Final Flashcards
Molecular genetics
Study of structure and function of genes and the regulation of their expression
Transmission genetics
“Classical genetics”
Study of how traits are transmitted from generation to generation
Population genetics
Study of heredity in a large group of individuals
Quantitative genetics
Study of polygenetic and multifactorial traits
Cytogenetics
Study of structure and function of cell, particularly the chromosomes
C value
Amount of haploid DNA in base pairs in organism
Genome
All the genetic material that an organism has
DNA
Deoxyribonucleic acid
Has H instead of OH at 2’ carbon
Contains thymine
Genetic material for all known prokaryotes and eukaryotes
RNA
Ribonucleic acid
Has OH at 2’ carbon
Contains uracil instead of thymine
Genetic material for some viruses
Antiparallel
Opposite
How two strands of DNA run in respect to each other
Double helix
Double-stranded DNA forms this
Nucleotide
Building block of DNA and RNA
Contains pentose sugar, nitrogenous base, and phosphate group
Major groove
Larger groove in DNA double helix
Results from angle of glycosidic bond
Minor groove
Smaller groove in DNA double helix
Results from angle of glycosidic bond
Nucleic acids
DNA and RNA (deoxyribonucleic acid and ribonucleic acid)
Phosphate group
-PO3 group
Present on nucleotides to allow for linkage between them (phosphodiester bond)
Deoxyribose sugar
Pentose sugar with H instead of OH on 2’ carbon
Ribose sugar
Pentose sugar with OH on 2’ carbon
Nitrogenous bases
Cyclic ring structure containing nitrogens
Pair with one another to form DNA helix
Phosphodiester bonds
Bonds between phosphate groups on nucleotides
Allows for linkage between nucleotides
Chromosomes
How DNA is packed in eukaryotes
Condensed to save space
Chromatin
DNA + protein in the nucleus
Histones
Proteins that help pack chromatin into nucleus
Positively charged: DNA is negatively charged
Consists of H1, H2A, H2B, H3, and H4
Nucleosome
DNA wound around histone core
Euchromatin
Chromatin that exhibits normal packing and unpacking in cell cycle
Contains genes that are actively being transcribed (loosely packed)
Typically devoid of repetitive sequences
Heterochromatin
Packed tightly
Not being actively transcribed
Epigenetics
A change in phenotype that doesn’t result from a change in the sequence of a gene
Change is heritable
Caused by switching on or off parts of genome in response to environment
Bidirectional replication
DNA replication proceeds in both directions due to the presence of 2 replication forks
Semiconservative replication
Parent strand is used as template and joins with new strand
Correct model of replication
Semidiscontinuous replication
Lagging strand of DNA is synthesized this way as a series of short fragments
Origin of replication
Place on DNA where replication begins
Replication bubble
Spot on DNA where replication is occurring
DNA strands are denatured, so DNA is temporarily single-stranded
Replication fork
Structure created during DNA replication
Consists of 2 denatured strands that can be synthesized off of
Leading strand
Strand of DNA that is synthesized off of in the 5’ to 3’ direction
Lagging strand
Strand of DNA that is synthesized off of in the 3’ to 5’ direction
Okazaki fragments
Sections of newly synthesized DNA
Formed on lagging strand
Helicase
Enzyme that breaks H-bonds between nucleotide bases in DNA replication
SSB protein
Protein that binds to single strands of DNA in replication, holding them apart
Primase
Enzyme that makes RNA primer in DNA replication
DNA polymerase
Enzyme that catalyzes phosphodiester bond formation between nitrogenous bases (dNTPs) in DNA replication
Ligase (DNA replication)
Enzyme that connects DNA strands in DNA replication
Topoisomerase
Enzyme that unwinds DNA in DNA replication
Transcription
Process of turning DNA into mRNA
Template strand
Strand to which RNA pol makes complementary RNA strand
Strand of DNA that is site of transcription
Centromere
Constitutive heterochromatin
Packed tightly: constricts chromosome
Mitotic spindle attaches to centromere in order to pull chromosomes apart during cell division
Telomere
Tandemly repeated DNA at the ends of linear chromosomes
Protects integrity of DNA from exonucleases (chew up ends of DNA: defense against foreign DNA)
RNA polymerase
Enzyme that transcribes RNA by linking together NTPs
Exons
Sequences that are expressed
Transcribed and translated
Introns
Euk genes only
Long insertions of non-coding sequences
Intervening sequences: transcribed, but not translated
Buffer against mutation and contain enhancer sequences
5’ capping
Methylated guanine nucleotide (5’ methyl G-cap) is added to 5’ end of mRNA
Protects RNA from exonucleases and ensures correct positioning of ribosome during translation
Polyadenylation
End of transcription Steps: 1. mRNA is cleaved at poly A site 2. mRNA is released 3. 50 to 250 adenine nucleotides are added to 3' end by poly A polymerase
Gene regulatory elements
Set of cis-acting (next to) sequence elements bound by trans-acting (from someplace else) factors
Contains core promoter, proximal elements (close to core promoter; enhancers or silencers), and distal elements (far away from core promoter; may be on other chromosome; enhancers or silencers)
Promoter
Region of DNA that initiates transcription of a particular gene
General transcription factors
Bind to core promoter, recruiting polymerase and causing basal transcription
Enhancers
Sequences of DNA that are bound by proteins called activators
When bound, transcription of gene is increased
Located further downstream or upstream from +1 site
Activators
Proteins that bind to enhancers, causing increased transcription of genes
2 major domains: DNA binding domain and transcription activation domain
Change shape, allow for binding to DNA
Repressors
Proteins that bind to silencers, causing decreased transcription of genes
Silencers
Sequences of DNA that are bound by proteins called repressors
When bound, transcription of gene is decreased
Located further downstream or upstream from +1 site
mRNA splicing
Modification of RNA in which introns are removed from exons
Alternative splicing
One gene can encode more than 1 protein because different combinations of exons are spliced together to create different proteins
Spliceosome
Removes introns from mRNA
rRNA
Ribosomal RNA
snRNA
Small nuclear RNA
Non-coding
Translation
Process of turning mRNA into proteins
Polypeptide
Polymers of amino acids that are connected by peptide bonds
Protein
Combination of polypeptides folded in a 3-D structure
Amino acids
Building blocks of proteins
Each different amino acid (20 in total) has a different R group that provide it different functions
Codon
Set of 3 mRNA nucleotides that code for an amino acid
Charged tRNA
tRNA loaded with an amino acid
Ribosome can transfer amino acid from tRNA to growing peptide strand
Anticodon
Triplet nucleotide sequence of tRNA that is complementary to that of mRNA
Genetic code
Set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells
Degeneracy
More than 1 codon occurs for each amino acid (3rd nucleotide might be different)
Allows for protection against mutation
Same as redundancy
Wobble
Base pairing between tRNA anticodon and mRNA codon doesn’t necessarily follow complementary base pairing rules at the 3rd nucleotide
Reason: energetic favorability
Open reading frame (ORF)
The codons of an mRNA that are read sequentially to specify amino acids
Ribosome
Site of translation
Polysome
Multiple ribosomes translating same RNA concurrently
Mutation
Change in nucleotide sequence
Mutagen
Substance that induces mutation in DNA
Examples: radiation, intercalating agents, some drugs
Nonsense mutation
Change from functional codon to stop codon
Often severe phenotypic effect, but effect depends on where mutation is and what amino acid is changed
Missense mutation
A change in a codon so that a different amino acid is added to the polypeptide
Phenotypic change depends on amount of difference from original
Frameshift mutation
Addition or deletion of 1 or more base pairs changes open reading frame
Missense or stop results
Deletion
Loss of nucleotide(s) from sequence
Neutral mutation
Change amino acid to another amino acid with similar chemical properties
Mild or no phenotypic effect
Silent mutation
Change 1 codon for 1 amino acid to a different codon for the same amino acid
Point mutation
Single base pair substitution
Gain of function mutation
Causes gene product to have more activity
Loss of function mutation
Results in partially or fully nonfunctional gene product
Null allele
Fully nonfunctional allele
Transposable elements
Segments of DNA that have the capacity to move in the genome
Chromatin remodeling
Histone core is moved so that the gene is accessible: allows transcription of genes blocked by histone
DNA methylation
CpG island is methylated, causing gene to be silenced
Methyl groups physically block transcriptional machinery
Can sometimes recruit histone deacetylases to modify histone tails
Histone acetylation
Histone acetyltransferases (HATs) cause masking of positive charge on histone tails, making DNA accessible Heritable change Process is reversible by histone deacetylases (HDACs), recruited by DNA methylation
RNAi (RNA interference)
- miRNA is transcribed
- miRNA is processed into shRNA (short hairpin RNA)
- RISC (RNA interference silencing complex) recognizes shRNA and picks it up
- RISC complex binds to mRNA
- RISC complex cuts off mRNA’s poly A tail
- mRNA is degraded
Hairpin RNA
RNA that makes a sharp hairpin turn
Can be used to silence gene expression through RNA interference
RNA half-life
Point in time at which half of RNA is degraded
Depends on structure, proteins bound, and poly A tail length (too short, degraded)
Aneuploidy
Number of chromosomes in individual’s cells isn’t a multiple of the normal haploid set
1 or more extra or missing chromosomes
Insertion
Addition of a base pair
Duplication
Doubling of part of chromosome
Translocation
Piece of 1 chromosome is placed onto another chromosome
Inversion
Segment of chromosome is taken out and re-inserted backwards
Fragile sites
Narrow sites of some chromosomes
Prone to breakage
Sister chromatid
Identical copy of a chromosome
Homologous chromosomes
Chromosomes that aren’t identical, but code for the same genes
Monohybrid cross
Cross between two individuals whose alleles differ for one gene
Dihybrid cross
Cross between two individuals whose alleles differ for two genes
Law of segregation
In meiosis I, homologous chromosomes end up at one pole or the other at random
Law of independent assortment
In meiosis I, chromosomes don’t influence each other’s segregation
Testcross
Cross of unknown genotype (homozygous dominant or heterozygous) with homozygous recessive individual
Allows for determination of unknown genotype
Codominance
Heterozygote shows the phenotypes of both homozygotes simultaneously
Ex- roan horses (both red and white hairs)
Incomplete dominance
Phenotype of heterozygote is intermediate to homozygotes
Ex- palomino horses (intermediate to chestnut and cremello)
Epistasis
1 gene masks the expression of another gene
Polygenic phenomenon
Haplosufficiency
1 dose of gene product supports life Autosomal recessive Homozygous wt= healthy Heterozygous= healthy Homozygous mutant= sick or dead
X-linked
Trait carried on the X chromosome
More commonly seen in males than females
Hemizygosity
Having unpaired genes
Ex- guys are this in respect to X-linked traits
SRY (sex-determining region of Y) in humans
Becomes active at 6-8 weeks during development
Encodes Testes Determining Factor (TDF), which controls the development of testes (absence of this causes gonads to develop into ovaries)
Barr bodies
Silencing of 1 X chromosome in females allows for the same level of expression for genes on the X chromosome in males and females
Entire chromosome isn’t completely inactivated- some parts are a little bit active
Gene dosage
The amount of gene product present in an individual
Pleiotropy
1 gene is responsible for multiple phenotypes
Penetrance
The % of individuals with a particular genotype who show the expected phenotype
Expressivity
Degree to which a phenotype is expressed
Severity of phenotype
Phenotypic variation
Differences in phenotype between individuals
Maternal effect
Mitochondria and mtDNA in egg cytoplasm are inherited in offspring
Phenotype of the offspring is determined by the genotype of the mother
Extranuclear inheritance (mtDNA)
DNA found in mitochondria
Polygenic trait
Trait that results from action by multiple genes
Most traits are these
Multifactorial
Influence from many genes along with environment
Discrete trait
Clearly defined by 1 or a few genes
No degrees of severity
Only a few traits follow this mode of expression
Quantitative trait
Measurable in numeric terms
Controlled by multiple genes and environmental factors
Have continuous variation
Continuous variation
Phenotypes are distributed along a continuum
Series of intermediate phenotypes that fall between 2 extremes
Heritability
How much of the phenotypic differences are due to genetic factors
Expressed in a number ranging between 0-1 (0- none, 1- all)
Quantitative trait loci
Loci that influence quantitative traits
Genetic drift
Changes in allele frequencies due to random sampling
Reduces genetic diversity
Ex- settlers killing off millions of bison on the Great Plains
Bottleneck effect
Population is drastically reduced in number, reducing genetic diversity
Not due to anything that would reduce selectively, like certain diseases
Founder effect
Population is established from a small number of breeding individuals
Reduced genetic diversity
Natural selection
Frequency of alleles that confer survival and reproduction increases in the population
Gene pool
All of the alleles in a population
Migration
Flow of alleles into and out of a population
Gene flow
An individual migrates and contributes its alleles to the gene pool of the new population
Selective mating
Mating of organisms in a non-random manner
Genomics
Study of an entire genome(s)
Functional genomics
Global analysis of function of sequences in a genome
Comparative genomics
Comparison of entire genomes from different species, individuals, or groups
Bioinformatics
Combination of biology and computer science
Transcriptomics
Study of complete set of transcripts that are produced by a genome under a specific condition
Reverse transcriptase
Enzyme that synthesizes DNA from RNA
Orthologous genes
2 or more different genes in 2 different organisms that have the same or similar function
Result of speciation
Paralogous genes
2 or more genes in an organism that have similar or identical function
Result of duplication
Homologous genes
Paralogs and homologs
Pharmacogenomics
Study of role of genetics in a drug response
PCR
Amplify millions of copies of DNA molecule from very small starting portion of DNA
Many cycles of 3 steps: denature DNA using heat, anneal primers to DNA, extend strand using Taq polymerase
cDNA
Complementary DNA: complementary to RNA
Real-time PCR
Measure increase in amount of PCR product during thermal cycling reactions
Measure specific cDNA as it’s being amplified: use reporter probe
Reporter probe in real-time PCR
Contains fluorescent marker and quencher
When quencher is close to fluorescent marker, no light is emitted
As polymerase makes strand, quencher is displaced from fluorescent marker, causing light to be emitted
RNAseq
Method that provides sequences of all transcripts in a sample
Steps:
1. Extract RNA from cells of interest
2. Reverse transcribe into cDNA
3. Sequence cDNA using Next Gen technology
Genetic engineering
Human manipulation of an organism’s DNA
Transformation
Getting a host (ex- E. coli) to take up a cloning vector to make clones of the sequence of interest
Clone
Identical copy
DNA marker
Specific region of DNA that varies among individuals
Used to create a detailed map of the individual’s genome
DNA polymorphisms
Changes in DNA sequence between individuals
SNPs (single nucleotide polymorphisms)
Changes in DNA sequence at a specific nucleotide
Copy number variants
Number of copies of genes present in a person’s genome
Cause changes between people
RFLP
Method of identifying SNPs
SNP changes restriction enzyme site: different number of fragments observed in gel electrophoresis
Shotgun sequencing method
- Extract DNA from human cells
- Cut DNA into small, overlapping fragments (contigs) using restriction enzymes (reaction is performed at suboptimal conditions- enzymes don’t cut at every site)
- Clone contigs to make genomic library
- Sequence each clone using Sanger sequencing
- Use computers to reassemble sequences of contigs by puzzling together overlapping sequences
- Deposit sequences into database, NCBI GenBank
Human genome project
Project in 1990s that focused on sequencing whole human genome (hadn’t been done yet)
Sanger method
- Cloning vector containing DNA of interest is amplified by PCR
- When polymerase randomly adds ddNTP with attached fluorescent probe, sequencing reaction stops
- Different sized segments of DNA are created
- Segments are separated by size using capillary gel electrophoresis (electrophoresis in a capillary tube)
- Detector identifies ddNTPs based on their unique fluorescence
- Sequence is recreated by reading ascending order of ddNTPs
Next generation sequencing
- Extract DNA
- Cut into contigs
- Affix DNA to solid support (bead, chip, etc.)
- One by one, wash dNTPs across the DNA
- If known dNTP is incorporated by polymerase, then light is emitted
- Reassemble overlapping sequences
Annotation
Identification and description of genes and their important sequences
Can be done using computer algorithms to predict open reading frames: look for promoters, start sites, and polyadenylation sites
Haplotype
Set of SNPs that are close together on a chromosome
SNPs are inherited together: low recombination rates
Cloning vector
Plasmid used in cloning Contains Ori (origin of replication), MCS (multiple cloning site), and gene for antibiotic resistance
Ligase (cloning)
Enzyme that re-seals phosphodiester bonds between sequence and cloning vector
Southern blotting
- Isolate DNA from organism of interest
- Cut DNA into small pieces using restriction enzymes
- Separate DNA fragments using gel electrophoresis
- Transfer DNA from gel to membrane/blot (DNA is in same position on blot as on gel)
- Incubate blot with labeled probe that is complementary to DNA of interest
- Visualize probe: see band on blot where DNA of interest is located
Restriction enzyme
Cuts DNA at specific site, creating sticky ends
Used to create space in MCS for sequence of interest to be inserted
Exonuclease
Cleaves sequence at its end
Endonuclease
Cleaves sequence in its middle
Transgene
Gene transplanted from one organism to another
Restriction mapping
Using restriction enzymes that cleave at known sequences to obtain structural information about a piece of DNA (find out how large it is and the sizes of fragments making it up)
Recombination hot spot
Region of the genome with increased recombination rates
Recombination cold spot
Region of the genome with decreased recombination rates
P value
Less than 0.05: fail to reject null hypothesis
Greater than or equal to 0.05: reject null hypothesis
Null hypothesis: statistical difference between observed numbers and expected numbers
Central dogma of molecular biology
DNA is transcribed into RNA which is translated into amino acids
FISH
- Solution of labeled probes is added to DNA sample in question while it is being denatured
- Sample is allowed to hybridize
- Probe will hybridize to the sample DNA if the specific sequence is present
Used in detection of genetic disorders that result from copy number changes
Spectral karyotyping (SKY)
Human karyotype is labeled with 24 uniquely labeled chromosome paints
Used to detect complex rearrangements, small translocations, and unknown chromosomes
Array-based comparative genomic hybridization (Array CGH)
Patient’s DNA and normal DNA are differently labeled and co-hybridized to arrays of DNA clones which span the entire genome (comparison is expected to yield ratio of 1:1, indicating equal DNA copy numbers in both samples)
If yellow, normal copy number
If red, deletion in patient’s DNA
If green, duplication in patient’s DNA
Whole exome sequencing
Analysis of the exons (coding regions) of thousands of genes simultaneously
p and q
p= frequency of dominant allele (B)
q= frequency of recessive allele (b)
p+q=1
Hardy-Weinberg equation
p^2 + 2pq + q^2 = 1
p^2= f(AA)
2pq= f(Aa)
q^2= f(aa)
Map units (mu)
Map units=% recombination
Map units= (number of recombinants/total number of progeny)*100
Progeny in lowest abundance result from…
Double crossover
Progeny in highest abundance result from…
Parental
How to tell which gene in a test cross is in the middle
DCO tells which gene is in middle: only one that isn’t switched (odd one out)
Roughly equal number of offspring in testcross
No linkage of genes
4 high numbers from 8 phenotypic classes in testcross
Odd trait out assorts independently and other two are linked
2 parental (high #), 4 SCO (intermediate #), and 2 DCO (low #) in testcross
Odd trait out is in middle and all traits are linked
