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237 Cards in this Set
- Front
- Back
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How many base pairs in the human genome?
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6.3 billion
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How many genes in the human genome?
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35,000
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T/F The complexity of the human phenotype is explained by our species' significantly higher number of genes?
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False
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What factors might explain an increase in complexity with regard to the human phenotype?
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multiple polymorphisms (SNPs)
tissue-specific splice variation post-translational modification variable expression of genes |
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The human genome is organized into two separate genomes. What are they?
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Nuclear and Mitochondrial
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How many genes in mitochondrial DNA? How many of these are protein-encoding?
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37, 13
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What is unique about the shape of the mitochondrial DNA?
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Circular
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What is unique about the gene sequences of mitochondrial DNA?
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They are contiguous, no introns
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T/F Some mitochondrial genes overlap
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True
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T/F Both nuclear and mitochondrial DNA have histone complexes?
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False
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Mitochondrial DNA has (maternal / paternal) inheritance.
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Maternal
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T/F The majority of mitochondrial proteins are encoded by the mitochondrial genes themselves.
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False
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How many chromosomes make up the nuclear genome?
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23
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Define heterochromatin
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densely packed regions of chromosomes (centromeres)
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T/F Heterochromatin and euchromatin are both transcribed.
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False, heterochromatin in not transcribed
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Define euchromatin
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less densely packed chromatin
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What percentage of the nuclear genome is made up of genes?
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35%
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What percentage of genes make up protein-encoding regions?
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5%
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T/F Extragenic DNA has a significant role in gene evolution, structure and regulation of transcription levels.
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True
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Define retrotransposon
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RT copy themselves and other elements and reinsert back into the genome
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Give an example of an autonomous retrotransposon
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LINE
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The Alu sequence is an example of what type of retrotransposon?
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SINE
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What is the size requirement for a LINE?
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> 5kb
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How would you categorize satellite DNA?
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A non-transcribed highly repetitive DNA element
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Where do you commonly find rRNA genes?
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in satellites of acentric chromosomes (13,14,15,21)
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rRNA makes up what percentage of the human genome?
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10%
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Give an example of a moderately repetitive DNA element?
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mini-satellites (VNTRs)
microsatellites (STRs) telomeric sequences rRNA and tRNA genes |
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Satellite DNA is transcriptionally (active/ inactive)
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inactive
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Satellite DNA makes up most (heterochromatin / euchromatin)
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heterochromatin
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Where do you find satellite DNA?
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clustered at the centromere
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What type of satellite DNA is found on all chromosomes and plays an important role in centromere function?
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alpha satellite
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Define telomere
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A specialized structure that caps the ends of chromosomes leaving no free-end tot he DNA.
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What base pairs, when repeated, constitute a telomere?
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TTAAAGGG
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What maintains the telomere length?
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telomerase
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The average gene has how many bp?
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3000
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What is the largest human gene?
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dystrophin (2.4 million bp)
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Which chromosome has the most genes? Which has the fewest?
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1, Y
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What does it mean to say that humans have "interrupted" genes?
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The genetic structure is comprised on exons (encoding regions) and introns (non coding regions)
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Define a UTR
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DNA sequence that is transcribed into RNA but not translated into protein
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What is the functino of UTRs?
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Regulate rate of transcription, determine the destination of mRNA, regulate the binding and stabilization of mRNA on ribosomes during translation
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What are some elements commonly found in the promoter region of the gene?
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CAAT box, TATA box
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What codon signals the transcription process to initiate?
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ATG
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What genetic sequence signals the transcription process to end?
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the PolyA tail
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What are the basic components of a nucleotide?
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Pentose sugar, nitrogenous base, phosphate group
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What are the basic components of a nucleoside?
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Pentose sugar, nitrogenous base
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The difference between ribose and deoxyribose is a ______ group attached to the _____ carbon.
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hydroxy, 2'
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The phosphodiester bonds of DNA are formed by phosphodiester groups attached to the ______ carbon of one sugar and the ______ carbon of the other.
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5' ; 3'
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Polymerization of polynucleotides occurs at the ____ end.
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3' hydroxyl
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T/F Human DNA forms a left-handed helix
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False, Right-handed
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T/F Hydrophobic bases face toward the inside of the helix
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True
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Where on the DNA helix do transcription factors interact?
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Major groove
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T/F DNA is only capable of forming a double helix
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False
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T/F Human DNA is alpha DNA
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False, Human DNA is beta
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What is another name for the short arm of DNA? The long arm?
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p, q
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At the 10nm stage, the DNA resembles what?
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Beads on a string
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At the 30nm stage, DNA resembles what structure?
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A chromatin fiber
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Name three types of excisional RNA
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snRNA, snoRNA, scRNA
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Where does transcription take place within the cell?
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Nucleus
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Where does translation take place within the cell?
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Cytoplasm
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T/F DNA synthesis associated with DNA repair occurs in all phases of the cell cycle.
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True
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In what phase of the cell cycle does DNA replication occur?
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S
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What are the steps in DNA replication?
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Initiation, Elongation, Joining/Termination
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What is the name of the protein complex that recognizes the origin of replication?
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Primosome
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What are the steps involved in itiation of DNA replication?
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The primosome recognizes the origin of replication
Separation of the parental strands Stabilization of exposed DNA |
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Which polymerase is the main polymerase in DNA replication?
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alpha
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Which polymerase repairs DNA?
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beta
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Which polymerase replicates mitochondrial DNA?
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gamma
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Which polymerase works on the leading strand and has exonuclease activity?
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delta
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What are the steps of elongation?
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helicase adn gyrase unwind the DNA strand
The replisome moves along DNA pol alpha and delta synthesize daughter strands |
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What is the processivity of DNA?
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1000 bases/min.
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What prevents unwound DNA from rewinding?
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SSBs
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What is the function of primase?
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synthesizes RNA primers on lagging strand
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What does DNA ligase do?
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connect ozakaki fragments
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What does topoisomerase do?
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prevent supercoiling
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What synthesizes the lagging strand?
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Pol alpha
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What enzyme is key to the function of telomerase?
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hTERT
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Give an example of a spontaneous deamination.
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Cytosine --> uracil
5-methylcytosine --> thymidine |
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Give an example of a spontaneous depurination.
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Guanine --> No base
Adenine --> No base |
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Repair occurs during which phase of the cell cycle?
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G1/S checkpoint
G2/M checkpoint |
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Define locus
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A specific location on a chromosome
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Define allele
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an alternate form of a gene
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Define mutation
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quantitative or structural chane in genetic material which may or may not lead to a change in the phenotype of the organism
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Define polymorphism
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When two or more variables (alleles) are present in a given population with a frequency of >1% (can be disease or non-disease causing)
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What type of mutations are the basis of tumor formation?
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Somatic
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What is the mean heterozygosity of the human genome?
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0.08%
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What is meant by allelic heterogeneity?
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Different mutations in the same gene can cause the same phenotype
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What is meant by locus heterogeneity?
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Mutations in different genes can cause the same phenotype.
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BRCA 1 and BRCA 2 are both associated with familial breast/ovarian cancer. This is an example of what?
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Locus heterogeneity
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What is meant by clinical heterogeneity?
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Mutations in the same gene can cause different phenotypes
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Define pleiotrophy
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A mutation within a single gene that affects multiple seemingly unrelated organ systems
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What group of disorders are known to be especially pleiotrophic?
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mitochondrial
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What are the four broad categories of genetic disease?
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Monogenic, chromosomal, polygenic, somatic cell defects
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What broad category do most genetic disorders fall under?
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Polygenic (multifactorial)
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What are some categories of chromosomal disorders?
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Polyploid, aneuploid, deletions, inversions, insertions, translocations, isochromosomes, dicentric or ring chromosomes
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Do multifactorial (polygenic) disorders display classical mendelian inheritance pattern?
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No
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Inborn errors of metabolism fall under a unique category of multifactorial disorders called what?
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Synergistic heterozygosity disorders
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Define penetrance
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The % of individuals with a specific genotype that express the associated trait or phenotype
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Define expressivity
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The variation in phenotype seen in affected people with the same genotype. "measure of affectedness"
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In the phrase "genomic imprinting", the "imprinting" refers to what?
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The silencing or turning off of a gene.
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How does imprinting take place
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methylation of chromosomal regions and regulatory elements
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T/F Imprinting patters are inherited
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True
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Genomic imprinting renders affected genes functionally ____________.
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Haploid
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Genomic imprinting is the basis for which two diseases?
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Prader-Willi
Angelman |
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Define mosaicism
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When two or more genetically different cells arise from the same zygote
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Define chimerism
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When two or more genetically different cells arise from different zygotes
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What percentage of Mendelian diseases are dominant?
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50
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What percentage of mendelian diseases are recessive
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35
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What percentage of mendelian diseases are x-linked
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10
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What type of disorder is Marfan syndrome?
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AD
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What type of disorder is neurofibromatosis I?
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AD
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What type of disorder is achondroplasia?
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AD
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Cafe au lait spots are indicitive of what disorder?
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Neurofibromatosis I
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What is a compound heterozygote?
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An individual with two damaged alleles that are each damaged at different loci
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The majority of inherited cancers demonstrate what inheritance pattern?
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AD
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Who had the 2-hit theory of cancer?
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Knudson
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What type of disorder is Tay-Sachs?
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AR
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What type of disorder is Galactosemia?
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AR
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What type of disorder is PKU?
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AR
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What type of disorder is CF?
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AR
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Which is more common, XLD or XLR?
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XLR
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What type of disorder is Rett syndrome?
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XLD
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What type of disorder is hemophilia A?
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XLR
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What type of disorder is muscular dystrophy?
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XLR
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What type of disorder is Alport syndrome?
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XLR
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What type of disorder is G6PDH deficiency?
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XLR
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T/F Affected males never transmit a mitochondrial disease.
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True
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T/F Affected females transmit a mitochondrial disease to all offspring regardless of gender.
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True
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Define heteroplasmy.
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There are variable numbers of mitochondria per cell (2-100). Zygotes receive different ratios of normal and abnormal mtDNA via the mother.
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Which phase of the cell cycle is the longest?
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Interphase
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At which phase of the cell cycle are chromosomes generally analyzed?
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Metaphase or prometaphase
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What are the three most common causes of chromosome abberations?
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malsegregation of chromosomes during mitosis or meiosis.
improper recombination during meiosis misrepair of broken chromosomes |
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Describe constitutional chromosomes abberations.
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Present in all cells, occur early in development, many are embryonically lethal
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Define euploid
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The normal chromosome complement.
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Describe metacentric chromosomes.
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Centromere is in/near the center.
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Describe submetacentric chromosomes.
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Centromere is non centrally located, but two distinct arms are visible
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Describe acrocentric chromosomes.
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The centromere is located far enough at one end of the chromosome that the p arm is almost missing.
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Describe telocentric chromosomes.
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The centromere is located at one extreme end of a chromosome
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Define polyploidy
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Extra sets of chromosomes
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Define aneuploidy
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Deleted or extra individual chromosomes. Ex. monosomy, trisomy
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What is trisomy 13?
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patau Syndrome
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What is trisomy 18?
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Edwards
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What is Klinefelter's?
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XXY
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What is Turner's
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X
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What are the two most common causes of aneuploidy?
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non-disjunction, anaphase lag
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Is a deletion an example of a balanced or an unbalanced chromosomal abnormality?
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unbalanced
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What type of disorder is Cri-du-chat?
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microdeletion
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Describe a robertsonian translocation.
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Breakage and head-to-head fusion of 2 acrocentric chromosomes.
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What type of disorder is AML?
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an inversion in chromosome 16
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What causes the formation of isochromosomes?
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abnormal exchanges between sister chromatids, close to centromeres. The two p arms might separate from the two 1 arms.
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What causes the formation of ring chromosomes?
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A chromosome breaks in two places adn the ends of the chromosome arms fuse together
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Distinguish between Double minutes and Episomes.
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DMs are small (500kb - 50MB) , paired acentric extrachromosomal fragments. Epismoes are the same but less than 100Kb
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Define the following abbreviations:
del inv dup inv dup r i dic t ins |
deletion
inversion duplication inversion & duplication ring isochromosome dicentric translocation insertion |
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Is the enhancer a cis or trans acting element?
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Cis
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Is the promoter a cis or trans acting element?
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Cis
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Are the transcription fractors cis or trans acting elements?
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Trans
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What is the function of RNA pol I
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Transcribes most rRNA genes
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What is the function of RNA pol II
|
transcribes most structural genes that encode protein (mRNA snRNA miRNA)
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What is the function of RNA Pol III
|
transcribes tRNA genes adn 5S rRNA
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What is the function of RNA pol IV
|
mitochondria
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What are the three levels of control with regard to gene regulation?
|
transcriptional control
post-transcriptional control epigenetic control |
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What is an example of epigenetic control?
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methylation
histone modification |
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What is the predominant level of gene regulation?
|
transcriptional control
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Define epigenetic
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genetic changes that are heritable but do not depend on changes in genome sequence
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Is the TATA box a cis or trans acting element?
|
CIS
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Is the CAAT box a cis or trans acting element?
|
cis
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Is the AP site a cis or trans acting element?
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cis
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Where is the core promoter located?
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-45 to +45
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Where is the proximal promoter located?
|
-50 to -200
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What is unique about tRNA promoters?
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They lie within the gene rather than upstream of it
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What do Histone acetyltransferases do?
|
They add acetyl groups to histones adn activate transcription
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What do histone deacetylases do?
|
remove acetyl groups
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Name four methods of DNA repair
|
Direct, Excision, Post-replication, mismatch
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Define uniparental diSOMY
|
Both genomes originate from same parent
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The abnormal 46XX conceptus of exclusive maternal origin lead to:
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ovarian teratomas
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The abnormal 46XX conceptus of exclusive paternal origin lead to:
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hydatidiform mole
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Hydatifform moles have a significant risk of transforming into a ______________
|
choriocarcinoma
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List and define the two types of UPD
|
Heterodisomy - both homologues from one parent
Homodisomy - 2 identical copies of the same gene |
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UPD is frequently the basis for which two genetic disorders?
|
Prader-Willi, Angelman's
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Describe an individual with prader-willi
|
hypotonia
morbid obesity cognitive impairment behavior problems hypogonadism, infertility short stature |
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Describe an individual with angelman syndrome
|
happy puppet
ataxia microcephaly severe learning disability poor weight gain |
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In PWS, expressed genes are only of (maternal / paternal) origin.
|
maternal
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In AS, expressed genes are only of (maternal / paternal) origin.
|
Paternal
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PWS and AS both have a chromosomal abnormaily in what region?
|
Deletion of 15q11-13
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The chromosomal abnormality in Angelman's syndrome causes an increased expressioin of _______________
|
UBE3A
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What is the most common type of mutation in the human genome?
|
Point mutations / polymorphisms
SNPs |
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What are the three types of point mutations
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SN substitution
SN insertion SN deletion |
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Transitions and Transversions are types of _____________
|
SNPs
Point Mutations |
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A transition is a ______________ to a ___________.
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purine, purine
pyrimidine, pyrimidine |
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A transversion is a ___________ to a ____________
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purine, pyrimidine
pyrimidine, purine |
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What is a silent mutation?
|
Nucleotide subsitiution, but amino acid remains the same
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Changes in which of the following bases within a codon are least likely to cause a phenotypic change:
1) 1 2) 2 3) 3 |
3
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Define missense mutation and list the two categories of missense mutations.
|
chagnes the amino acid. can be conservative (change to similar aa) or non-conservative (change to functionally different aa)
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Repetitive DNA sequences:
1) comprise about 30% of human genome 2) include ALU sequences 3) include VNTR's and STR's 4) include telomeric sequences 5) all of the above |
5) all of the above
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What level of G-banding resolution does the chromosomal designation 4q21.23 describe?
|
sub-sub-band
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What factors might explain why some individuals with the same disease genotype show variable disease severity?
|
modiying genes, differential methylation patterns, mosaicism, effect of environmental factors
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Which type of RNA is part of the spliceosome?
|
snRNA
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What percentage of the genome encodes for protein. What percentage of gene sequences encode for protein?
|
<10%
<5% |
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Name all of the highly repetitive transcribed DNA elements:
|
Retrotransposons, LINES, SINES, LTR's
|
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Name all of the highly repetitive non-transcribed DNA elements:
|
Satellite DNA, DNA transposons
|
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Name all of the moderately repetitive transcribed DNA elements:
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rRNA genes, tRNA genes
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Name all of the moderately repetitive non-transcribed DNA elements:
|
minisatellites (VNTRs), microsatellites (STRs), telomeres
|
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Telemores are technically what type of DNA element?
|
minisatellites
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What sequence constitutes a telomere? How many times must it be repeated?
|
TTAGGG, 5-20
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LINEs make up what percentage of the human genome?
|
21%
|
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SINEs make up what percentage of the human genome?
|
13%
|
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List some examples of genes with highly conserved domains/motifs.
|
histones, alpha globins, beta globins, immunoglobulins, TCR genes, HLA genes, HOX genes, PAX genes
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How did gene familes likely arise?
|
Due to gene duplication and subsequent divergence.
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Define pseudogene
|
Defective copy of a functional gene.
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Nucleic acids are polymers of __________
|
nucleotides
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The nitogrenous base attaches to the ____ carbon of the pentose sugar.
|
1'
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List some base modifications found in the human genome:
|
5mC, inosine
|
|
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miRNA controlls the expression of mRNA via __________ ______________.
|
steric hendrance
|
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T/F DNA replication is initiated at multiple sites of origins every 50 to 100kb
|
True
|
|
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T/F DNA replication occurs bi-directionally
|
True
|
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During DNA replication, which polymerase forms an RNA primer to initiate the replication process?
|
DNA pol alpha
|
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Which DNA polymerase(s) have exonuclease acitivity?
|
only delta
|
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DNA primase is comprised of what polymerase?
|
DNA pol alpha
|
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How long does each cell take to complete replication and proofreading?
|
4 to 8 hrs
|
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What are the four most common sources of DNA damage?
|
spontaneous depurination & deamination, replication, recombination, endog. & exogenous damaging agents
|
|
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How often do DNA polymerases encorporate an incorrect base?
|
1 every 10^6 to 10^10 bases
|
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What are the two types of excision repair?
|
BER, NER
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Define Base Excision repair
|
removes and replaces a single damaged nucleotide
|
|
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Define Nucleotide Excision repair
|
removes and replaces longer stretches of damaged nucleotides (2-30 bases)
|
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At least 8 different DNA glycosylases are used in which type of repair?
|
BER
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List the 7 mismatch repair genes:
|
MLH1, MSH2, MSH3, MSH6, PMS1, PMS2, GTBP
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Name a disease related to MMR deficiency?
|
HNPCC
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What are the two levels of genetic testing for HNPCC
|
Microsatellite instability testing, detection of mutation in MMR genes
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Forward slippage of DNA polymerase during replication leads to ____________
|
deletions
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Backward slippage of DNA polymerase during replication leads to ______________
|
insertions
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What does a test in HNPCC patients of tumor versus germline pattern in the same patient tell us
|
whether an expansion/contraction of repeats has occured in the tumor. Indicates slippage
|
|
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If an individual is positive for HNPCC what are the likely results of an MSI test?
|
They will be high. Greater than 1/5 of loci
|
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What causes xeroderma pigmentosum
|
a defect in any of 7 different NER enzymes
|
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What type of DNA damage is common in xeroderma pigmentosum patients exposed to UV light?
|
pyrimidine dimers
|
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Familial brest and ovarian cancer are caused by what?
|
Errors in BRCA1 and 2 that inhibit the cell from repairing DSBs
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|
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Name a disease that is related to an impaired cellular response to DNA damage:
|
Fanconi's anemia, li_fraumeni Syndrome
|
|
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General transcription factors bind where on teh DNA sequence during transcription?
|
Core promoter
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What amino acids in histones to methyltransferases target?
|
arginine adn lysine
|
