Trans - Human Genome Flashcards
2
Q
Percentage of genes in genome
A
2-3%
3
Q
Correlation between genome size and organism complexity
A
None
4
Q
Definition of telomere
A
Ends of chromosome
5
Q
Original definition of genome
A
Collection of genes contained within a haploid chromosome set
6
Q
Modern definition of genome
A
Locatable region of genomic sequence corresponding to a unit of inheritance associated with regulatory regions, transcribed regions, and/or other functional sequence regions
7
Q
Definition of centromere
A
Central region of chromosome
8
Q
Arms of chromosome?
A
Chromatid
9
Q
Shorter arm of chromosome
A
P arm
10
Q
Longer arm of chromosome
A
Q arm
11
Q
Number of rings in purine
A
Two
12
Q
Number of rings in pyrimidine
A
One
13
Q
Which bases are purines?
A
Adenine, Guanine
14
Q
Which bases are pyrimidines?
A
Cytosine, Thymine
15
Q
Correlation between GC content and melting point
A
Higher GC content, higher melting point
16
Q
Which is more preferred for expression? AT or CG?
A
AT
17
Q
Correlation between GC content and level of expression
A
Higher GC content, more silenced genes
18
Q
Definition of intron and exon
A
[1] Intron –> region of DNA not expressed;
[2] Exon –> expressed region of DNA
19
Q
Parts of the UTR/Leading sequence
A
[1] Enhancer
[2[ Promoter
[3] Operator
[4] Consensus sequence
20
Q
Consensus sequence in a) prokaryotes, b) eukaryotes
A
[A] Pribnow box (TATAAT);
[B] Hogness box (TATA)
21
Q
Parts of coding sequence
A
[1] Start codon (AUG);
[2] Introns and exons;
[3]. Stop codon (UAA, UAG, UGA)
22
Q
Number of bonds in CG linkage
A
3
23
Q
Name and define the regions associated with the alternating introns and exons
A
[1] Pre Region –> signal region, determines where the protein will go;
[2]. Pro Region –> determines posttranslational modification
[3] Mature Region –> encodes the protein
24
Q
Parts of the UTR/trailing sequence
A
[1] 2nd termination signal
[2] Cleavage signal (AAUAA) containing poly-A tail
25
Q
Central dogma of molecular biology
A
[1] Replication –> DNA duplication;
[2] Transcription –> RNA synthesis
[3] Translation –> protein synthesis
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Definition of open reading frame
Region of DNA corresponding to coding sequence
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Composition of human genome
[1] euchromatic portion;
| [2] constituitive heterochromatin
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Where can constituitive heterochromatin be found?
[1] Centromeres;
[2] Long arm of Y chromosome
[3] Short arm of acentric chromosomes (13, 14, 15, 21, 22)
[4] Secondary constriction of long arm of 1, 19, 16
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Percentage composition of bases in genome
GC --> 41%; AT --> 59%
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What are Giemsa bands?
[1] Dark bands --> low GC, 37%
[2] Light bands --> high GC, 45%
both bands seen in karyotype
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Number of base pairs in human genome
3200 M
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Number of genes in human genome
30,000 - 35,000
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Percentage of genes coding untranslated RNA
5-10%
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Mechanism of gene distribution
Hybridization of CpG islands to metaphase chromosomes
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Composition of nuclear genome
[1] 95.5% noncoding DNA
| [2] 4.5% conserved DNA --> 3% untranslated & regulatory, 1.5% coding DNA
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General trend in abundance of euchromatin and heterochromatin in genes
Chromosome 1 has highest amount of euchromatin and heterochromain, amount decreases as chromosome number increases
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Definition of pseudogenes
Multiple copies of genes serving as rescue genes in case original genes get damaged
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Number of BP in mitochondrial genome
16,569
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Number and characteristics of genes in mitochondria
37 genes --> 22 tRNA, 2rRNA, 13 protein coding
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[T/F] mitochondrial genes have introns
F
41
Structure and significance of D-loop in mitochondrial genome
Triple stranded region, origin for replication of mitochondrial genome
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Endosymbiont theory
Mitochondria may have originated from symbiotic prokaryotic bacteria
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Subunits of nuclear rRNA
[1] large subunit (28S, 5.8S, 5S)
| [2] small subunit (18S)
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RNA polymerase I
ribosomal synthesis
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Significance of mitochondria in apoptosis
Contains cytochrome C --> critical component in apoptosis
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Subunits of mitochondrial rRNA
16S & 23S
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Function of tRNA
Carries amino acids during translation
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Significance of snRNA
Involved in RNA maturation, spliceosomal RNA
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H/ACA snoRNA subfamily
guides site-specific pseudourylation of uridine to produce pseudouridine in rRNA
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Significance of snoRNA
Guides site-specific base modification in rRNA & snRNA
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Significance of miRNA
Antisense regulator of genes --> bind to complementary sequence in 3'-UTR to inhibit translation
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Significance of noncoding 7SK RNA
Negative transcriptional inhibition of RNA polymerase II elongation
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Significance of SRA1 RNA
Coactivator of steroid receptors
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Characteristics of classical gene families
[1] High degree of sequence homology
| [2] Products have short conserved amino acid motifs
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Example of conserved amino acid motifs in classical gene families
[1] DEAD (Asp-Glu-Ala-Asp)
| [2] WD (tryptophan-aspartate)
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Characteristics of gene superfamilies
[1] No significant conserved amino acid motifs;
| [2]. Share general common structural features
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Examples of gene superfamilies
[1] Immunoglobulin superfamily --> immunoglobulin genes, T cell receptor genes, HLA genes;
[2] Globin superfamily --> alpha and beta globin, neuroglobin, myoglobin;
[3] G protein-coupled receptor superfamily --> mediate ligand induced signaling between extracellular and intracellular environments
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Characteristics of pseudogenes
[1] Copied at the level of genomic DNA by tandem gene duplication
[2] Contain all elements of a gene but have inappropriate termination codons in exons
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pericentromeric genes
contain sequences that have been copied recently during evolution and are located on several chromsomes
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Examples of identical proteins coded by different genes
Histone, ubiquitin
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Number of bonds in AT linkage
2
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BLAST
[1] Basic local alignment search tool
| [2] Searches for sets of optimal local alignments based on a query
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Ways that a species' genome may change (4)
[1] Expansion --> gene duplication
[2] Genesis --> creation of new genome
[3] Exchange
[4] Deletion
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Definition of retrogenes
Nonprocessed pseudogenes that are integrated in a chromosome next to a promoter and expressed
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Mechanisms which govern changes at the protein level are most likely due to: _____
Nucleotide substitution, insertion, deletion
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Definition of comparative genomics
New field of biological research dealing with the comparison of genomes of different species
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Changes may give rise to new genes which become fixed if ____________
they give the organism an advantage in natural selection
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Definition of neutral theory
[a] Molecular evolution caused by random genetic drift through mutations that are selectively neutral or nearly neutral;
[b] Describes cases in which natural selection is not strong enough to outweigh random events
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Definition of
a) synonymous substitution,
b) non synonymous substitution
[a] substitution in DNA that does not alter the amino acid sequence of the coded protein
[b] substitution in DNA that alters the amino acid sequence of the coded protein
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Definition of positive selection
[1] Darwinian selection fixing advantageous mutations;
[2] Equal to molecular adaptation and adaptive molecular evolution
[3] ex. people who have sickle cell anemia are less affected by malaria
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Definition of purifying selection / negative selection
Natural selection against deleterious mutations
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Types of nucleotide substitution (6)
Given 2 nucleotide sequences, we can ask how their similarities and differences arose from a common ancestor.
[1] single substitution --> 1 change 1 difference;
[2] multiple substitution --> 2 changes 1 difference;
[3] coincidental substitution --> 2 changes 1 difference;
[4] parallel substitution --> 2 changes, no difference;
[5] convergent substitution --> 3 changes, no difference;
[6] back substitution --> 2 changes, no difference
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Transition vs Transversion
Types of substitution:
[1] Transition --> purine for purine, pyrimidine for pyrimidine
[2] Transversion --> purine for pyrimidine
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Significance of purifying selective force
Prevent accumulation of mutation at important functional sites, resulting in sequence conservation
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Enumerate the types of mutation, and their characteristics
[1] Based on effect --> lethal vs nonlethal;
[2] Based on size/position --> Point mutation (missense, nonsense, frameshift);
[3] Based on substitution --> transition vs subversion
76
Differentiate missense, nonsense, and frameshift mutations
[1] missense --> single nucleotide change causes a different amino acid to be coded;
[2] nonsense --> single nucleotide change causes premature stop codon;
[3] frameshift --> insertions or deletions that change the reading frame (not divisible by 3)
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The nucleotide sequences of a pair of homologous genes have a (higher or lower?) information content than the amino acid sequences of their coded proteins
Higher, due to the fact that synonymous mutations change the DNA without changing the protein
78
Which occurs more frequently? Transitions or transversions? Why?
Transitions occur 2x more frequently than transversions --> easier to replace for the same type
79
[T/F] all mitochondrial genes code for stop codons
F, some are added posttranscriptionally
80
[T/F] some coding sequences of mitochondrial genes are overlapping
T
81
Euchromatin in nuclear genome - number of BP, characteristics
3000 Mb; transcriptionally active
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RNA polymerase II
mRNA, sRNA, miRNA synthesis
83
RNA polymerase III
synthesis of tRNA, rRNA 5S, misc small RNAs
84
subtelomeric genes
unstable and prone to duplication
85
C/D box snoRNA subfamily
guides site-specific methylations in rRNA
86
missense mutation
single nucleotide change causes different amino acid to be coded
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nonsense mutation
single nucleotide change causes stop codon to be coded
88
frameshift mutation
addition or deletion of nucleotide changes the reading frame
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stop codons
UAA, UAG, UGA
90
start codon
AUG
