IB 204 Exam 1

DNA Polymerase III

Enzyme that catalyzes the production of DNA, stranding in a 5’ to 3’ direction

• requires a template and primer

DNA polymerase I

Enzyme that removes DNA from primer sequences and fills gaps with DNA during replication on the lagging strand, has 5’ to 3’ polymerase activity, exonuclease activity in both directions

Taq DNA polymerase

A thermostable enzyme used in DNA synthesis from the thermophilic organism Thermus aquaticus

DNA ligase

Enzyme that catalyzes the formation of phosphodiester bond between adjacent nucleotides

• involved in sealing ‘nick's’ (gaps in a single strand of DNA)

Gyrase/topoisomerase

Enzymes that catalyze changes in the topological state of DNA, such as relaxing supercoiling

ssDNA

Single stranded DNA

Primase

ssDNA-dependent RNA polymerase that synthesizes RNA primers during DNA replication

Helicase

Enzyme that unwinds the double helix by breaking hydrogen bonds between bases

Single stranded (ss) binding protein

Protein that bind single stranded DNA facilitating access of DNA polymerases

MCM2-7 complex

A eukaryotic DNA helicase

Licensing factor

Protein or complex of proteins that allows an origin of replication to begin DNA replication at that site

Kinase

Protein that attaches phosphate group to another molecule, often for the purpose of regulation

Telomere

DNA-protein structures found at both ends of a chromosome, protect genome from degradation, unnecessary recombination, and inter-chromosomal fusion

Telomerase

The enzyme responsible for maintenance of the length of telomeres by addition of guanine-rich repetitive sequences

End replication hypothesis

Proposal that the ends of linear DNA cannot be replicated completely

Germ cell

Reproductive cell, such as egg or sperm produced by meiosis in sexually reproducing organisms

Somatic cell

Any cell that is not a reproductive cell

Mutagen

Compound which causes mutations to DNA

Carcinogen

Compound which causes cancer (can be naturally occurring or mad-made)

Auxotroph

Mutant organism unable to grow without provision of a nutrient

Insertion

Mutation involving insertion of one or more nucleotides within a sequence of DNA

Deletion

Mutation involving loss of one or more nucleotides within a sequence of DNA

Substitution

Mutation involving replacement of one nucleotide with another within a sequence of DNA

InDel

An abbreviation describing the type of mutation

• “insertion or deletion”

Missense

Outcome of a mutation resulting in a change of the codon and resulting amino acid sequence of a gene

Nonsense

Outcome of a mutation resulting in generation of a stop codon

Silent

Outcome of a mutation that results in no change in the amino acid sequence of a protein

Reading frame

Specific choice out of three different ways to read a sequence of nucleotides

Frameshift

Outcome of a mutation caused by insertion or deletion of a nucleotide that changes which downstream sequences are read by the ribosome

Nick (DNA)

Gap in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand

Mismatch (base pair)

Where two bases are paired together that do not match, introducing changes in DNA sequence

DNA adduct

Piece of DNA covalently bound to a chemical that can impede DNA replication

Base excision repair

Mechanism of repairing damage to individual base pairs involving removal and replacement

• recognizes specific modifications and involves enzymes such as DNA glycoslyases

Nucleotide excision repair

Mechanism for repairing single stranded DNA damage caused by chemicals, UV radiation or other mutagens, through the removal and replacement of segments of DNA

Deamination

Loss of an amino group from 5-methylcytosine creating thymine or from cytosine creating uracil

Cyclins

Proteins that control the progression of a cell through the cell cycle by activating cyclin-dependent kinases (CDK)

Cyclin dependent kinase

A group of protein kinases (enzymes which catalyze addition of a phosphate group) which control progression through the cell cycle

p53

Protein involved in regulating cell cycle progression in response to DNA damage

Bengin tumor

Growth of cells that does not invade tissues or spread to different areas of the body (non-cancerous)

Malignant tumor

Cancerous tumor that can invade tissues and spread to other parts of the body

Angiogenesis

Formation of new blood cells

Tumor supressor gene

Gene which works to regulate cell division which when inactivated can cause cancer

• these genes are recessive meaning both alleles must be inactive before inhibition of cell division is removed

Two-hit theory of cancer

Dominant pre-disposition to cancer comes from a germ-line mutation while tumorigenesis occurs through a second somatic mutation

Kinase

Enzyme which catalyzes the transfer of a phosphate group from ATP to another molecule

Rb (retinoblastoma protein)

Tumor suppressor protein involved in control of the G1 checkpoint

Checkpoint

Control point to pause the cell cycle to ensure necessary conditions have been met before progression

Proto-oncogene

Gene which causes cells to become cancerous when mutated

• turns into an oncogene

Oncogene

Mutated gene which causes cancer

• dominant, meaning that only allele needs to be activated to promote cell division

HER2

Human epidermal growth factor receptor

• controls growth differentiation of cells in response to hormone signaling

ras

Group of genes which encode proteins that regulate cell proliferation as part of a signaling cascade

raf

Family of serine/theronine protein kinases involved in the cellular proliferation signaling cascade

• activated by ras

v-src (SARK)

Viral src oncogene

c-src

Chromosomal src proto-oncogene

Sanger (dideoxy) sequencing

Method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides

Dideoxy trinucleotide phosphates (ddNTPs)

Nucleic acids with bases A, T, C, or G attached, that lack a 3’ hydroxyl group

p53

Transcription factor involved in initiating DNA damage repair

p21

Protein which binds to and inhibits CDK-cyclin complexes, preventing cell-cycle progression

ATM kinase (Ataxia-Telangiectasia Mutated kinase)

Enzyme involved in detection of dsDNA breaks and stabilizing p53 through phosphorylation