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Questions and Answers

What role does the template strand play in transcription?

It determines the amino acid sequence of proteins.

It is the strand that becomes mRNA.

It serves as a guide for RNA synthesis. (correct)

It directly bonds to ribosomes during translation.

Which of the following correctly categorizes the lac operon?

Repressible operon

Negative regulation operon

Inducible operon (correct)

Constitutive operon

What process is regulated by transcription factors in eukaryotic gene regulation?

Transcription initiation (correct)

Translation initiation

Protein degradation

RNA processing

Which of the following mutations contributes to cancer development by affecting tumor-suppressor genes?

Mutation of p53 (D) Signup and view all the answers

To increase chromatin condensation, what changes are necessary regarding histone modification?

Decrease histone acetylation and increase methylation. (C) Signup and view all the answers

What occurs in a hypertonic environment compared to a cell's interior?

The solute concentration outside the cell is greater. (B) Signup and view all the answers

Which type of molecules can cross the plasma membrane easily without assistance?

Small non-polar molecules (C) Signup and view all the answers

Which type of diffusion requires energy to move substances?

Active diffusion (C) Signup and view all the answers

What role does cholesterol play in membrane permeability?

It decreases membrane fluidity and affects permeability. (B) Signup and view all the answers

Which of the following statements regarding tonicity and osmosis is true?

In a hypotonic solution, water moves into the cell. (A) Signup and view all the answers

What is the primary role of G-Protein Coupled Receptors (GPCRs) in signal transduction?

They initiate cellular responses by altering ion movement. (D) Signup and view all the answers

What effect does phosphorylation have on a protein?

It changes the protein's conformation and activates it. (C) Signup and view all the answers

What characterizes second messengers in cellular signaling?

They are small, non-protein molecules that can diffuse freely within the cell. (D) Signup and view all the answers

Which of the following describes the concept of 'diversity' in signal regulation?

It refers to the ability of a single ligand-receptor interaction to produce various responses. (D) Signup and view all the answers

What is the significance of 'termination/control of signal' in cellular responses?

It helps restore homeostasis by stopping unnecessary signaling. (A) Signup and view all the answers

What is the primary role of the first ETC in the light reactions?

Generates ATP (C) Signup and view all the answers

Which process occurs when RuBP combines with O2 instead of CO2?

Photorespiration (A) Signup and view all the answers

Which type of plant photosynthesis is characterized as energy inefficient but maximizes photosynthesis?

C4 and CAM photosynthesis (B) Signup and view all the answers

What product does the Calvin Cycle produce that serves as a precursor to glucose?

G3P (A) Signup and view all the answers

How does the cyclic flow in the light reactions differ from the linear flow?

It only produces ATP (B) Signup and view all the answers

What happens to ADP and NADP+ produced during the Calvin Cycle?

They are reused in the light reactions (D) Signup and view all the answers

Which component of PSII is considered the strongest biological oxidizing agent?

Chlorophyll (A) Signup and view all the answers

Why is photorespiration considered a wasteful process?

It consumes ATP without forming sugar (B) Signup and view all the answers

What is the primary purpose of polymerase chain reaction (PCR)?

To amplify DNA sequences (B) Signup and view all the answers

During fertilization, what do two haploid gametes form?

A diploid zygote (D) Signup and view all the answers

Which step in the PCR process follows denaturation?

Annealing (C) Signup and view all the answers

What is a characteristic of retroviruses in gene delivery?

They utilize DNA to replicate (C) Signup and view all the answers

Which component is primarily used to visualize specific mRNAs during the probe/FISH method?

Fluorescence (C) Signup and view all the answers

In gel electrophoresis, which charge do DNA fragments carry?

Negative charge (D) Signup and view all the answers

How are plasmids useful in recombinant DNA technology?

They are easy to isolate and manipulate (C) Signup and view all the answers

What is the primary function of reverse-transcriptase in RT-PCR?

To convert RNA into complementary DNA (B) Signup and view all the answers

Which type of compounds will water not adequately dissolve due to their nonpolar nature?

Lipids (D) Signup and view all the answers

What structural feature characterizes saturated fatty acids?

They are solid at room temperature. (A) Signup and view all the answers

Which compound is formed by the dehydration of two monosaccharides?

Disaccharide (A) Signup and view all the answers

What is the primary bond that links amino acids in a protein?

Peptide bond (D) Signup and view all the answers

What type of lipid is defined by having a glycerol backbone and two fatty acid tails?

Phospholipid (D) Signup and view all the answers

Which level of protein structure refers to the three-dimensional folding of a polypeptide?

Tertiary structure (D) Signup and view all the answers

Which statement is true regarding aquaporins?

They are proteins that facilitate water transport across membranes. (A) Signup and view all the answers

Which type of bond connects nucleotides in a nucleic acid?

Phosphodiester bond (A) Signup and view all the answers

Which carbohydrate is indigestible to humans and primarily serves a structural role in plants?

Cellulose (D) Signup and view all the answers

What distinguishes nucleic acids from proteins in terms of their building blocks?

Nucleic acids consist of nucleotides. (B) Signup and view all the answers

Study Notes

Exam Information

Exam date: Friday December 13th, 10:30 AM CST
Exam duration: 75 minutes; officially closes at 3pm
Location: Canvas, "Quizzes" tab, same as previous exams
Exam format: ALL multiple choice questions, no free response questions
Content breakdown: 50% Weeks 12, 13, and 14; 50% Weeks 1-11
Point value: 106 points (21.2% of total grade)
Number of questions: 53, each worth 2 points

Content Review by Weeks

"Unit 4": Weeks 12, 13, 14
Unit 1: Weeks 1-4
Unit 2: Weeks 5-8
Unit 3: Weeks 9-11

Week 12: Cell Communication and Signaling

Cell signaling: communication between cells, ligand binding to a receptor causes a response
Signal transduction: how the signal is transmitted within the cell

Cellular Messaging

Cell signaling: communication between cells
Simplest explanation: ligand binding to a receptor which causes responses
Seen in prokaryotes and eukaryotes

Local Signaling

Autocrine signaling: cell targets itself, often related to negative feedback
Direct contact: through cell junctions, cell junctions allow communication between the cytoplasm of neighboring cells
Gap junctions: animals
Plasmodesmata: plants/algae
Paracrine signaling: a signaling molecule targets nearby cells, only works with cells in close proximity because signal spreads via diffusion

Long Distance Signaling

Endocrine signaling: animals use hormones that move through bloodstream
Bloodstream carries message to target cell in a remote part of the body
The message (hormone) will only bind to the cell with the correct receptor in the body

Synaptic Signaling

Synaptic signaling: neurotransmitter (chemical message) is converted into electrical signal in neurons; allows for responses
Outside the cell: high Na+ and Cl-; inside the cell: high K+
At rest, inside of the cell is negative; outside is positive
Charges shift during signal transmission; inside temporarily becomes more positive
At end of signal transduction, influx of Ca2+ allows for release of neurotransmitter to pass signal onto next neuron.
Signal released: Neurotransmitter
Signal received by: neurons, creates a response

3 Stages of Cell Signaling

Reception: binding of signal molecule to receptor à conformational change of receptor & activation of enzymes
Transduction: relayed through the cell, proteins change shape in a cascade
Response: activation of cellular response

Receptors to Know

G-protein coupled receptors: ligand binds, converts GDP → GTP, GTP activates an enzyme that starts the cascade
Receptor tyrosine kinases: Dimerization (two signaling molecules bind), cytoplasmic regions become phosphorylated, activating relay proteins
Ion channel receptors: signaling molecule binds, opens channel, ions move across, causes cellular response
Steroid receptors (intracellular): steroid hormones cross membrane to reach intracellular receptors, some bind directly to DNA (non-polar/lipid-soluble messengers), ex: estrogen to different receptors

Transduction: Phosphorylation/Dephosphorylation

Phosphorylation (add phosphate group via kinase) à changes conformation/becomes active
Dephosphorylation (via phosphatase) à restores the protein to inactive form
Phosphorylation cascade (multiple relays of phosphorylation)

Transduction: Second Messengers

Small, non-protein molecules: diffuse freely through the cell
Participate in GPCRs and RTKs
Ex: Ca2+ (normally at very low levels inside cell; when enters cell, can act as 2nd messenger)

Signal Regulation

Specificity: ligand-receptor specificity; same molecule at same location, different response based on proteins
Amplification: make a signal bigger (megaphone analogy); same molecule binds to different receptors, different responses (tissue specialization)
Diversity; overall efficiency of response - proteins in pathway grouped by scaffolding proteins
Termination/control of signal: resetting by removing stimuli or degrading components

DNA/Chromosomal Structure

Chromatin: loose form of DNA and proteins, present when cell is not dividing
Chromosomes: condensed/tightly packed form of DNA, found only during cell division
Chromatids: singular copy of a chromosome, sister chromatids (two copies via duplication), connected at the centromere.

The Cell Cycle

Interphase: cell spends most time here, includes G1 (growth, protein synthesis), S (synthesis, DNA replication), G2 (growth prep for division)
M phase: mitosis and cytokinesis
Prokaryotes: Binary fission - DNA replication → chromosome segregation → cytokinesis (2 exact copies)

Mitosis

Eukaryotic nuclear division, chromosome number is constant across daughter cells
Prophase: chromatin condenses, mitotic spindle forms, nucleolus dissolves
Prometaphase: nuclear envelope fragments, spindle "grabs" chromosomes at kinetochores
Metaphase: spindle complete, chromosomes align at metaphase plate
Anaphase: chromatids separate, pulled toward opposite poles
Telophase: daughter nuclei form, mitotic spindle disappears
Cytokinesis: division of cytoplasm, cleavage furrow (animal) or cell plate (plant)

Human Ploidy

Somatic cells: diploid (2n) - Two copies of genetic material subdivided into chromosomes; any cell that's not a reproductive cell
Human somatic cells: 22 pairs of autosomes and 2 sex chromosomes
Autosome: anything not a sex chromosome
Gamete cells: haploid (n) - single copy of each chromosome (unpaired)
Allele: alternative version of a gene; may produce different phenotypes

Diploid vs Haploid

Diploid cells (2n): two copies of each chromosome
Haploid cells (n): one copy of each chromosome
Meiosis results in 4 haploid cells (from one diploid cell)
In mitosis, a diploid cell gives rise to 2 diploid daughter cells

Homologous Chromosomes

"Homologous" refers to similarity between structures, one from mom, one from dad
NOT genetically identical
Similar in size and shape, genes in same order, but can be different alleles

Meiosis

Cell division, sexually-reproducing organisms, consists of 1 replication and 2 divisions producing gametes.
Meiosis I separates homologous chromosomes. Meiosis II separates sister chromatids
Prophase I: duplicated chromosomes pair with homologs (synapsis). Crossing over
Metaphase I: homologous pairs line up facing poles
Anaphase I: pairs of homologs separate to poles
Telophase I: each half cell is haploid
Prophase II: spindle apparatus forms, chromosomes condense
Metaphase II: sister chromatids at plate
Anaphase II: sister chromatids separate and cohesin separates
Telophase II: nuclei form; chromosomes decondense

Crossing Over

Reciprocal exchange of genetic material between two non-sister chromatids during prophase I of meiosis
Non-sister chromatids broken at corresponding positions
DNA breaks are repaired, joining DNA from one non-sister chromatid to the corresponding position of another

Independent Assortment

Random arrangement of pairs of homologous chromosomes at the center of the cell during metaphase I
Meiosis allows for novel combinations of traits not seen in the previous generation (genetic variation)

Animal Life Cycle

Haploid gametes (egg and sperm) produced by meiosis
Two gametes fuse during fertilization => diploid zygote
Zygote goes through mitosis to form a multicellular body
Other eukaryotic life cycles: plants/algae have alternation of generations; fungi/protists have spores; many life cycles spent as haploid

Week 14: Genomes and Biotechnology

Recombinant DNA: Plasmids (vehicles) are non-chromosomal DNA, easy to isolate and manipulate
Ways to introduce: natural genetic recombination, adding methyl groups to nucleotides
Retroviruses (RNA viruses): insert DNA into a cellular chromosome (reverse transcriptase).

Polymerase Chain Reaction (PCR)

PCR used to amplify DNA (make copies); exponential generation
Cycle 1 consists of 3 steps: Denaturation, Annealing, Extending

DNA Technology (Probes/FISH)

Probes/FISH: single-stranded RNA or DNA sequence used to search for its complement in a sample genome; fluorescence allows visualization; identifies presence or location of specific mRNAs
Reverse-Transcriptase-Polymerase Chain Reaction (RT-PCR): uses RNA as template for reverse transcription to complementary DNA (cDNA) for PCR amplification and gene detection.

Gel Electrophoresis

Separates and visualizes DNA according to molecular size
DNA negatively charged (travels towards anode)
Smaller fragments travel further; larger fragments closer to cathode.

DNA Microarrays

Used to study the expression of all genes in different tissues at different times or under different conditions
Microarray consists of tiny amounts of many single-stranded genes fixed to glass slide

CRISPR-Cas9 system

Gene editing technology
Cas9 enzyme cuts both strands of DNA complementary to guide RNA
After cut, DNA is repaired, and nucleotides may be introduced.
Also used to disable/knock out the target gene for studying.

Small Nucleotide Polymorphism (SNPs)

Each SNP represents a difference in a nucleotide
3 million SNPs in human genome
Majority of variation in human genomes is in noncoding regions (rarely directly involved in disease)

Stem Cells

Embryonic (pluripotent): Undifferentiated à any cell type, obtained from embryos
Adult: Limited number of cell types
Induced pluripotent stem cells: reprogrammed adult cells to act like embryonic cells; used for therapeutic treatments

Cloning

Therapeutic cloning: use of cloned embryos as source for stem cells to treat disease
Cloning plants (using single cell cultures, easy to genetically engineer)
Cloning animals (fusing nucleus of differentiated body cell into an unnucleated egg cell)
Only a small percentage of cloned embryos normally develop to birth; many show defects, epigenetic changes can conflict with developmental needs, flaws with mtDNA

Genomics and Bioinformatics

Forensic applications: every individual's genetic profile is unique due to highly repetitive STRs (short tandem repeats); STRs help in solving cold cases
Bioinformatics: use of computer programs/mathematical models to organize biological data

Transposable Elements

Transposable elements: stretches of DNA that can move within genomes in prokaryotes and eukaryotes
Makes up ~75% of human repetitive DNA
Helps to facilitate recombination and may facilitate recombination, carry genes to new positions
May create sites for RNA splicing – genome evolution

Comparing Genomes

Chromosome sets contribute to diversity, chromosomal mutations, some genes diverged, multigene families.
Comparing genome sequences provides clues to evolution and development; comparing highly conserved genes
Branch points on a phylogenetic tree represent divergence from a common ancestor; genome size and organism complexity are unrelated.

Week 1-2: Chemical Bonds, Water, and Carbon

Covalent bonds: sharing of valence electrons (nonpolar is equal; polar is unequal); ionic bonds: electron transfer (cations and anions); Intermolecular forces (Van der Waals and hydrogen bonds); Isomers: same molecular formula, different structure/properties
Water: hydrogen bonds, hydroxide (OH) and hydronium (H3O⁺) ions, cohesive, adhesive, high specific heat, evaporative cooling, excellent solvent
Hydrogen bonds in water result inability to break up other compounds (sugars, Amino Acids) compared to Lipids (non-polar).

Week 3: Monomers and Macromolecules

Carbohydrates: monosaccharides, dehydration synthesis forms glycosidic linkages; disaccharides, polysaccharides (storage, structural)
Lipids: not true polymers; fats (ester bond of glycerol and fatty acids), phospholipids (2 fatty acids and 1 glycerol); steroids (4-ring structure); saturated vs. unsaturated
Proteins: amino acids joined by peptide bonds (four levels of structure - primary, secondary, tertiary, quaternary), enzyme structure and function; shape dictates function
Nucleic acids: nucleotides joined by phosphodiester bonds; DNA (double stranded, A-T and C-G, deoxyribose), RNA (single stranded, A-U and C-G, ribose).

Aquaporins

Proteins embedded in plasma membrane allow water movement between extracellular and intracellular spaces
Key features of shape: amphipathic (hydrophilic/hydrophobic regions) to interact with both aqueous and hydrophobic regions
Amino acid characteristics: charged/polar amino acids on top and bottom interacting with water; hydrophobic regions interact with phospholipid tails

Week 4: Prokaryotes and Eukaryotes, Origins, and Cell Structure

Prokaryotes vs. Eukaryotes: differences in cell structure, presence/absence of organelles and nucleus
Large surface area to volume ratio important for prokaryotes

Week 5: Membrane Structure and Function and Gradients

Plasma membrane structure (selective permeability, temperature, cholesterol, types of fatty acids)
Types of transport: passive (no ATP needed, ex: osmosis, diffusion) vs. active (ATP needed); osmosis vs. diffusion
Tonicity: hypertonic (higher solute outside cell), hypotonic (lower solute), isotonic (equal)
Membrane proteins: integral, peripheral, transmembrane; functions of membrane proteins

Week 6: Energy Transformation, ATP, and Enzymes

Gibbs Free Energy (G), endergonic (requires energy), exergonic (releases energy), ΔG; Spontaneous vs. non-spontaneous reactions
Enzymes = catalysts, decrease activation energy; specific temp & pH
Enzyme inhibitors (competitive, non-competitive, allosteric)
Enzyme-substrate interactions (lock-and-key, induced fit model); ATP role in energy coupling; cell respiration and photosynthesis

Week 7: Cellular Respiration

Redox reactions (oxidation, reduction, hydrogen atoms)
Types of phosphorylation: substrate-level, oxidative phosphorylation)
3 types of catabolic pathways: aerobic respiration (36-38 ATPs), anaerobic respiration (varied outcome, less ATP), fermentation (2 ATPs)
Cellular respiration stages: Glycolysis, Pyruvate Oxidation, Citric Acid Cycle (Krebs cycle), Oxidative Phosphorylation
Lactic acid fermentation, alcoholic fermentation

Week 8: Photosynthesis

Stages of photosynthesis (light reactions, Calvin cycle)
Electron transport pathways: linear, cyclic electron flow, role in ATP/NADPH production
Calvin cycle stages (carbon fixation, reduction and sugar formation, regeneration of RuBP)
Alternative mechanisms of carbon fixation (photorespiration; C3, C4, and CAM)

Week 9: DNA Structure, Replication, and Heredity

Different experiments leading to understanding of DNA (Morgan, Griffith, Avery, McCarthy, MacLeod, Hershey, Chase, Chargaff, Wilkins, Franklin, Watson, Crick, Meselson)
Semiconservative replication model, steps and enzymes (replication, DNA polymerase I vs III, prokaryotes vs. eukaryotes, DNA repair, mismatch repair and nucleotide excision repair)

Week 10: The Genetic Code, Transcription, Translation, and Mutations

Universal genetic code (redundant, not ambiguous, start/stop codons)
Transcription (DNA → mRNA, RNA polymerase, template vs coding strand)
Translation (mRNA → protein, initiation, elongation, termination, wobble, signal-recognition particle)
Prokaryotic vs. eukaryotic processes (polyribosome, coupling, transcription complex)
Mutations (frameshift, substitution mutations: silent, missense, nonsense)

Week 11: Gene Regulation and Expression

Prokaryotic gene regulation (operons: lac operon, trp operon, inducible and repressible)
Eukaryotic Gene regulation (Chromatin structure, Transcriptional regulation, RNA processing, post-translational modifications, embryonic development-cytoplasmic determinant, induction, Cancer development-mutation of proto-oncogenes/tumor suppressor genes like p53)

Question about Chromatin Condensation

Increased chromatin condensation requires decreased histone acetylation or increased methylation.

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