Trans - Human Genome Flashcards
Percentage of genes in genome
2-3%
Correlation between genome size and organism complexity
None
Definition of telomere
Ends of chromosome
Original definition of genome
Collection of genes contained within a haploid chromosome set
Modern definition of genome
Locatable region of genomic sequence corresponding to a unit of inheritance associated with regulatory regions, transcribed regions, and/or other functional sequence regions
Definition of centromere
Central region of chromosome
Arms of chromosome?
Chromatid
Shorter arm of chromosome
P arm
Longer arm of chromosome
Q arm
Number of rings in purine
Two
Number of rings in pyrimidine
One
Which bases are purines?
Adenine, Guanine
Which bases are pyrimidines?
Cytosine, Thymine
Correlation between GC content and melting point
Higher GC content, higher melting point
Which is more preferred for expression? AT or CG?
AT
Correlation between GC content and level of expression
Higher GC content, more silenced genes
Definition of intron and exon
[1] Intron –> region of DNA not expressed;
[2] Exon –> expressed region of DNA
Parts of the UTR/Leading sequence
[1] Enhancer
[2[ Promoter
[3] Operator
[4] Consensus sequence
Consensus sequence in a) prokaryotes, b) eukaryotes
[A] Pribnow box (TATAAT);
[B] Hogness box (TATA)
Parts of coding sequence
[1] Start codon (AUG);
[2] Introns and exons;
[3]. Stop codon (UAA, UAG, UGA)
Number of bonds in CG linkage
3
Name and define the regions associated with the alternating introns and exons
[1] Pre Region –> signal region, determines where the protein will go;
[2]. Pro Region –> determines posttranslational modification
[3] Mature Region –> encodes the protein
Parts of the UTR/trailing sequence
[1] 2nd termination signal
[2] Cleavage signal (AAUAA) containing poly-A tail
Central dogma of molecular biology
[1] Replication –> DNA duplication;
[2] Transcription –> RNA synthesis
[3] Translation –> protein synthesis
Definition of open reading frame
Region of DNA corresponding to coding sequence
Composition of human genome
[1] euchromatic portion;
[2] constituitive heterochromatin
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
Percentage composition of bases in genome
GC –> 41%; AT –> 59%
What are Giemsa bands?
[1] Dark bands –> low GC, 37%
[2] Light bands –> high GC, 45%
both bands seen in karyotype
Number of base pairs in human genome
3200 M
Number of genes in human genome
30,000 - 35,000
Percentage of genes coding untranslated RNA
5-10%
Mechanism of gene distribution
Hybridization of CpG islands to metaphase chromosomes
Composition of nuclear genome
[1] 95.5% noncoding DNA
[2] 4.5% conserved DNA –> 3% untranslated & regulatory, 1.5% coding DNA
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
Definition of pseudogenes
Multiple copies of genes serving as rescue genes in case original genes get damaged
Number of BP in mitochondrial genome
16,569
Number and characteristics of genes in mitochondria
37 genes –> 22 tRNA, 2rRNA, 13 protein coding
[T/F] mitochondrial genes have introns
F
Structure and significance of D-loop in mitochondrial genome
Triple stranded region, origin for replication of mitochondrial genome
Endosymbiont theory
Mitochondria may have originated from symbiotic prokaryotic bacteria
Subunits of nuclear rRNA
[1] large subunit (28S, 5.8S, 5S)
[2] small subunit (18S)
RNA polymerase I
ribosomal synthesis
Significance of mitochondria in apoptosis
Contains cytochrome C –> critical component in apoptosis
Subunits of mitochondrial rRNA
16S & 23S
Function of tRNA
Carries amino acids during translation
Significance of snRNA
Involved in RNA maturation, spliceosomal RNA
H/ACA snoRNA subfamily
guides site-specific pseudourylation of uridine to produce pseudouridine in rRNA
Significance of snoRNA
Guides site-specific base modification in rRNA & snRNA
Significance of miRNA
Antisense regulator of genes –> bind to complementary sequence in 3’-UTR to inhibit translation
Significance of noncoding 7SK RNA
Negative transcriptional inhibition of RNA polymerase II elongation
Significance of SRA1 RNA
Coactivator of steroid receptors
Characteristics of classical gene families
[1] High degree of sequence homology
[2] Products have short conserved amino acid motifs
Example of conserved amino acid motifs in classical gene families
[1] DEAD (Asp-Glu-Ala-Asp)
[2] WD (tryptophan-aspartate)
Characteristics of gene superfamilies
[1] No significant conserved amino acid motifs;
[2]. Share general common structural features
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
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
pericentromeric genes
contain sequences that have been copied recently during evolution and are located on several chromsomes
Examples of identical proteins coded by different genes
Histone, ubiquitin
Number of bonds in AT linkage
2
BLAST
[1] Basic local alignment search tool
[2] Searches for sets of optimal local alignments based on a query
Ways that a species’ genome may change (4)
[1] Expansion –> gene duplication
[2] Genesis –> creation of new genome
[3] Exchange
[4] Deletion
Definition of retrogenes
Nonprocessed pseudogenes that are integrated in a chromosome next to a promoter and expressed
Mechanisms which govern changes at the protein level are most likely due to: _____
Nucleotide substitution, insertion, deletion
Definition of comparative genomics
New field of biological research dealing with the comparison of genomes of different species
Changes may give rise to new genes which become fixed if ____________
they give the organism an advantage in natural selection
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
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
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
Definition of purifying selection / negative selection
Natural selection against deleterious mutations
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
Transition vs Transversion
Types of substitution:
[1] Transition –> purine for purine, pyrimidine for pyrimidine
[2] Transversion –> purine for pyrimidine
Significance of purifying selective force
Prevent accumulation of mutation at important functional sites, resulting in sequence conservation
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
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)
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
Which occurs more frequently? Transitions or transversions? Why?
Transitions occur 2x more frequently than transversions –> easier to replace for the same type
[T/F] all mitochondrial genes code for stop codons
F, some are added posttranscriptionally
[T/F] some coding sequences of mitochondrial genes are overlapping
T
Euchromatin in nuclear genome - number of BP, characteristics
3000 Mb; transcriptionally active
RNA polymerase II
mRNA, sRNA, miRNA synthesis
RNA polymerase III
synthesis of tRNA, rRNA 5S, misc small RNAs
subtelomeric genes
unstable and prone to duplication
C/D box snoRNA subfamily
guides site-specific methylations in rRNA
missense mutation
single nucleotide change causes different amino acid to be coded
nonsense mutation
single nucleotide change causes stop codon to be coded
frameshift mutation
addition or deletion of nucleotide changes the reading frame
stop codons
UAA, UAG, UGA
start codon
AUG
