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What is the primary purpose of homologous chromosomes during meiosis?

To control the timing of cell division

To produce identical daughter cells

To prevent mutation during cell replication

To promote genetic variation through crossover (correct)

Which phase of meiosis is characterized by the formation of chiasmata?

Prophase I (correct)

Metaphase I

Anaphase II

Telophase II

What is a consequence of a cell moving past the G1 checkpoint without repairing damaged DNA?

The damaged DNA will be replicated (correct)

The cell will stop dividing indefinitely

The cell will undergo programmed cell death

The cell will enter a growth phase

Which protein complex is essential for a cell to transition from G2 to mitosis?

Maturation Promoting Factor (MPF) Signup and view all the answers

How does genetic variation occur during meiosis?

Through both crossover and independent assortment Signup and view all the answers

During what process are four genetically distinct daughter cells formed?

Meiosis II Signup and view all the answers

What best describes independent assortment in meiosis?

Chromosomes align randomly at the metaphase plate Signup and view all the answers

Which of the following statements about sister chromatids is correct?

Sister chromatids are identical copies of a chromosome Signup and view all the answers

What explains the presence of 35-45 tRNAs for 61 codons?

Each tRNA can recognize multiple codons for the same amino acid due to wobble pairing Signup and view all the answers

Which type of mutation is responsible for sickle cell anemia?

Missense Signup and view all the answers

What occurs during the interphase of the cell cycle?

DNA replication in the S phase Signup and view all the answers

What is the role of the centromere in cell division?

Serves as a platform for kinetochore attachment Signup and view all the answers

What describes the state of chromosomes during anaphase?

Chromosomes are reeling in towards the poles Signup and view all the answers

Which of the following processes is NOT associated with cell division?

RNA splicing Signup and view all the answers

Which statement best describes sister chromatids?

Identical copies of a chromosome formed during DNA replication Signup and view all the answers

During which phase of the cell cycle do cells prepare for mitosis?

G2 phase Signup and view all the answers

During anaphase, how do chromosomes behave?

They walk along the microtubules toward the centrosomes. Signup and view all the answers

In which phase do chromosomes first visibly condense?

Prophase Signup and view all the answers

What role does the Rb protein play in the cell cycle?

It inhibits cell division. Signup and view all the answers

What is the main function of Cyclin D and CDK4/6 complexes during the cell cycle?

To remove the Rb protein and bypass the G1 checkpoint. Signup and view all the answers

What characteristic defines proto-oncogenes?

They regulate normal cell division. Signup and view all the answers

How do oncogenes contribute to cancer development?

They cause abnormal and rapid cell division. Signup and view all the answers

What marks the M checkpoint during cell division?

Ensuring kinetochores are attached at the metaphase plate. Signup and view all the answers

What is the role of tumor suppressor genes (TSG) like p53?

To initiate DNA repair and regulate the cell cycle. Signup and view all the answers

What is the significance of hyperactive Ras protein mutations?

They lead to uncontrolled cell division even in the absence of growth factors. Signup and view all the answers

How do cancer cells exhibit loss of anchorage dependence?

They can metastasize through the circulatory system. Signup and view all the answers

Study Notes

Midterm 2 Review - BIO 93 TRIO

F24 BioSci Peer Tutors: Victoria Vo, Sophie Cohen, Charlotte Phan, Hannah Song

Lecture 10: ATP

Hydrolysis of ATP is exergonic.
Hydrolysis of ATP can be coupled with endergonic reactions to make them spontaneous.
Energy is stored in the phosphate bonds of ATP.
Repulsion between negatively charged phosphate groups in ATP allows easy energy release when broken.

Lecture 10: Enzymes

Catalytic protein.
Greatly affected by pH and temperature. Optimal human enzyme temperature is 37°C.
General Structure:
- Substrate: molecule acted upon by the enzyme
- Active site: area of enzyme where reaction occurs
- Enzyme-substrate complex: the combination of enzyme and substrate
- Enzyme: catalyzes a reaction
- Products: result of enzyme activity
Steps of Enzyme Action:
- 1. Substrate binds to enzyme at active site.
- 2. Induced fit.
- 3. Enzyme performs catalytic activities.
- 4. Releases the product.
Inhibition of Enzymes:
Competitive inhibition
- Inhibitor
- Enzyme
- Substrate
Noncompetitive inhibition
- Inhibitor
- Enzyme
- Substrate
- Allosteric site
Enzyme-Catalyzed Reaction:
- Lowered activation energy
- AG does not change
- Enzyme is not consumed in reaction
- Speeds up reaction

Poll Question (Page 3)

Which one of these processes DO NOT require the use of energy?
- a) Endocytosis and exocytosis
- b) Activation of TKR (Tyrosine Kinase Receptors)
- c) Activation of GPCR (G-protein coupled receptors)
- d) Na+/K+ pump
- e) Hydrolysis of ATP

Poll Question (Page 6)

Which of the following PAIRS of statements are true?
- a) Noncompetitive inhibitors bind to the allosteric site.
- b) Enzyme inhibitors increase the activation energy of a reaction.
- c) Competitive inhibitors bind to both allosteric and active site.
- d) Although substrates can bind to the allosteric site, it mostly binds to the active site.
- e) Inhibitors and activators can bind to the allosteric site or active site, but substrates can only bind to the active site.

Lecture 11: Cellular Respiration

Glycolysis:
- 1 glucose molecule -> 2 pyruvates -> 2 ATP
Intermediate Step (Pyruvate Oxidation):
- No ATP made.
Citric Acid Cycle:
- active transport via MPC
- 2 acetyl coA + 6 NADH + 2 FADH
Oxidative Phosphorylation:
- 26-28 ATP

Poll Question (Page 8)

Which steps of cellular respiration include substrate level phosphorylation?
- a) Glycolysis and Pyruvate Oxidation
- b) Pyruvate Oxidation and Kreb Cycle
- c) The ETC and Chemiosmosis
- d) Glycolysis and the Citric Acid Cycle

Poll Question (Page 9)

At what step of cellular respiration does the body diverge to fermentation if oxygen is not present?
a) Before glycolysis
b) Before pyruvate oxidation
c) Before the Kreb cycle
d) Before Oxidative Phosphorylation

Lecture 11: Fermentation

Lactic Acid Fermentation:
- Muscle cells
- Lactate exported to liver.
- Reformed into glucose.
- 2 ATP per glucose.
- No CO2 released.
Alcohol Fermentation:
- Bacteria and Yeast
- Release 2 CO2/glucose.
- 2 ATP/glucose.

Lecture 12: Photosynthesis

6CO2 + 6H2O → sunlight → C6H12O6 + 6O2
Site of photosynthesis: Chloroplast
2 parts: Light reactions and Calvin cycle
Photosynthesis is a REDOX reaction.
- H2O oxidized → O2
- CO2 reduced → sugar

Pt. 1: Light Reaction

Light absorption directly correlates to action spectrum
Light reactions take place in the thylakoid membrane
Photosystems II and I convert light energy into chemical energy
Uses light energy with photosystems to excite electrons.
Electron transport chain moves electrons into thylakoid space which creates ATP and NADPH.
Water is split and oxygen is released.

Pt. 2: Calvin Cycle

Input: CO2, NADPH, ATP.
Output: NADP+, ADP + Pi, G3P.
3 phases: Carbon fixation, Reduction, Regeneration.

Poll Question (Page 15)

If ATP synthase on the thylakoid membrane was inhibited, what would happen to the pH of the thylakoid space?
- a) Increase
- b) Decrease
- c) Stay around same
- d) First increase, then decrease

Poll Question (Page 16)

If rubisco became denatured in Bob's stroma, which of the following stages in the Calvin cycle would be disrupted?
- a) Carbon reduction
- b) Carbon fixation
- c) RuBP regeneration
- d) G3P to glucose process

Lecture 13: The Molecular Basis of Inheritance

Griffith Experiment:
- R strain (nonvirulent) → mouse lives
- S strain (virulent) → mouse dies
- Heat-killed S strain → mouse lives
- Mix of heat-killed S strain and living R strain → mouse dies
- Concluded that a transforming principle moves from dead S to live R
Hershey-Chase Experiment:
- Proteins were stained with radioactive sulfur.
- Nucleic acids were stained with radioactive phosphorus.
- Radioactive phosphorus was found in bacteria pellet.
- DNA is the hereditary material.
DNA Structure:
- of adenine = # of thymine
- of cytosine = # of guanine
- A pairs with T; C Pairs with G
- Purines must pair with pyrimidines
- A and T have two hydrogen bonds, C and G have three.
- X-ray crystallography determined structure of DNA
- DNA is a double helix with two strands and hydrophobic interior (bases) and hydrophilic exterior (phosphate backbone).

Poll Question (Page 22)

In a single strand of DNA, guanine comprises 27%. How much thymine is present?
- a) 73%
- b) 36.5%
- c) 27%
- d) Impossible to determine

Poll Question (Page 23)

What is the arrow pointed towards in this image?
- a) Origin of replication
- b) Replication bubble
- c) Replication fork
- d) Answers A and C

Poll Question (Page 24)

Which image displays the correct DNA replication method?
- a) [Image of DNA replication with each strand separate and mixed]
- b) [Image of DNA replication with the strands shown as one and splitting]
- c) [Image of DNA replication with strands splitting and copying and showing mixture]

Poll Question (Page 25)

Which of the following DNA molecules has a site that is most likely to be an origin of replication?
- Provides possible answers and asks students to identify which one is more likely
- Look for sequences with repeating base pairs like A-T or G-C

DNA Replication and Repair (Lecture 14)

DNA is semiconservative.
DNA replicates in the 5'→ 3' direction.
Replication begins at origins of replication.
Replication proteins are crucial to DNA replication (helicase, polymerase, SSBP, etc).

DNA Synthesis (Page 28)

DNA polymerase can only add new nucleotides to the 3' hydroxyl group of existing DNA strands
Replication is a 5' → 3' process.

Replication Proteins (Page 29)

List of proteins including: helicase, SSB, topoisomerase, primase, DNA polymerase III, DNA polymerase I, and ligase with detailed function of each.

DNA Proofreading and Repair (Lecture 14)

Mismatch repair of DNA
- Repair enzymes correct errors.
Nucleotide excision repair - Repairs damaged DNA
Shows possible diagrams to identify what is occurring

Poll Question (Page 32)

During DNA replication in a human cell, helicase malfunctions. What effect would this have on the replication process?
- a) The replication fork would continue but leading strands would be synthesized at a slower rate.
- b) Primase would synthesize primers but they would not bind to DNA due to the lack of exposed single strands.
- c) DNA polymerase III would be unable to synthesize new DNA strands because the parental DNA remains double stranded.

Poll Question (Page 33)

If Peter the Anteater introduces a mismatch base during synthesis, what is the most likely consequence if mismatch repair is functioning normally?
- a) The mismatch will be recognized and corrected to the correct base pair.
- b) DNA ligase will detect the mismatch and remove the incorrect nucleotide.
- c) The mismatch will remain uncorrected, potentially leading to a permanent mutation

Poll Question (Page 34)

A scientist is studying DNA synthesis with a mutation in DNA Polymerase III. What would likely happen to the replication process?
- a) DNA synthesis on the leading strand will stop, but lagging strand synthesis will continue normally.
- b) DNA synthesis will start at the origin but is unable to elongate effectively.
- c) Okazaki fragments would be directly joined together.

Poll Question (Page 35)

What does Drug C most likely inhibit? (Requires information from a given graph).

Lecture 15: Transcription

Protein links genotype and phenotype: Genes produce proteins via transcription and translation.
Transcription: production of mRNA from DNA.
Involves RNA polymerase, binding to promoter region of a gene.
RNA polymerase separates DNA strands and produces a transcribed RNA strand complementary to one strand of the DNA.
Translation: formation of a protein sequence based on mRNA, occurs at ribosomes.
Base pairs code for amino acids: 3 base pairs code for an amino acid (codon).

Prokaryotic vs. Eukaryotic Transcription and Translation

Prokaryotes have coupled transcription and translation (transcription & translation happen at the same time).
Eukaryotes have separated transcription and translation; transcription occurs in the nucleus and translation occurs mainly at ribosomes in the cytoplasm.

Transcription (Initiation, Elongation, Termination) (Page 40)

Summarize each phase, including actions of RNA polymerase.

RNA Processing (Page 45)

Prokaryotes: RNA transcripts act as mRNA right away. - Functions: - Facilitate mRNA export. - Protect RNA from degradation. - Helps attach ribosomes for translation.
Eukaryotes: Eukaryotes need modifications to pre-mRNA before functioning as mRNA.
- Involves RNA splicing by spliceosomes.

tRNA (Page 46):

Function: Each tRNA carries a specific amino acid depending on its anticodon.
- tRNA and aminoacyl-tRNA synthetase match each tRNA to its specific amino acid.
Structure of tRNA - explains the structure with H bonding, for example, important sections like T-loop, anticodon loop

Translation (page 47 and 48):

Summarize steps of translation (Initiation, Elongation, Termination).

Protein Location (Translation) (Page 49):

How SRP and signal peptide work within protein translation, including the roles of signal-cleaving enzyme and the ER membrane pore.

Point Mutations (Page 50):

Types of point mutations (Nucleotide pair substitution, insertions, and deletions).
Show possible examples.

Poll Question (Page 51)

Why is there on average 35-45 tRNAs for 61 codons?
- a) tRNAs are not involved in protein synthesis, so the number does not correlate with amino acid count.
- b) There are multiple anticodons for each amino acid.
- c) Each tRNA can recognize multiple codons for the same amino acid because of wobble pairing.
- d) There's only one codon for each amino acid.

Poll Question (Page 52)

What kind of mutation occurred for sickle cell anemia?
- a) Nonsense
- b) Missense
- c) Silent
- d) Insertion

Lecture 17: Cell Division Pt. 1

Where do we see cell division?
- Reproduction
- Tissue renewal and repair (e.g., wound healing)
- Growth and development

Chromosome Structure (Page 55):

Structure of chromosomes including:
- A chromosome is a single DNA molecule made of proteins wrapped around strands of DNA.
- Sister chromatids are identical copies of a chromosome.
- Centromeres are platforms for kinetochores (spindle microtubules attachment points)

Cell Cycle: 2 Main Phases (Page 56):

Interphase:
- G1: Cell physically grows larger, copies organelles, synthesizes necessary macromolecules.
- S: DNA replication occurs.
- G2: More cell growth and preparation for mitosis.
M Phase: Mitotic phase which includes series of activities leading to forming two daughter cells (including Prophase, Prometaphase, Metaphase, Anaphase, Telophase, and Cytokinesis).

Cell Cycle- to M Phase (Page 57):

Sequence of steps occurs during the phases of mitosis detailed in the diagram.

Poll Question (Page 58 and 59):

Given this diagram, during anaphase are chromosomes “reeled in” or “walk in”?
- a) Reeled in
- b) Walked in

Poll Question (Page 60):

In what phase do chromosomes condense? a) Prophase b) Prometaphase c) Metaphase d) G2 phase

Lecture 18: Cell Division Pt. 2

Checkpoints:
- G1 checkpoint: Cell size, nutrients, growth factors, DNA damage, hormones and signals.
- G2 checkpoint: DNA damage, DNA replication completeness, Sufficient MPF complexes.
- M checkpoint: Ensures kinetochores are attached to chromosomes at metaphase plate during prometaphase.

Proto-oncogenes and Oncogenes (Page 63):

Proto-oncogene: Normal gene role in regulating cell division and growth.
- Encode proteins to stimulate cell division, inhibit cell differentiation, and halt cell death.
Oncogene: Mutated version of proto-oncogene, causes abnormal and rapid cell division (cancer).
- Increased cell division, decreased differentiation, and inhibition of cell death.
Explains hallmarks of cancer cells.

Regulating Genes of Cell Division (page 64):

Explains Ras proteins, mutation of ras, and function of tumor suppressor genes.

Meiosis (Page 65):

Briefly describe the process of meiosis in this section including meiosis 1 and 2. - Each homologous chromosome duplicates, forms two sets of chromosomes with two sister chromatids. - Chiasmata formation. Crossover and separation of homologous chromosomes; Formation of two non-identical daughter cells. - Separation of sister chromatids happens

Genetic Variations (Page 66):

Includes Crossover, Independent Assortment of Chromosomes, and Random Fertilization.
- Explains how and why genetic variations occur during cell reproduction.

Poll Question (Page 67):

Which of the following is the correct definition of a homologous chromosome?
- a) A chromosome not directly involved in sex determination of offspring - b) A pair of sister chromatids of the same chromosome - c) A pair of chromosomes that have the same length and gene loci - d) The chromosome responsible for determining the sex of the offspring

Question (Page 68):

If a cell bypasses the G1 checkpoint without repairing damaged DNA, what could be the consequence?
- The cell will replicate damaged DNA and increase risk of mutations.

Question (Page 69):

Which protein complex is crucial for the cell to pass from the G2 checkpoint into mitosis?
- Cyclin E-Cdk2 complex
- Maturation Promoting Factor (MPF)

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