Genetics Exam I

Mitosis

Cell division that generates two genetically identical cells

Cell Cycle

G1 (Gap I): Phase of growth and metabolism

S phase: DNA synthesis (doubling of homologous chromosome pairs)

G2 (Gap II): Growth, DNA Checkpoint, and repair

M phase: Cell Division (mitosis)

Prophase (Mitosis)

Chromosomes condense and centrioles divide

Prometaphase (Mitosis)

Fully condensesd chromosomes move toward the cell equator, centrioles reach opposite poles, and spindle fibers form

Anaphase (Mitosis)

Centromeres split and sister chromatids are pulled to opposite poles

Telophase (Mitosis)

Chromosomes are at the poles and cytokinesis occurs

Cytokinesis (Mitosis)

Division of the cytoplasm

Astral Microtubules

Mitotic microtubules that extend from the MTOC out to the cell periphery/cortex

Kinetochore Microtubules

Mitotic microtubules that extend from the MTOC to chromosomes

Polar Microtubules

Mitotic microtubules that extend from one pole to the other

Meiosis

Cell division that generates four, haploid cells

Meiosis I

First division in meiosis where homologous chromosomes are separated

Meiosis II

Second division in meiosis during which sister chromatids are separated

Gametes

Haploid cells produced by meiosis (sperm & ovum)

Polar Boidies

Produced along with one haploid ovum/egg during meiosis

Aneuploidy

Gain or loss of one or more individual chromosomes (primarily results from nondisjunction during meiosis)

Euploidy

Addition of complete haploid sets of chromosomes

Nondisjunction

Process that primarily leads to aneuploidies during meiosis

Trisomy

Condition involving the addition of a single chromosome

Polyploidy

More than two haploid sets of chromosomes

Autopolyploidy

Additional of one or more chromosome sets that are identical to the haploid complement of the same species

Allopolyploidy

Combination of chromosome sets from different species

Amphidiploids

Organisms resulting from allopolyploid

Impacts commercialization of plants

Metaphase I (Meiosis I)

Homologous chromosome pairs align at metaphase plate

Anaphase I (Meiosis I)

Homologous chromosomes are pulled to poles

Telophase I

Cytoplasm divides (→ two cells with one of each chromosome [paternal or maternal])

Metaphase II (Meiosis II)

Chromosomes align at the metaphase plate

Anaphase II

Sister chromatids separate and are pulled to opposite poles of the cell by spindle fibers

Sister Chromatids

Two identical halves of a chromosome

Telophase II (Meiosis II)

Chromosomes gather at the two poles of the cell and the cell divides (cytokinesis) forming four unique haploid daughter cells

Theory of epigenisis

Adults arise from the growth of a fertilized egg undergoing successive developmental events to form an adult organism

Theory of Preformation

Adults arise from the growth of fully formed organisms already present in the sperm or egg

Nucleotides

Building blocks of DNA (Nitrogenous Base + Pentose + Phosphate Group)

Purine (Nitrogenous Base)

9-member double ring (Adenine, Guanine)

Pyrimadine (Nitrogenous Base)

6-member single ring (Cytosine, Uracil, Thymine)

Phosphodiester Bond

Links two sugars in a polynucleotide backbone

5’ End

End of a polynucleotide where the phosphate group attaches at #5-C

3’ End

End of a polynucleotide where the hydroxyl group is located at the #3-C

Spectrophotometer

Instrument that measures the spectral components of a substance, used to measure nucleic acid concentration by their absorption of UV light at 260nm

A260 Reading (Optical Densitiy)

Measure of light absorption at 260nm

Directly proportional to DNA concentration (A260 of 1 = 50 μg/ml dsDNA)

Hyperchromic Shift

An increase in UV absorption that occurs with DNA denaturation (separation of DNA strands)

Molecular Hybridization

Method to locate specific DNA sequences by created an identifiable complementary RNA probe unique to the sequence of interest, which is mixed with denatured single strands of DNA and allowed to anneal during slow cooling

FISH (Florescence in situ Hybridization)

Method used to analyze DNA using a flourescently labeled complementary RNA probe, unique to a sequence of interest, to locate specific DNA sequences

Gel Electropheresis

Method used to separate DNA molecules based on their charge and size (typically using a porous agarose matrix where DNA fragments move toward the positive anode and are visualized with a DNA dye)

Polymerase Chain Reaction (PCR)

Method used to amplify specific DNA sequences (used as an analytical method)

DNA Sequencing

Method used to determine the order of nucleotides in a DNA molecule (used as an analytical method)

Initiation (DNA Replication)

Helicase unwinds double helix and single strand binding proteins keep unwound strands open

Elongation (DNA Replication)

DNA polymerase adds precursor dNTPS (deoxynucleotide triphosphates) to the 3’ OH end, building new strands in the 5’ to 3’ direction

Termination (DNA replication)

RNA primers are replaced with DNA sequences and ligases covalently links Okazaki fragments

Chromosomal Recombination

Exchange of material between homologous chromosomes

Endonuclease Nicking (Homologous Recombination Step I)

Endonuclease cuts DNA strands

Stand Displacement (Homologous Recombination Step II)

One DNA strand moves out of its original position

Ligation (Homologous Recombination Step III)

DNA strands joined together

Branch Migration (Homologous Recombination Step IV)

Strands have exchanged then move along the DNA molecule

Duplex Separation (Homologous Recomination Step V)

Separation of DNA duplexes

Rotation/Holliday Structure (Homologous Recombination Step VI)

DNA duplexes undergo rotation, forming cross-shaped intermediate (Holliday Structure)

Histones

Positively charged proteins around which negatively charged DNA wraps, forming nucleosomes; amino acids in their tails are positively charged

Solenoids

Higher order structure formed when nucleosomes coil and stack onto each other

Chromatin Fiber

Looped domains formed by the coiling and stacking of solenoid fibers

Nucleosome Core Particles

Composed of eight histone proteins (two of each H2A, H2B, H3, H4)

Euchromatin

Open chromatin conformation

Gene activation and active transcription

Heterochromatin

Closed chromatin conformation

Gene repression

Interchromatin Compartment

Regions within the nucleus containing transcription factories and RNA processing machinery

Elongation (Transcription)

RNA nucleotides are added complementary to the template DNA strand (Uracil replaces Thymine)

Termination (Transcription)

Terminator sequences within DNA signal transcription to stop, recruiting proteins that cleave the transcript and causes RNA polymerase to dissociate from DNA

RNA Processing

Modifications that RNA undergoes before being translated into protein (addition of 5’ cap, splicing of introns, and addition of Poly-A tail)

5’ Cap

Modification added to the 5’ end of mRNA for protection and ribosome attachment

Poly-A Tail

Am modification, consisting of a long chain of adenine nucleotides, added to the 3’ end of mRNA for stability and nuclear export

tRNAs

RNA molecules responsible for reading the mRNA message and bringing the corresponding amino acids to the ribosome during translation

A site (Ribosome)

Amino acid or acceptor site on ribosome where charged tRNA binds

P site (ribosome)

Peptides site on the ribosome where peptide bond is formed between amino acids

E site (Ribosome)

Exit site on ribosome where uncharged tRNAs leave

Primary Structure (protein)

Linear sequence of amino acids in polypeptide chain

Secondary Structure (protein)

Local folded structures within a polypeptide (such as α-helices and β-pleated sheets)

Tertiary Structure (protein)

The overall three-dimensional shape of a single polypeptide chain

Quanterany Sequence (protein)

The arrangement of multiple polypeptide chains (subunits) in a protein complex

Cis-acting Sites

Specific DNA sequences located in or around genes that are recognized and bound by regulatory proteins to influences gene expression (TATA-box, enhancers, silencers)

General Transcription Factors

Proteins that bind to cis-acting sites to initiate basal levels of transcription; they assemble in a specific order to form a pre-initiation complex (PIC) and some recruit RNA polymerase II (RNAPII)

Histone Tail Modification

Chemical changes to the tails of histone proteins (acetylation, methylation, etc.) that alter their interaction with DNA, affecting chromatin conformation and gene accessibility

Histone acteyltransferases (HATs)

Enzymes that add acetyl groups to histones, reducing their positive charge and typically promoting gene activation

Histone decatylases (HDACs)

Enzymes that remove acetyl groups from histones, increasing their positive charge and typically promoting gene expression

Histone methyltransferatses (HMTs)

Enzymes that add methyl groups to histones, which can be repressive or activating depending on the specific modification

Chromatin Remoldeling Complexes

Promoting complexes that reposition or remove nucleosomes, altering chromatin conformation to control DNA accessibility

DNA Methylation

The addition of a methyl groups to cytosine base, primarily in CpG island by DNMTs (DNA methyltransferases). It inhibits transcription factories binding and recruits repressive chromatin remodelers, leading to repressed gene expression

DNA methyltransferase (DNMTs)

Enzymes responsible for adding methyl groups to DNA

RNA Degredation Pathways

Mechanisms by which mRNA molecules are broken down

Decapping (removal of 5’ cap)

Deadenylation (shortening of poly-A-tail)

Internal cleavage by nucleases

Small interfering RNAs (siRNAs)

Longer, double-stranded RNA molecules involved in RNA-induced gene silencing (from viral infection, transposing, synthetic sources)

MicroRNAs (miRNAs)

Single-stranded RNA molecules with a double-stranded stem-loop structure, involved in RNA-induced gene silencing (from cell’s own genome)

DICER Complex

Protein complex that processes longer double-stranded RNAs into shorter siRNA or miRNA molecules during RNA-induced gene silencing

RISC (RNA-induced silencing complex)

Protein complex that denatures processed short RNAs and degrades the sense strand, mediating mRNA degradation or translation inhibition

RITS (RNA-induced transcriptional silencing complex)

Protein complex that recruits chromatin remodeling enzymes to mediate chromatin modification and transcription repression

Long noncoding RNAs (lncRNAs)

Class of ncRNAs that regulate gene expression by forming RNA-protein complexes with chromatin regulators, recognizing specific genomic locations, participating in chromatin remodeling, and interacting with transcription factors

Noncoding RNAs (ncRNAs)

RNA molecules transcribed from the genome that are not translated into protein, but instead play regulatory roles

Histone Code

The sum of patterns and interactions of histone modifications on nucleosomes that influence gene expression