IB 203 Genetics UIUC Exam 1 Key terms Fall 2026

A set of vocabulary flashcards covering key terms in molecular biology, cell cycle regulation, DNA repair, and replication.

Sanger (dideoxy) sequencing

A 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

A transcription factor involved in initiating DNA damage repair and regulating cell cycle progression in response to DNA damage.

p52

A protein which binds to an inhibits CDK-cyclin complexes preventing cell-cycle progression.

ATM kinase

Ataxia-Telangiectasia Mutated kinase is an enzyme involved in detection of dsDNA breaks and stabilizing p53 through phosphorylation.

Proto-oncogene

A gene which causes cells to become cancerous when mutated (turns into an oncogene).

Oncogene

A mutated gene which is causes cancer. Oncogenes are dominant, meaning that only one allele needs to be activated to promote cell division.

HER2

Human epidermal growth factor receptor, controls growth a differentiation of cells in response to hormone signaling.

ras

A group of genes which encode proteins that regulate cell proliferation as part of a signaling cascade.

raf

A family of serine/threonine protein kinases involved in the cellular proliferation signaling cascade. Activated by Ras.

v-src

Pronounced "SARK" viral src oncogene

c-src

Chromosomal src proto-oncogene

Tumor supressor gene

A gene which works to regulate cell division which when inactivated can cause cancer. Tumor suppressor 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

An enzyme or protein that catalyzes the transfer or attachment of a phosphate group to another molecule, often for the purpose of regulation.

Rb (retinoblastoma protein)

A tumor suppressor protein involved in control of the G1 checkpoint

Checkpoint

A control point to pause the cell cycle to ensure necessary conditions have been met before progression.

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.

Benign tumor

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

Malignant tumor

A cancerous tumor that can invade tissues and spread to other parts of the body.

Angiogenesis

The formation of new blood cells

Nick (DNA)

A 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

A 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.

Germ cell

A 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

A compound which causes mutations to DNA

Carcinogen

A compound which causes cancer (can be naturally occurring or man-made)

Auxotroph

A mutant organism unable to grow without provision of a nutrient.

Insertion

A mutation involving insertion of one or more nucleotides within a sequence of DNA.

Deletion

A mutation involving loss of one or more nucleotides within a sequence of DNA

Substitution

A 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

The 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.

DNA Polymerase III

Enzyme that catalyzes the production of DNA strands in a $5'$ to $3'$ direction. Requires a template and primer.

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.

DNA polymerase I

Enzyme that removes RNA 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 'nicks' (gaps in a single strand of DNA).

Gyrase/topoisomerase

Are 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

An 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

A protein or complex of proteins that allows an origin of replication to begin DNA replication at that site.

Mutation Causes

DNA replication errors, DNA damage, Imperfect DNA repair

Somatic Mutation

Not heritable, only effects 1 type of tissue

Germline Mutation

A mutation that occurs in the germ cells, which can be passed on to offspring and affect every cell in the organism.

Ames Test

Uses Salmonella (a strain of bacteria) to test whether a given chemical can cause mutations in DNA (mutagen). The strains of Salmonella can’t make histidine, which allows the colony to grow, so if colonies grow after exposing the bacteria to the chemical, the chemical caused a mutation. A positive Ames test indicates a mutagen but does not necessarily mean it is a carcinogen. Larger organisms have metabolisms that can turn nonmutagenic chemicals into mutagenic ones, and vice versa. Rat enzymes used to mimic metabolic processes.

AMES test experiment steps

1. Start: his⁻ Salmonella + small amount of histidine

2. Add: rat liver extract

3. Test: add the test compound

4. Plate: put bacteria on histidine-free medium

5. Incubate: let colonies grow

6. Compare: test plate vs. control plate

7. Interpret: more colonies than control = mutagenic

3 Pieces of evidence to define a carcinogen

• Short term assays (AMES test)

• Long term animal tests over 2 yrs

• Epidemiology

and verified by WHO

DNA damage like UV damage can cause polymerase stalling at replication fork. Why is this bad?

Can cause dsDNA breaks that lead to error prone DNA repair

TLS

type of DNA polymerase that subs in polymerase alpha when DNA damage is detected.

TLS insertion process

1. DNA Polymerase alpha stalling due to DNA damage

2. Ubiquitin sends Ub tag to PCNA to release DNA pol alpha

3. DNA pol a replaced with TLS to bypass damage and continue replication

Scientific Method

1. Make an observation

2. Ask a question

3. Form a hypothesis

4. Conduct experiments/ collect data

5. Analyze data and draw conclusions

Retinoblastoma

Cancer of the eye

Explain how some cancers are heritable with reference to the two-hit hypothesis and retinoblastoma

Some cancers are considered heritable because an individual’s susceptibility to developing cancer is increased when they inherit a mutated or dysfunctional allele. The two-hit hypothesis states that both alleles of a tumor suppressor gene must be inactivated or lost for that tumor suppressor to lose its normal function and contribute to cancer development. These two “hits” can occur as two somatic mutations during a person’s lifetime, or a person can inherit the first mutation and later acquire the second.

In the case of retinoblastoma, when an individual inherits a mutation that inactivates one allele of the RB tumor suppressor gene, they only need one additional mutation in the remaining healthy allele for both copies to be inactivated. In sporadic retinoblastoma, however, both RB alleles must acquire separate somatic mutations in the same retinal cell, which is much less likely. Sporadic bilateral retinoblastoma would be even less likely because separate cells in both eyes would each have to independently acquire two mutations in the RB gene.

6 Hallmarks of Cancer

1. Sustained Division

2. Replicative Immortality

3. Activation Invasion and Metastasis

4. Evade Growth Suppressors

5. Angiogenesis

6. Resisting Cell Death

What initiates lung cancer in non-smokers?

air pollution causes an inflammatory response that can promote tumor development.

Somatic Mutation Theory of Cancer

Cancer develops because mutations gradually accumulate in body cells over time.

1. First Causative mutation → Tumor population 1

2. Then one of those cells gets a second causative mutation. That cell may have a new advantage, like dividing faster or surviving better. It divides and creates → Tumor population 2

3. Then different cells continue picking up additional mutations.

4. Eventually, the tumor contains multiple genetically different groups of cancer cells

Those different groups are called subclonal populations.

Where do the mutations come from if they're non-smokers?

natural aging

Inflammatory model

Mutated cells may already exist, but inflammation helps activate/promote their growth.

According to current understanding of cancer development, which of the following is proposed. Cancer...

Often requires mutations in 4 or more different genes