o What is uniparental disomy?
Both chromosomes are from one parent
o What are trinucleotide repeat disorders?
Multiple repeats of trinucleotide that disrupt the gene dosage and cause a mutation
o How is mitochondrial inheritance non-classical? What is the effect of heteroplasmy on
disease severity for mitochondrial diseases?
Mitochondrial inheritance= Maternal inheritance. Heretroplasmy= different levels of
mutation in the mitochondria. The % determine if it is a mutation or normal gene

DNA Replication, Damage, and Repair

• When in the cell cycle is the DNA replicated? At what stage is the chromosome number and
alignment checked?
 S phase, Metaphase
• How are the two strands of DNA replicated differently?
Antiparallel strands. Leading strand is continuous while the lagging is discontinuous form the
okazaki fragments
• Describe the role of the following proteins in DNA replication:
o Single-stranded DNA binding proteins: Prevent reannealing of the strands, stabilize single
stand DNA and attracts proteins
o Helicase: unwind helix or duplex
o Primase: Create primer
o Topoisomerase: alter the supercoiling of double-stranded DNA, act as swivels
o Sliding clamp: make DNA synthesis processive
o Clamp loader: Open the clamp (use ATP)
• How are the bits of RNA in the newly synthesized strands removed? By a specialized nucleases
(DNA pol 1)
• How does telomerase ensure the fidelity of the chromosomes?
Synthesis of DNA from RNA template, Add repetitive TTAGGG units, the extended end serves as a
template for priming lagging stand synthesis
• For each of the following repair methods, list:
o the kind of damage repaired
o the errors it can introduce (if any)
o basic mechanism
o whether it is single- or double-stranded
o a disease associated with failure in that method
Do this for the following repair methods
o Base excision repair
o Nucleotide excision repair
o Transcription-coupled repair
o Mismatch repair
o Homologous recombination
o Non-homologous end joining
Kind or damage Error it can Basic Single or double Disease ex.
repaired introduce mechanism stranded
Mismatch Mismatch bases Single Colon cancer
repair
Base excision Remove endogenous Single Neurogenerative
repair events Ex. disease
Depurination or
deamination
Nucleotide Environmental damage Single X-derma
excision repair pigmentosum
Homologous genetic recombination After DNA Double Breast cancer
recombination that occurs during replication
meiosis
Non genetic recombination G1 Double SCID
homologous that occurs during
recombination meiosis between non
homologous
chromosomes
Transcription RNAP II repaired Single
coupled repair
Transcription RNA DNA
• In what ways does RNA differ from DNA? Nucleotide Uracil Thymine
Sugar Ribose Deoxyribose
• What are the minimal requirements for Stands Single Double RNA
synthesis?
DNA template, UTP instead of TTP, NO primer is needed, 5’-3’ direction, DNA dependent RNA pol:
pro= 1 RNA pol, Euka= 3 RNA pol
• What marks the start site in eukaryotic transcription?
TATA box
• What are the 5’ and 3’ post-transcriptional modifications? What is their significance in translation?
5’ Cap, 3’ poly A tail. Inc stability of the RNA. Processed RNA will be called mRNA, transported to
cytoplasm for translation
• Define the following terms (as they apply to eukaryotic genes): upstream, downstream, promoter,
UTR, exon, intron.
Upstream: Left, where transcription start. Downstream: right, where transcription ends.
Promoter: sequence of DNA needed to turn a gene on or off. UTR: untranslation region. Exon:
coding region of mRNA. Intron: Non-coding region in DNA
• Describe how splicing works.
A branch attach G donor site. 1-G attack is 2’-5’. Lariat is created.
Introns are removed from the pre-mRNA by the spliceosome and exons are spliced back together
• What unique post-transcriptional processing is done on rRNA?
Chemical modification, cleavage, 18S= small ribosomal subunit, 5S+28S= Large ribosomal subunit

Translation
• Describe the function of the three sites of the ribosome
E site: where growing chain exist, P site: hold tRNA with growing chain, A site: accepts tRNA with
bound to a.a
• Describe the structure of tRNAs, including where the anticodon and amino acid attachment sites
are located.
tRNA clover structure. Codon-anticodon attach at anticodon loop. aa attach to 3’ end at ACC aa
• Describe how tRNAs get loaded with amino acids.
Aminoacyl tRNA synthase -use ATP- enzymes that catalyza coupling of aa to it’s tRNA
• What is the role of the wobble base interactions in decoding the nucleotide signal?
Wobble is to 3rd base, multiple codons can code for a single amino acid
• Describe the process of elongation of the peptide chain.
The ribosome continues to translate each codon in turn. Each corresponding amino acid is added to
the growing chain and linked via a bond called a peptide bond. Peptide bond is formed by peptidyl
transferase at A site.
• What are key signals for termination of translation?
Stop codon reach A site, release factors (eRF1 and 2)
• How is proofreading done by the ribosome?
1. Pro: EF-Tu and EF-G. Euka: eEF1 and 2
2. Coupling GTP hydrolysis to transition in the different ribosome states allows for faster protein
synthesis
3. rRNA folds around the codon-anticodon interaction site is influences by correct base pairing
which trigger GTP hydrolysis by GTPase
• How can the ribosome be used as a target for antibiotics?
Aminoglycosides: inhibit prokaryotic translation. Chloramphenicol: binds at the peptidyl transferase
center within the large subunit
• Where are proteins usually synthesized? What are exceptions?
 Cytoplasm. Except mitochondrial proteins. Mammalian cells are compartmentalized
• When do proteins usually fold?
During translation

Cytogenetics
• What is karyotyping? What is the purpose of stains in karyotyping?
The process by which photographs of chromosomes are taken in order to determine any
chromosomal abnormalities. Staining to identify structure in DNA. G bounding – AT rich DNA (use
trypsin). Dark band= gene poor
• Chromosome rearrangements
o How clinically significant are duplications?
Affect the gene dosage. Duplication involve 5% of haploid human genome
o What is the evolutionary importance of gene duplications?
Produce new gene functions.
o What is the difference between terminal and interstitial deletions?
Terminal deletion= Loss of the end of the chromosome= Single break. Interstitial= two
breaks are induced
o How do deletions lead to the phenomenon of psuedodominance?
When dominant allele is deleted, thus recessive allele phenotype is expressed
o What is the difference between paracentric and pericentric inversions?
Paracentric= Away from centromere
Pericentric= Inversion around the centromere
o What are Robertsonian translocations? Are they reciprocal or not?Chromosomal
translocation with fusion of the long arms of the acrocentric chromosomes 14 and 21in a
female individual. The short arms of the two chromosomes involved are lost. yes

• Aneuploidy
o Which are the few human aneuploidies consistent with human life?
Down syndrome, and sex chromosome aneuploidies: turner (single X female), Klinfelter
(double x male)
o What kinds of aneuploidy are there?
§ Nul (-2)
§ Mono (-1)
§ Tri(+1)
§ Tetra(+2)
o When does the error that leads to aneuploidy occur?
§ Non-disjunction in miosis 1: homologues chromosomes not separating
§ Non-disjunction in miosis 2: sister chromatids not separating
o What is the main risk factor for trisomy? Maternal age
o What is uniparental disomy? 2 copies of a chromosome come from the same parent, instead
of 1 copy coming from the mother