exam 2 bio review

conservative model

parental DNA remains together while newly formed daughter strands become paired

semi-conservative

each of the 2 parental DNA strands acts as a template for new DNA to be synthesized so that each newly formed daughter strands is paired with an “old” strand

dispersive model

both copies of DNA have double-stranded segments of parental DNA and newly formed DNA interspersed

meselson-stahl experiment

The experiment proved that DNA replication is semiconservative: every time a cell divides, each of the two resulting DNA molecules consists of one strand from the original molecule and one newly synthesized strand

polymerase chain reaction (PCR)

allows scientists to rapidly replicate lots of DNA

gel electrophoresis

allows scientists to determine what DNA was replicated in PCR

• where smaller DNA travels further

end-replication problem in eukaryotes

loss of genetic information due to RNA primers inability to “clip onto” the lagging strand (lack of space)

telomeres

protective, repetitive, non-coding regions at the end of linear chromosomes; prevents loss of coding regions of DNA during replication and unraveling/sticking of chromosome ends

telomerase

protein found in eukaryotic cells that extend telomeres by writing telomeric DNA

• in cancer, egg, sperm, and stem cells

centrifugation

separates heavy from light DNA

DNA polymerase

“proofreads” the replicated DNA for mitosis

• replaces errors

exonuclease activity (nuclease)

removal and replacement of incorrect nucleotides by cleaving the phosphodiester backbone

DNA ligase

seals gaps in DNA backbone

mismatch repair

incorrectly added bases are detected, removed, and replaced

base excision repair

only the damaged base is removed and replaced

nucleotide excision repair

1+ damaged bases are removed and replaced

if errors in replication are not repaired

mutations occur

induced mutation

caused by environment

• chemicals, xrays, UV light, lab experiments, etc

spontaneous mutation

naturally caused, randomly occurring

DNA mutations in non-coding DNA

most mutations occur in this type since it makes 97% of our DNA

• affects the expression of genes

• mutations still occur in coding regions

codon

sequence of 3 nucleotides

• represents an amino acid or start/stop signal of protein synthesis

point mutation

change of a single nucleotide for another

missense (point) mutation

one nucleotide change resulting in a different amino acid

• sickle cell anemia

nonsense (point) mutation

one nucleotide change resulting in a stop codon (UAA, UGA, UAG)

• duchenne muscular dystrophy

silent (point) mutation

single nucleotide change resulting in no change of amino acid

frame shift mutation

addition/deletion of nucleotide(s) that shift all following amino acids making them wrong (frameshift error)

• creates new proteins useless to the cell (stop codons)

• more severe than point mutations

• thalassemia + tay sachs disease

insertion/deletion of whole codons

no frameshift errors; may pose severe effects

spontaneous mutations

result from intracellular processes

• meiosis, inherent instability of nucleotide bases, DNA polymerase error, base pair degradation

induced mutations

result from external mutagens

external mutagens

factors that cause permanent change in DNA

• radiation, chemicals, infectious agents

DNA mutations are always harmful (T or F)

false, mutations that help organisms adapt will be more common over time

key principles of modern cell theory?

1) All organisms consist of cells. 2) Energy flow occurs within cells. 3) Cells are the basic structural/organizational unit. 4) Hereditary information is passed on. 5) All cells come from pre-existing cells. 6) All cells have the same chemical composition.

three primary functions of cell division?

1) Reproduction (creates new single-celled organisms). 2) Growth & development (from zygote or cuttings). 3) Tissue renewal/repair (replaces worn-out/damaged cells).

Define chromosome

Threadlike structure carrying genetic info/genes

Define plasmid

small, independent loops of non-essential DNA in prokaryotes

Define nucleosome

Eukaryotic structural unit made of DNA wrapped around histone proteins

How do prokaryotic and eukaryotic chromosomes differ?

Prokaryote: Single circular DNA, naked (no histones), plasmids present.
Eukaryote: Linear DNA, associated with histone proteins, no plasmids, 2+ distinct chromosomes

How do prokaryotes reproduce

binary fission

steps of binary fission

circular DNA replicates at origin; cell elongates; chromosomes separate; cell pinches into two identical daughter cells

What is the eukaryotic cell cycle and its general outcome?

The series of events following DNA replication that leads to cell division, producing 2 identical daughter cells (except in meiosis)

What is cell differentiation, and which cells typically divide?

the process where a less specialized cell becomes a specialized cell. Mostly undifferentiated cells (stem cells) divide.

What are the two main phases of the eukaryotic cell cycle?

interphase: Cell growth and chromosome copying (G1, S, G2)
Mitotic (M) Phase: Chromosome separation (mitosis) and physical cell division (cytokinesis)

What occurs during G1, S, G2, and G0 of interphase?

• G1: Cell growth & organelle/non-DNA content duplication.

• S: Chromosome replication (DNA synthesis).

• G2: Cell growth & error checks/repairs on duplicated DNA.

• G0: Cell cycle arrest/resting phase.

Define homologous chromosomes

Matched pairs of chromosomes

Define chromatids

Replicated copies of a chromosome

Define centromere

Connection point between sister chromatids where spindle fibers attach

What are the key outcomes and prerequisites of mitosis?

Produces 2 genetically identical daughter clone cells (half original size, then grow). It begins strictly following DNA replication.

What is the condition of DNA during Interphase prior to mitosis?

DNA is fully replicated, loosely coiled, and not visible under a light microscope

What events occur in Early Prophase?

Nuclear envelope disintegrates, chromosomes coil/condense, replicated centrioles move to opposite poles, and astral rays/spindle fibers form.

What events occur in Late Prophase? (prometaphase)

Chromosomes are pairs of sister chromatids joined at the centromere; kinetochores on centromeres attach to spindle fibers.

What key event defines Metaphase?

Chromosomes line up along the metaphase plate in the center of the cell

What key events occur during Anaphase?

Centromeres split, sister chromatids separate into individual chromosomes and are pulled to opposite poles along spindle fibers

What key events occur during Telophase?

Cytoplasm constricts (cleavage furrow), nuclear membranes reform, nuclei enlarge, and chromosomes uncoil back into chromatin.

What is cytokinesis and when does it begin/end

Physical division of the cell. Begins with cleavage furrow formation, continues through telophase, and its completion marks the end of cell division.

How does cytokinesis differ between animal and plant cells?

• Animal Cells: Form a cleavage furrow using a contractile ring.

• Plant Cells: Form a cell plate inside using Golgi vesicles.

What is meiosis and its primary functions?

Sexual cell division forming 4 genetically unique haploid gametes.
Halves chromsome number (2n > n); introduces genetic diversity via random alignment and crossing over

What is crossing over and between what structures does it occur?

Exchange of genetic material between non-sister chromatids of homologous chromosome pairs during meiosis, increasing variability

Define Diploid (2n) and haploid (n) in human contexts

Diploid (2n): normal somatic cell count with 2 chromosome sets (Humans: 2n = 46)
Haploid (n):gamete chromosome count containing one set (Humans: n = 23)

Outline the basic sequence and product of Meiosis.

DNA replicates once before Meiosis I, followed by two consecutive divisions (Meiosis I & Meiosis II) producing 4 haploid daughter cells

What happens during Meiosis I?

Non-sister chromatids cross over, and homologous chromosome pairs separate, reducing chromosome number from $2n$ to $n$

What happens during Meiosis II?

Sister chromatids separate, giving each daughter cell an equal share of unreplicated chromosomes.

What causes Down Syndrome (Trisomy 21)?

Non-disjunction (chromatids failing to separate correctly during meiosis), resulting in an extra copy of chromosome 21

What are the 3 main cell cycle checkpoints

G1 + G2 Checkpoints, M Checkpoint

G1 Checkpoint

Checks cell size, nutrients, social signals, and undamaged DNA.

G2 Checkpoint

Checks faithful chromosome replication, undamaged DNA, and mitosis-activating proteins.

M Checkpoint

Checks that all chromosomes are properly attached to spindle fibers.

what external factors regulate cell growth in vitro (outside living organism) vs in vivo (inside living organism)?

In Vitro: Availability of essential nutrients and density-dependent inhibition (overcrowding prevents division)
In Vivo: Growth factors (e.g., PDGF) and anchorage dependence (cells must attach to a substrate).

Necrosis

Uncontrolled cell death from loss of homeostasis (toxins, hypoxia) without gene coordination

Apoptosis

Programmed, tightly controlled cell death triggered when cells are unneeded or damaged

What are caspases and how are they activated?

Digestive enzymes that cleave specific cytoplasmic/nuclear proteins to cause cell death. Activated from inactive procaspases via a proteolytic caspase cascade.

proteolytic caspase cascade

extra/intra-cellular signals from immune cells / organelle damage that activate procaspases (inactive) into caspases (active)

What happens if a cell passes checkpoints with damaged DNA?

It is either destroyed by the immune system or becomes cancerous.

• G1 is the most common point of failure

Tumor Suppressor Genes

Code for proteins that prevent uncontrolled division (e.g., P53, P21, Rb)

Proto-oncogenes

Code for proteins that promote cell division (e.g., Cdk); become cancer-causing oncogenes when mutated

Transformation

A single cell becomes cancerous.

Benign Tumor

Non-invasive mass of abnormal cells staying in one spot

Malignant Tumor

Invasive cells that spread (metastasis) and impair organ function

What structural features distinguish cancer cells under a microscope?

Abnormal chromosome numbers and multipolar or malformed spindle apparatuses.

Taxol (Chemotherapy)

Forcibly stabilizes microtubules, preventing spindle breakdown and stopping division.

CAR-T Cells (Immunotherapy)

Patient T-cells are extracted, reprogrammed to recognize cancer, and reinjected

Define DNA replication and state when it occurs in prokaryotes vs eukaryotes

Process of copying the genome. Occurs prior to binary fission in prokaryotes, and during the S phase of interphase in eukaryotes.

What are the 2 basic steps of DNA replication

1) DNA unwinds/strands separate. 2) New strand is synthesized using old strand as template

What are the 3 essential ingredients of DNA replication?

Parental template DNA, specialized proteins, and nucleotide triphosphates

Name the 3 proteins involved in DNA unwinding

Helicase, topoisomerase, Single-Strand Binding (SSB) Proteins

Helicase

Opens DNA double helix by breaking hydrogen bonds.

Topoisomerase

Relieves unwinding strain by cutting and resealing DNA.

Single-Strand Binding (SSB) Proteins

Bind single strands to keep them from rewinding

Name the 4 proteins involved in DNA strand synthesis

Primase, DNA Polymerase, Ligase, and Sliding Clamp

Primase

Synthesizes short RNA primers to initiate synthesis

DNA Polymerase

Adds complementary nucleotides (5’ to 3') and replaces RNA primers

Ligase

Seals gaps/nicks in sugar-phosphate backbone

Sliding Clamp

Holds DNA Polymerase in place during synthesis

What bond holds the 2 DNA strands together?

hydrogen bonds

what bond is in the sugar phosphate backbone

phosphodiester bond

Leading Strand

Continuous synthesis toward the helicase (3’ to 5’)

Lagging Strand

Discontinuous synthesis away from helicase (5’ to 3’)

Okazaki Fragments

Short DNA pieces synthesized on lagging strand, later joined by ligase

origin of replication

specific genomic sequence where replication begins

replication fork

unwound “bubble” structure where strands separate and replicate in both directions

Which direction are nucleotides added, by base-pairing, and what bonds form?

Added in 5’ to 3’ direction (A-T, G-C). Hydrogen bonds form between base pairs, and phosphodiester bonds form along the backbone