Biol 1a Lec FINAL EXAM Study Guide CSUF

Inductive reasoning

• specific observations → general claim

  • (Ex: Bob died. Jim died. Susan died. Mary died. Conclusion: People are mortal)

Deductive reasoning

• general idea → more specific

  • (Ex: All people are mortal. Sheila is a person. Therefore, Sheila is mortal)

Basic science vs Applied science

• Basic science: aims to answer fundamental questions about biology

• Applied science: uses the information from basic science to solve real-world problems

Compare and contrast the scientific method (in textbook), with the scientific process (in PowerPoint slides and described in class).

• Textbook: Observation, Question, Hypothesis, Prediction, Experiment, Result

• Powerpoint: more complex, going back and forth through the steps

Determine the number of protons, electrons, and neutrons in an atom using the information on a periodic table

• Protons = ?

• Neutrons = ?

• Electrons = ?

• Atomic # = ?

• Mass # = ?

• Protons = mass # - neutrons

• Neutrons = mass # - protons

• Electrons = protons

• Atomic # = protons (DONT CHANGE)

• Mass # = protons + neutrons

What is an isotope? How are they important in biology?

• Isotope: differ in the number of neutrons

• Important bc they’re used in:

  • Carbon dating, detecting macromolecules, X-ray imaging

Define covalent bond, ionic bond and hydrogen bond

• Covalent Bonds: sharing of electrons, partial neg/pos charges

• Ionic Bonds: steals electrons rather than sharing, leaving a +/- charge

• Hydrogen bonds: (H w/ anything)

What are the four properties of water that make it ideal for life?

• Water is the solvent of life

  • Polar solvent: dissolves polar substances

  • Hydrophilic (water-loving)

• Ice Floats on Water

  • Solid water is less dense than liquid water

• Moderation of Temp by Water

  • Requires more energy to raise the temp of water, more flexible

• Cohesion and adhesion of Water Molecules

  • Cohesion: water H-bonds to itself

  • Adhesion: water H-bonds to other things

Polymer vs Monomer

• Monomer: macromolecules made from single subunits, or building blocks

• Polymer: monomers combined to form larger molecules

Dehydration hydration vs Hydrolysis

• Dehydration Reaction: when covalent bonds are formed between the monomers, a water molecule is released as a byproduct

• Hydrolysis: when polymers are broken down into monomers using water molecules, means “split water”

What are the 4 macromolecules?

Carbohydrates, Lipids, Proteins, and Nucleic Acids

Carbohydrates (functions and examples)

• Function: Provide energy and structural support

• Examples: Starch (plants), glycogen (animals), cellulose (plant cell walls).

Lipids (functions and examples)

• Function: Store energy, provide insulation, and form cellular membranes.

• Examples: Fats, oils, phospholipids, steroids

Proteins (functions and examples)

• Function: Perform various cellular tasks, including catalyzing reactions (enzymes), signaling, and structural support.

• Examples: Enzymes (amylase), structural proteins (collagen), hormones (insulin)

Nucleic Acids (functions and examples)

• Function: Store and transmit genetic information.

• Examples: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

Compare and contrast prokaryotes and eukaryotes.

• Prokaryotes: 

  • Unicellular

• Eukaryotes: Multi-celled organisms

  • 100-100,000 times larger

  • More complex: endomembrane system, Cell wall, chloroplasts

• Cell Similarities: DNA, Plasma membrane, Cytoplasm, Ribosomes

  • Plasma membrane: an outer covering that separates the cell’s interior from its surrounding environment

  • Cytoplasm: consisting of a jelly-like cytosol within the cell in which other cellular components are found

  • DNA: genetic material of the cell

  • Ribosomes: synthesize proteins

Redox reaction

2 reactions happening at the same time, paired oxidation and reduction reactions

Glycolysis (location, inputs, outputs)

• Located: cytosol, outside mitochondria bc glucose isn't allowed

• Inputs: glucose 

• Outputs: 2 pyruvate, 1 ATP at substrate level

Pyruvate oxidation (location, inputs, outputs)

• Located: in matrix of mitochondria 

• Inputs: pyruvate

• Outputs: Acetyl CoA

Citric Acid Cycle (location, inputs, outputs)

• Located: Matrix of the mitochondria 

•  Input: Acetyl-CoA

• Output: NADH, FADH2, ATP

Oxidative phosphorylation/Electron Transportation chain (location, inputs, outputs)

• Located: mitochondria

• Input: Electrons via NADH and FADH2

• Output: ATP Oxidative

Light Reaction (purpose, location, inputs, outputs)

• Purpose: Capture light energy to produce energy-rich molecules.

• Location: Thylakoid membranes (chloroplast).

• Inputs: Light energy, water (H₂O), ADP, NADP⁺.

• Outputs: ATP, NADPH, oxygen (O₂).

Calvin Cycle (purpose, location, inputs, outputs)

• Purpose: Use energy from ATP and NADPH to synthesize glucose from CO₂.

• Location: Stroma (chloroplast).

• Inputs: CO₂, ATP, NADPH.

• Outputs: Glucose (or G3P), ADP, NADP⁺, Pi.

Calvin Cycle and Light Reaction dependency on each other

• Calvin Cycle: relies on ATP and NADPH produced by the light reactions.

• Light reactions:  regenerate NADP⁺ and ADP, which are reused in the Calvin Cycle

What is the role of NAD+, FAD and NADP+ in cellular respiration and photosynthesis?

• NAD+ and FAD are coenzymes

• Coenzymes: nonprotein substances that associate and activates an enzyme

• NAD+ and FAD role in cellular respiration: electron shuttles, keep em bounded so they aren’t floating everywhere, make sure the electrons end up in the right place

How can a proton gradient be used to do work in the cell?

• Electrochemical gradient: difference of charge across the plasma membrane

• Established from active transport bc they require ATP (energy), causing an imbalance of charges

Cellular Respiration (location, oxidize, reduce, inputs, outputs)

• Location: mitochondria

• Oxidized: glucose → CO2

• Reduced: oxygen → water

• Inputs: Glucose, O2

• Outputs: CO2, H2O, ATP

Photosynthesis / light reactions (location, oxidize, reduce, inputs, outputs)

• Location: Chloroplast

• Oxidized: water → oxygen

• Reduced: CO2 → glucose

•  Inputs: CO2, H2O, ATP

• Outputs: Glucose, O2

Light reactions and Cellular Respiration simularities

• Both involve electron transport chains and chemiosmosis to produce ATP.

• Both involve redox reactions.

• Both require specialized organelles (mitochondria for respiration, chloroplasts for photosynthesis).

• Both have cycles (Krebs in respiration, Calvin in photosynthesis) to process energy intermediates

Mitosis (summary, role, function)

• Summary: supports growth, maintenance, and stability in the organism

• Role: Ensures growth, tissue repair, and asexual reproduction of somatic (body) cells

• Function: Produces two genetically identical diploid (2n) daughter cells from a diploid parent cell

Meiosis (summary. role, function)

• Summary: ensures genetic variation and continuity of life

• Sperm/Egg genetic diversity

• Function: Reduces the chromosome number by half, producing four genetically unique haploid (n) cells from a diploid (2n) parent cell

Mitosis and Meiosis similarities

• Cell Division Processes: nuclear division to produce new cells.

• Phases: PMAT (prophase, metaphase, anaphase, telophase)

• Preceded by Interphase: Both are preceded by interphase, during which DNA replication occurs (S phase).

• Spindle Formation: Use spindle apparatus to separate chromosomes.

• Cytokinesis: Both are usually followed by cytokinesis, dividing the cytoplasm and forming daughter cells.

• Chromosome Movement: Both involve the alignment, separation, -and movement of chromosomes

Mitosis and Meiosis Differences

• Mitosis ensures genetic consistency for growth and repair, producing two identical diploid cells.

• Meiosis introduces genetic diversity and halves the chromosome number to produce gametes, crucial for sexual reproduction

Starting with a cell of 2n=8, what would the parent and each daughter cell look like for mitosis and Meiosis

• Mitosis: 

  • Parent Cell: Contains 8 chromosomes arranged as 4 homologous pairs

  • Daughter Cells: Two identical diploid (2n=8 and 2n=8) cells, each with the same chromosome content as the parent cell

• Meiosis

  • Meiosis I: Homologous chromosomes separate:

    • Daughter Cell 1: n=4n = 4n=4 (e.g., chromosomes A, B, C, D).

    • Daughter Cell 2: n=4n = 4n=4 (e.g., chromosomes A', B', C', D').

  • Meiosis II: Sister chromatids separate:

    1. Four haploid (n=4n = 4n=4) daughter cells, each containing a unique set of chromosomes, facilitating genetic diversity

What are the ways that meiosis increases genetic diversity?

• Crossing over: prophase 1 of meiosis, exchange material at points called chiasmata

• Independent assortment: metaphase 1 of meiosis, maternal and paternal chromosomes are distributed into daughter cells at random

• Random Fertilization: any sperm, any egg

• Mutation: can happen during DNA replication of interphase prior to meiosis, or during meiosis

• Segregation of Alleles: anaphase 1 or 2 of meiosis

What are the two laws that Mendel developed?

• Law of Segregation

• Law of Independent Assortment

Law of Segregation (experiment & how are they related to meiosis?)

• Each individual has two alleles for a given trait, and these alleles segregate (separate) during gamete formation, so each gamete receives only one allele

• Experiment: pea plants with two different traits produced offspring that all expressed the dominant trait, but the following generation expressed the dominant and recessive traits in a 3:1 ratio

• Meiosis: This law reflects the separation of homologous chromosomes (and their alleles) during anaphase I of meiosis. Each gamete ends up with only one allele for each gene

Law of Independent Assortment

• During gamete formation, different pairs of alleles (on separate chromosomes) segregate independently of each other

• Experiment: Mendel performed dihybrid crosses, studying two traits simultaneously (e.g., seed shape and seed color).

  • F1 generation showed only the dominant phenotypes for both traits.

  • F2 generation displayed a 9:3:3:1 ratio, suggesting that the inheritance of one trait did not affect the inheritance of the other.

• Meiosis: reflects the random orientation of homologous chromosome pairs during metaphase I of meiosis

  • The way one pair aligns and segregates does not influence other pairs, leading to a variety of genetic combinations in gametes

Dominance vs Co-dominance vs Incomplete dominance

• Dominance: regular Rr = R shows up bc dominant

• Co-dominance: 2 dominant genes (RR), both show up

  • (Co = together)

• Incomplete dominance: Rr = R gene isn’t completely expressed as it’s in the presence of a recessive gene

What is an x-linked trait? Why are the more common in males than females?

• X-Linked trait: trait whose gene is located on the X chromosome. 

  • Often display specific inheritance patterns because males and females have different combinations of sex chromosomes

• More common in males bc: they have only one X chromosome and any recessive allele on it will be expressed

  • Less common in females bc they would need 2 copies of the recessive allele (1 on each X chromosome)

Explain how recombination frequency relates to map units on a chromosome. What does 50% recombination mean? 32%?

• Recombination frequency: measure of how often two genes on the same chromosome are separated during crossing over in meiosis. It reflects the likelihood that a recombination event occurs between two loci (gene positions) on a chromosome

  • 20% would mean they are relatively close to each other on the chromosome

  • 2% means they are tightly linked, meaning crossing over between them is rare

  • Higher the % = further away on chromosome

Semi-conservative replication

DNA synthesis with half parent DNA and half new DNA

What is the start of transcribed strands? the stops?

• stop = UAA, UAG, UGA

• start = AUG (met)

What is the function of mRNA, tRNA and rRNAs in translation? Describe each one.

• mRNA: read the codon and the protein product is made.

  • m = messanger, RNA has a message from DNA

  • transcription

• rRNA: is a major constituent of ribosomes on which the mRNA binds

  • r = ribosome

• tRNA: carries the correct amino acid to the protein synthesis site

  • Translates RNA = protein

  • Translation

Simple visual of how mRNAs, rRNAs, and tRNAs interact

Codon vs Anticodon

• Codon: a sequence of three nucleotides that together form a unit of genetic code in a DNA or RNA molecule.

  • (bottom)

• Anticodon: three unpaired bases on a tRNA that is complementary to one mRNA

  • (top)

What are the 2 parts of the Ribosome Structure?

• Small subunit: Binds to mRNA and is responsible for decoding the genetic message

• Large subunit: Facilitates peptide bond formation between amino acids during protein synthesis.

3 sites of a ribosome structure

• A Site: Entry site for tRNA molecules carrying the next amino acid to be added to the growing polypeptide chain

  • Matches the incoming tRNA anticodon to mRNA codon

• P Site: Holds the tRNA carrying the growing polypeptide chain

  • Transfers the polypeptide to the amino acid attached to the tRNA in the A site

• E Site (Exit): Holds the tRNA that has transferred its amino acid to the growing chain

  • tRNA exits the ribosome through this site to be recycled

What are the main differences between gene expression and gene regulation between prokaryotes and eukaryotes?

• Prokaryotes: have simpler, faster, and mostly transcription-level regulation

  • do transcription AND translation in the cell bc it has no nucleus

• Eukaryotes: have more complex, multi-level regulation with extensive mRNA processing and epigenetic control

  • transcription in nucleus, translation outside

  • Does gene regulation EVERYWHERE

Describe the function of a transcription factors in gene expression.

Transcription factors are essential regulators of gene expression, controlling when and how much of a gene is transcribed. They serve as a bridge between the genome and cellular or environmental signals, ensuring precise gene regulation necessary for proper cellular function and development.

Describe the RNA processing steps that occur in eukaryotes. What is alternative splicing?

• Rna processing steps in eukaryotes

  1. 5' capping

  2. 3' polyadenylation

  3. splicing

• Alternative splicing: adds diversity to the proteome by generating multiple protein isoforms from a single gene, increasing the complexity of gene expression

Operon, and Inducible vs Repressible operon

• Operon: a unit made up of linked genes that are thought to regulate other genes responsible for protein synthesis

• Inducible: normally off

• Repressible: normally on

Explain the different mechanisms of gene regulation for eukaryotes.

• Transcriptional: Chromatin remodeling, transcription factors, epigenetics

• Post-Transcriptional: Alternative splicing, RNA editing, mRNA stability, RNA interference

• Translational: Ribosome binding, mRNA localization

• Post-Translational: Protein modifications, folding, and degradation