315: Unit 1

Glycolysis

the anaerobic breakdown of glucose to pyruvate, with the net energy gain of 2 molecules of ATP

Oxidative metabolism

the use of molecular oxygen as an electron acceptor in the breakdown of organic molecules

Ribosomes

a particle composed of RNA and proteins that is the site of protein synthesis

Mitochondria

responsible for synthesis of most ATP in eukaryotic cells by oxidative phosphorylation

Chloroplast

responsible for photosynthesis in the cells of plants and algae

Lysosomes

contains enzymes that break down biological polymers

Peroxisomes

carry out oxidative reactions

Vacuoles

large membrane-enclosed sac in the cytoplasm of eukaryotic cells; in plant cells vacuoles store nutrients and waste, degrade macromolecules, and maintain turgor pressure

Endoplasmic Reticulum

an extensive network of membrane-enclosed tubules and sacs involved with protein sorting and processing as well as in lipid synthesis

Rough ER

region of ER covered with ribosomes and involved in protein metabolism

Smooth ER

region of ER that is the major site of lipid synthesis in eukaryotic cells

Chromatin

complexes between eukaryotic DNA and proteins; makes DNA compact

Histones

small proteins containing a high proportion of basic amino acids that facilitate binding to the negatively charged DNA molecule

Nucleosomes

consisting of DNA wrapped around a histone octamer; are the basic structural unit of chromatin

Centromeres

sites at which microtubules attach to chromosomes during mitosis

Kinetochore

a specialized structure consisting of proteins attached to a centromere that mediates the attachment and movement of chromosomes along the mitotic spindle

Telomeres

a repeat of simple-sequence DNA that maintains the end of linear chromosomes

DNA Polymerase

enzyme that catalyzes the synthesis of DNA

Replication fork

where 2 parental strands separate and daughter strands are synthesized

Okazaki fragments

a short DNA fragment synthesized to form the lagging strand

DNA ligase

seals break in DNA strand

Primase

synthesizes short fragments of RNA (primers)

Helicase

breaks H-bonds and unwinds DNA

Single stranded DNA binding proteins

stabilize unwound DNA by binding to single stranded regions

Topoisomerase

catalyzes the reversible breakage and rejoining of DNA strands so they don’t get too twisted

Histone chaperones

proteins that remove histones ahead of the replication fork during DNA replication in eukaryotic cells and reinsert them into the DS DNAs behind the replication fork

What are the steps in DNA replication?

Initiation, Elongation, Termination

What is the initiation site for DNA synthesis?

Origin of replication

What is the catalytic activity of DNA polymerase?

DNA polymerase catalyzes the elongation of a DNA strand by adding nucleotides to the 3’- hydroxyl group of a primer

What is the reaction the DNA polymerase catalyzes?

The DNA polymerase has 5’ to 3’ polymerase activity and forms a phosphodiester bond.

What are the DNA polymerase’s substrates?

The DNA polymerase’s substrates are dNTPs (deoxynucleoside triphosphates), a template strand, and a primer.

What is the proofreading activity in DNA polymerase?

The 3’ to 5’ exonuclease function which detects and removes mismatched nucleotides

5’ to 3’

Refers to 5’ phosphate and 3’ hydroxyl group

Exonuclease

an enzyme that removes nucleotides one at a time from the ends (5’ to 3’) of a nucleic acid strand

Endonuclease

an enzyme that cleaves phosphodiester bonds within the internal parts of a nucleic acid strand

Telomerase

a specialized ribonucleoprotein enzyme that maintains the ends of the linear chromosomes, known as telomeres, by adding repetitive DNA sequences

Pyrimidine dimers

adjacent pyrimidines on the same strand of DNA are joined by the formation by the formation of a cyclobutane ring resulting from the saturation of the double bonds between carbon 5 and 6

Base excision repair

single damaged bases are recognized and removed; glycosylase recognizes mutated base and cuts it out, endonuclease cleaves the DNA chain, phosphodiesterase removes sugar from the backbone, and the gap is repaired by polymerase and ligase

DNA glycosylase

an enzyme that cleaves the bond linking the base (uracil) to the deoxyribose of the DNA backbone

Nucleotide Excision Repair

damaged bases (ex: thymine dimers) are removed as part of an oligonucleotide containing the lesion; protein complex recognizes distortion in DNA, helicase unwinds the DNA, endonuclease cleaves on either side of the damage, the fragment is displaced, and polymerase and ligase fill in the gap

Non Homologous End Joining

double strand break repair; often introduces insertions and deletions; clean off ends of broken DNA and just stick it together

Homology Directed Repair

uses an undamaged homologous DNA strand to repair a ds break; double stranded break recruits 5’ to 3’ exonuclease, recombinase is recruited to 3’ overhangs, and recombinase catalyzes the invasion and exchange of one DNA strand for another

Synthesis Directed Strand Annealing

ds break repair through homologous chromosome as a template

Holliday Junctions

junction between ds DNA that can form as part homology-directed repair of ds breaks in genomes of eukaryotic cells

Translesion DNA synthesis

cells use it to copy DNA past a damaged spot that would otherwise stop the normal replication machinery; specialized error prone polymerase temporarily replace normal enzymes to bypass the lesion risking mutations but preventing cell death; normal DNA polymerase gets stuck, and it can’t read through, specialized DNA polymerase recruited and adds a few bases, specialized DNA polymerase is replaced by a normal polymerase, the lesion is excised after synthesis (nucleotide excision repair)

Why does translesion DNA synthesis cause mutations?

it relies on specialized error-prone polymerases with no proofreading and flexible active sites

What are the steps in nucleotide excision and repair of thymidine dimers?

Protein complexes scan the DNA to find structural distortions caused by thymine dimers, enzymes unwind and open the DNA around the damaged thymine, endonucleases make cuts on both sides of thymine dimer, DNA polymerase bind to the resulting single strand gap, and DNA ligase creates a final phosphodiester bond to seal the remaining nick in the sugar phosphate backbone

Mismatch repair

specialized enzymes chop out and remove a single-stranded segment of DNA containing an incorrectly paired base; (muts wrap around and slide down DNA) protein complex recognizes distortion in DNA, helicase unwinds the DNA, exonuclease nicks and chews out a stretch of DNA (excision), and then replication continues as normal