BIOL 207

Genetics

The study of genes, heredity, and genetic variation.

Genetic material

Must be able to contain large amounts of complex information, replicate faithfully, encode the phenotype, and have the capacity to vary.

DNA

Consists of two complementary and antiparallel nucleotide strands that form a double helix.

X-ray crystallography

The gold standard technique to resolve the 3D structure of biological molecules.

Complementary DNA bases

A pairs with T, C pairs with G.

Genes

The basic unit of heredity.

Genome

The complete set of genetic material in a cell.

Model organisms

Common characteristics include short generation time, production of numerous progeny, ability to carry out controlled genetic crosses, ability to be reared in a laboratory environment, availability of numerous genetic variants, and an accumulated body of knowledge about their genetic systems.

Ribosomes

RNA molecules with enzymatic activity.

Nucleotide polymer strands

DNA is composed of two nucleotide polymer antiparallel strands, with the phosphate sugar backbone to the outside.

Base pairs

Held together by hydrogen bonds on the inside.

DNA synthesis

During DNA synthesis, the phosphate group of one nucleotide is covalently bound to the 3' carbon of deoxyribose sugar of another nucleotide.

Prokaryotic DNA replication

Most prokaryotes have circular DNA with one origin of replication recognized by the initiator complex (DnaA).

DNA polymerase

Can only attach nucleotides to a pre-existing 3'-OH group.

Primase

Synthesizes short RNA primers and complexes with helicase at the replication fork.

DNA ligase

Joins the Okazaki fragments together.

Single stranded binding proteins (SSBs)

Protect single stranded DNA and prevent secondary structures from forming.

DNA gyrase

Relieves torsion by cutting DNA.

Eukaryotic chromosomes

Associated with histone proteins, helping to package DNA in a highly organized and condensed manner.

Nucleosomes

Reassembled quickly following replication.

Base pair error rate

Less than one error in every billion base pairs.

Origin recognition complex (ORC)

Attaches to each origin of replication and loads helicase onto dsDNA during the G1 stage of the cell cycle.

Telomeres

Ends of eukaryotic chromosomes, consisting of many repeats of a short sequence.

Telomerase

Ribonucleoprotein enzyme that elongates the ends of eukaryotic chromosomes and has specialized reverse transcriptase activity.

Double stranded breaks

Normally, double stranded breaks in chromosomes are unstable and lead to chromosome degradation, telomeres must act to stabilize and protect the double stranded ends.

Telomere associating proteins

Bind to the free end of the DNA.

Diploid cells

Carry two sets of genetic information.

Haploid cells

Carry one set of genetic information.

Anaphase

Sister chromatids separate, becoming individual chromosomes that migrate towards spindle poles.

Telophase

Chromosomes arrive at spindle poles, the nuclear envelope reforms, the condensed chromosomes relax.

Cytokinesis

Cytoplasm divides, cell walls form in plant cells.

Cell cycle

Produces two cells that are genetically identical to each other and to the cell that created them.

Chromosome fragments without centromeres

Are lost in mitosis.

G0 phase

Stable non-dividing period.

Interphase

Includes G1, growth and development of the cell; S, synthesis of DNA; G2, preparation for division.

Prophase

Chromosomes condense and mitotic spindle forms.

Prometaphase

Nuclear envelope disintegrates, spindle microtubules anchor to kinetochore.

Metaphase

Chromosomes align on the metaphase plate.

Mitosis

Is for cellular reproduction.

Meiosis

Produces gametes for sexual reproduction.

Prophase one

Is the first stage of meiosis.

Holliday model of recombination

Involves synapsis, crossing over, and the formation of holliday junctions.

Synapsis

Close pairing of homologous chromosomes.

Tetrad

Closely associated four-sister chromatids of two homologous chromosomes.

Crossing over

Crossing over of chromosome segments from the sister chromatid of one chromosome to the sister chromatid of another chromosome.

Daughter cells in meiosis

Are genetically variable.

Cohesins

Proper chromosome and sister chromatid segregation depends on these proteins.

Double strand break model of recombination

Involves alignment of two double stranded DNA molecules from homologous chromosomes, followed by a double stranded break.

Base substitutions

Include transitions (purine-purine) and transversions (purine-pyrimidine), with transitions being more common.

Insertions and deletions

Alter the reading frame and may change many codons.

Depurination

Loss of a purine.

Deamination

Loss of an amino group.

Strand slippage

Occurs when one of the DNA strands forms a small loop, resulting in the omission of a nucleotide on the new strand after synthesis.

Unequal crossing over

Occurs when homologous chromosomes misalign during crossing over, resulting in one having a deletion and the other having an insertion.

Expanding nucleotide repeats

A set of nucleotides that increase in copy number.

Expanding nucleotide repeats

Set of nucleotides that increase in copy number.

Base substitutions

Can cause missense, nonsense, and silent mutations.

Reverse mutation

Reverses original mutation back to original state.

Chromosome rearrangement

Alter the structure of chromosomes.

Types of chromosome mutations

Duplication, deletion, inversion, translocation.

Duplications and deletions

Cause problems lining up during meiosis one.

Unequal crossing over

Can cause duplications and deletions.

Unbalanced gene dosage

Can result from duplications and deletions.

Aneuploidy

Alters the number of chromosomes.

Polyploidy

One or more complete sets of chromosomes are added.

Insertions or deletions

Can cause frameshift mutations or in-frame mutations.

Loss of function mutation

Partial or complete absence of gene product function, usually recessive.

Gain of function mutation

Gene product has a new function, usually dominant.

Conditional mutation

Phenotype seen under certain conditions.

Lethal mutation

Causes premature death.

Suppressor mutation

A mutation that hides or suppresses the effect of another mutation.

Homozygous deletions

Usually lethal.

Heterozygous deletions

Movement of genetic material between non-homologous chromosomes.

Nondisjunction

During meiosis and mitosis, usually lethal, exception is x chromosome in mammals.

Incomplete crossovers

During meiosis results in the majority of aneuploidy in humans.

Mismatch repair

Repair mechanism for DNA.

Nucleotide excision repair

The two strands of DNA are separated, a section of the DNA containing the distortion is removed, DNA polymerase fills in the gap, and DNA ligase seals the filled in gap.

Homology directed repair

Occurs shortly after DNA replication.

Base excision repair

No template used, is error prone.

Plasmids

Circular DNA molecules from bacteria.

Linkers

Synthetic DNA fragments containing restriction sites.

Selectable markers

Genes that encode a marker, typically visual or growth selective.

T4 DNA ligase

Covalently seals "nicks" in sugar phosphate bonds on two ends.

Origin of replication (ori)

Encoded in a DNA sequence inside the plasmid, allowing plasmids to replicate independently of the genome.

PCR reaction mixture

Contains DNA template, primers, dNTPs, DNA polymerase, and buffers.

Thermocycler

Allows repeated cycling of the first three steps in PCR.

ddNTPs

Special nucleotides used in DNA sequencing.

Crispr

Clustered regularly interspaced short palindromic repeats.

Crispr-CAS

Developed in bacteria to combat invading DNA elements, similar to an adaptive immune system.

Protospacers

Foreign DNA sequences that match spacer sequences unique sequences.

Pre-crRNA

Transcribed from the Crispr array into a single long precursor RNA.

Non-homologous end joining

An error-prone method to fix double strand breaks.

Homology directed repair

Less error-prone but also less efficient method to fix double strand breaks.

Forward genetics

Begins with a phenotype due to random mutations.

Reverse genetics

Begins with interest in a gene of unknown function.

Microsatellites

Short tandem repeats, variable number of copies.

DNA barcoding

Identify different species using DNA.

Transcriptional unit

Stretch of DNA encoding RNA molecule and sequences necessary for its transcription.

Transcriptional apparatus

RNA polymerase and array of accessory proteins.

Elongation

The process of adding nucleotides to the RNA molecule during transcription.