genetics Flashcards
Transmission genetics
Study of the transmission of genes from generation to generation
molecular genetics
Study of the structure and function of genes at the molecular level
population genetics
Study of the genetic differences within and between populations or individuals
quantitative genetics
Study of the effects of many genes
Trait
A characteristic feature of an organism
* Tend to run in families in predictable ways
* Controlled by one or more genes
* May not be visible (DNA sequences)
genotype
The genetic variant present at a given location in the genome
* Variants of a genotype are alleles
* Can be represented by symbols (e.g., BB, Bb or bb)
phenotype
An individual’s observable traits
* Determined by the interaction between their genotype and the environment
chromosome
A structure composed of DNA and proteins that bears genetic information
gene
A section of DNA that codes for a polypeptide or RNA
gene locus
A specific location of a gene along a chromosome
alleles
Different molecular forms of the same gene
* There may be many alleles at a locus
ploidy
The number of copies of a genome an organism has
haploid
Having a single set of chromosomes (i.e., only 1 allele per locus, “n”)
diploid
Having two sets of paired chromosomes (i.e., 2 alleles per locus, one on each copy of a chromosome; “2n”)
cell cycle (4 main events)
- Cell division signals
- DNA replication
- DNA segregation
- Cytokinesis These events occur differently in prokaryotes and eukaryotes
cell division in prokaryotes
Cell division is called binary fission, replication of the entire single-celled organism
Cell division signals are usually external factors such as nutrient concentration and environmental conditions
how many chromosomes do prokaryotes have?
1 circular chromosome
2 important prokaryote chromosome regions
ori—where replication starts (origin)
ter—where replication ends (terminus)
prokaryote DNA segregation
When replication is complete, ori regions move to opposite ends of the cell, segregating the daughter chromosomes
prokaryote Cytokinesis
Cell membrane pinches in, protein fibers form a ring
New cell wall materials are synthesized, resulting in separation of the two cells
cell division eukaryotes
Cell division is through mitosis (or in some tissues, meiosis)
Cell division is regulated based on the needs of the entire organism
eukaryotic DNA replication
- Eukaryotes have more than one chromosome
- Replication starts at may origins on each
- Replication is limited to one part of the cell cycle
interphase (e)
Nucleus is visible
Cell functions occur Has 3 subphases:
* Growth 1 (G1)
* Synthesis (S)
* Growth 2 (G2)
G1 phase (e)
- Chromosomes are single (unreplicated)
- Duration is variable, from minutes to years
- Ends at the G1-to-S transition, when commitment is made to DNA replication and cell division
S phase (e)
- DNA replicates
- Sister chromatids remain together until mitosis
G2 phase (e)
- Cell prepares for mitosis, e.g., by synthesizing the structures that move the chromatids
M phase (e)
Includes mitosis and cytokinesis
Mitosis
Leads to the production of two nuclei that are genetically identical to each other and to the nucleus of the cell that entered the cell cycle in G1
Subdivided into prophase, prometaphase, metaphase, anaphase, and telophase
Asexual reproduction is based on mitosis
A single-celled organism reproduces itself with each cell cycle
Some multicellular organisms also reproduce asexually
Meiosis
Sexual reproduction requires meiosis
* Offspring are not identical to the parents
* Gametes are created by meiosis
* Gametes and offspring differ genetically from each other and from the parent
Two nuclear divisions, but DNA is replicated only once
Reduces chromosome number from diploid (2n) to haploid (n)
Ensures each haploid product has a complete set of chromosomes
Meiosis generates genetic diversity that is the raw material of evolution
crossing over
Exchange of genetic material between non-sister chromatids
sexual life cycles
Evolution has generated many different versions of the sexual life cycle.
* All involve meiosis to produce haploid cells
* Fertilization and meiosis alternate
* Haploid (n) cells or organisms alternate with diploid (2n) cells or organisms
monohybrid crosses
Cross parental varieties with contrasting traits for a single character
law of segregation
The two copies of a gene separate during gamete formation. Each gamete receives only one copy.
law of independent assortment
Copies of different genes assort independently
The second law is now understood in the context of meiosis.
* Chromosomes segregate independently during formation of gametes, and so do any two genes located on separate chromosome pairs
multiplication rule
Probability of two independent events happening together: multiply the probabilities of the individual events Tossing two coins: probability that both will come up heads = ½ × ½ = ¼
addition rule
The probability of an event that can occur in two different ways is the sum of the individual probabilities
In F2, there are two ways to get Rr, thus ¼ + ¼ = ½
alleles
New alleles arise through mutation
Are stable, inherited changes in the DNA
the wild type
an allele that is common, and thought of as the “default” phenotype
polymorphic
A gene with multiple alleles
epistasis
when the phenotypic expression of one gene is influenced by the products of other genes
penetrance
the proportion of individuals with a genotype that develop the expected phenotype
expressivity
the degree to which a phenotype is expressed in an individual
qualitative traits
those that have discrete qualities often controlled by alleles at a single locus
Sex Chromosomes and Linkage
In mammals
- Females have two X chromosomes (XX), males have one X and one Y (XY)
- Male mammals produce two kinds of gametes— half carry a Y and half carry a X
Sex of the offspring depends on which gamete fertilizes the egg
- Male mammals produce two kinds of gametes— half carry a Y and half carry a X
Sex Chromosomes and Linkage
In birds
- Males have two Z chromosomes (ZZ), females have one Z and one W (ZW) In bees:
- Males are haploid, females are diploid In Galapagos giant tortoises:
Sex is dependent on the temperature eggs are incubated at (no sex chromosomes!)
- Males are haploid, females are diploid In Galapagos giant tortoises:
Sex Chromosomes and Linkage
In birds
- Males have two Z chromosomes (ZZ), females have one Z and one W (ZW)
Lyonization
- Early in embryo development, one of the two X chromosomes inactivates by supercoiling to a Barr Body
DNA structure key features
- It is a double-stranded helix
- It is right-handed helix
- It is antiparallel
- The strands are held together by complementary base pairing
- The outer edges of the bases are exposed in major and minor grooves
The sugar–phosphate backbones form a coil around the outside of the helix; the nitrogenous bases point toward the centre
Hydrogen bonds between complementary base pairs hold the two strands of the DNA helix together
van der Waals forces occur between adjacent bases on the same strand
Antiparallel strands: direction is determined by sugar phosphate bonds
Phosphate groups connect the 3ʹ C of one sugar with the 5ʹ C of the next
One strand has a free 5ʹ phosphate group—the 5ʹ end
The other chain has a free 3ʹ hydroxyl group—the 3ʹ end
The double-helix structure is essential to DNA function:
T
- With millions of nucleotides, the base sequences store a huge amount of genetic information
- Precise replication in cell division is possible by complementary base pairing
Nucleotide sequences determine sequences of amino acids in proteins; proteins determine phenotypes.
tRNA (transferRNA) function
translation of mRNA into proteins requires a protein, links information in mRNA codons with specific amino acids in protein.
This function performed by transfer.
Two key roles:
1. tRNA reads mRNA codons correctly 2. tRNA transfers amino acid to the growing peptide chain (corresponding to the mRNA codon)
codons
- Series of three nucleotides in mRNA that code for an amino acid
Codons direct the placement of specific amino acids into a protein
negative regulation
binding of repressor protein blocks transcription (stops RNA polymerase from binding to promoter).
positive regulation
binding of activator protein stimulates transcription (allows RNA polymerase to bind to promoter).
operator
genetic sequence which allows proteins responsible for transcription to attach to the DNA sequence
mutation
a change in the nucleotide sequence that can be passed on from one cell or organism to another.
somatic mutations
occur in body cells; passed to daughter cells in mitosis but not to offspring.
germ line mutations
occur in cells that give rise to gametes; passed to offspring at fertilization
Loss of function mutations:
gene is not expressed at all, or protein does not function; nearly always recessive.
Gain of function mutation
produces a protein with altered function; usually dominant. Common in cancer—new proteins stimulate cell division.
point mutations
insertion or deletion of a single base pair, or substitution of one base pair for another.
silent mutation
substitution that results in a codon that codes for the same amino acid.
missense mutation
substitution resulting for a different amino acid.
nonsense mutation
base substitution results in a stop codon somewhere in the mRNA
loss of stop mutation
base pair substitution that changes a stop codon to a sense codon; extra amino acids are added to the polypeptide.
frame-shift mutation
insertion or deletion of a base pair. Alters the mRNA reading frame (consecutive triplets) during translation; produces nonfunctional proteins.
chromosomal rearrangements
- Chromosomal rearrangements result in extensive changes in DNA.
- DNA molecules can break and rejoin, grossly disrupting genetic sequences.
Can be caused by damage to chromosomes by mutagens or by errors in chromosome replication.
- DNA molecules can break and rejoin, grossly disrupting genetic sequences.
deletion
chromosome breaks in two places and rejoins, leaving out part of the DNA.
duplication
homologous chromosomes break at different positions and reconnect to the wrong partners.
inversion
chromosome breaks and rejoins with one segment flipped.
translocation
segment of DNA breaks off and attaches to another chromosome; can cause duplications and deletions.
retroviruses
- Retroviruses insert their DNA into the host genome at random.
- If the insertion is within a gene, it can cause a loss of function mutation.
- The viral DNA can remain in the host genome and be passed from one generation to the next.
It is called an endogenous retrovirus.
transposons
- Transposons (transposable elements) also insert themselves into genes and cause mutations.
- They can move from one position in a genome to another and usually carry genes to encode enzymes for this movement.
- Short sequences can be left behind and become mutations.
- Some transposons replicate and copies are inserted into new sites.
- Some genomic DNA is sometimes carried along with the transposon, resulting in gene duplication.
Gene duplication events play an important role in evolution.
induced mutation
agent from outside the cell (a mutagen) causes a change in DNA.
ionization induced mutation
Ionizing radiation (X-rays, gamma rays, radiation from unstable isotopes) creates highly reactive free radicals.
- Free radicals can change bases into forms not recognized by DNA polymerase.
Ionizing radiation can also break the sugar-phosphate bonds of DNA, causing chromosomal abnormalities.
ionization induced mutation
Ionizing radiation (X-rays, gamma rays, radiation from unstable isotopes) creates highly reactive free radicals.
- Free radicals can change bases into forms not recognized by DNA polymerase.
Ionizing radiation can also break the sugar-phosphate bonds of DNA, causing chromosomal abnormalities.
UV induced mutation
UV radiation (from sun or tanning beds) is absorbed by thymine, causing it to form covalent bonds with adjacent bases and disrupt DNA replication
restriction endonucleases
Enzymes that cut double stranded DNA at specific sequences
Endonucleases
cut inside the sequence.
Exonucleases
cut from the extremities.
Ribonucleases, RNase
nucleases that cut RNA
DNA Polymerases
They copy a DNA strand into another DNA strand
DNA polymerisation
base extension in the 5’ to 3’ direction.
Three main types of DNA polymerases in bacteria
- DNA pol. I: main enzyme for DNA replication in bacteria.
The DNA polymerases used in PCR belong to this group - DNA pol. II: involved in DNA repair
- DNA pol. III: involved in DNA replication
processivity
number of nucleotides added to the new strand per second.
fidelity
rate of errors (wrong nucleotides added)
RNA polymerases in eukaryotes
RNA polymerase I: Large ribosomal RNAs.
RNA polymerase II: Messenger RNA.
RNA polymerase III: transfer RNA and small RNA.
RNA polymerases in prokaryotes
The same RNA polymerase produces messenger RNA and non coding RNA (rRNA, tRNA, sRNA).
Reverse Transcriptases
- RNA-dependent DNA polymerase
- Transcribe single-stranded RNA into single-stranded complementary DNA (cDNA).
vectors
- They are small DNA molecules having regulatory and coding sequences.
- Foreign DNA can be inserted into them.
- They are used as carriers of foreign DNA into host cells.
Origin of replication
replication of the vector, together with the foreign DNA fragment inserted into it.
Genetic markers
selection of cells which have taken up the plasmid DNA.
Multiple cloning site
a site where DNA is inserted
Transfer DNA (some vectors)
transfer a gene into a target genome.
Plasmids
Double stranded circular bacterial DNA used for molecular cloning to amplify or express insert DNA into bacterial hosts.
Phagemids or phasemids
DNA cloning vectors derived from phage DNA and containing an origin of replication. They are used to amplify insert DNA via bacteriophage replication into host cells.
Cosmids
Minimal phage vectors lacking the origin of replication.
Bacterial Artificial Chromosome: BAC
Large DNA vectors engineered from the F plasmid which behaves like a chromosome.
They are used to carry large insert DNA up to 300 Kb and are used to create and store genomic libraries.
They are very useful in genome studies.
Bacterial Artificial Chromosome: BAC
Large DNA vectors engineered from the F plasmid which behaves like a chromosome.
They are used to carry large insert DNA up to 300 Kb and are used to create and store genomic libraries.
They are very useful in genome studies.
Yeast Artificial Chromosome: YAC
YAC vectors act like real chromosomes in yeast and can store very long DNA fragments (over 150 kb in size).
Used in genomic studies
Molecular probes
- Labelled polynucleotide DNA or RNA fragments, variable in size (100-1000 bp), natural or synthetic.
- Used for detection of DNA or RNA targets present in complex samples via hybridization by sequence complementarity.
Oligonucleotides (oligos)
- Short (6-60 nucleotides) oligonucleotide sequences.
- Single strand oligos: used as primers for DNA and RNA amplification.
double strand oligos
used as adapters that are ligated to DNA fragments to facilitate cloning and other applications.
Genome sequencing
determining the base sequences of an entire genome
Transcriptom
subset of the genome expressed as RNA in a particular cell or tissue at a particular time.
probes
Labelled RNA or DNA fragments with a known sequence used to detect a complementary sequence in a DNA or RNA population.
Genomics: Genome analysis
Sequencing of the transcriptome (total expressed genes in a tissue) or the entire genome
Sequencing DNA libraries containing fragments representing the entire genome of a given organism.
Transcriptome analysis:
Expressed Sequence Tags (ESTs)
Random sequencing of thousands of clones from a cDNA library prepared from a given tissue at specific conditions.
