Honors Biology Semester 2 Cumulative Exam Study Guide

Ch.2 - The Chemical Context of Life

Polar vs. Nonpolar Bonds and Molecules

Chemical bonds determine the properties of molecules and their interactions in biological systems.

• Polar bonds: Electrons are shared unequally, resulting in partial charges (e.g., water).

• Nonpolar bonds: Electrons are shared equally, resulting in no charge separation (e.g., methane).

• Polar molecules have regions of partial charge, enabling hydrogen bonding and solubility in water.

Hydrogen Bonding

Hydrogen bonds are weak attractions between a hydrogen atom and an electronegative atom (often oxygen or nitrogen).

• Important for the structure of water, DNA, and proteins.

• Responsible for many properties of water, such as high specific heat and cohesion.

pH

pH measures the concentration of hydrogen ions in a solution.

• Acidic solutions have pH < 7; basic solutions have pH > 7.

• Biological systems maintain pH through buffers.

• Formula: $\text{pH} = -\log_{10}[\text{H}^+]$

Ch.3 - Carbon and the Molecular Diversity of Life

Biological Molecules: Structure and Function

Biological macromolecules are essential for life and include carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates: Energy storage and structural support. Monomers are monosaccharides (e.g., glucose).

• Lipids: Hydrophobic molecules including triglycerides (energy storage), phospholipids (membranes), and steroids.

• Proteins: Diverse functions including enzymes, structure, and signaling. Made of amino acids.

• Nucleic Acids: DNA and RNA store and transmit genetic information.

Protein Structure

Proteins have four levels of organization:

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (alpha helices, beta sheets) stabilized by hydrogen bonds.

• Tertiary Structure: Overall 3D shape due to interactions among side chains.

• Quaternary Structure: Association of multiple polypeptide chains.

Nucleic Acids: DNA vs. RNA

• DNA: Double-stranded, deoxyribose sugar, stores genetic information.

• RNA: Single-stranded, ribose sugar, involved in protein synthesis.

Ch.4 - A Tour of the Cell

Prokaryotic vs. Eukaryotic Cell Structure

Cells are classified as prokaryotic or eukaryotic based on their internal structures.

• Prokaryotes: No nucleus, simple organelles (e.g., bacteria).

• Eukaryotes: Nucleus, complex organelles (e.g., plants, animals).

Endomembrane System and Organelles

• Includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles.

• Functions in synthesis, transport, and processing of proteins and lipids.

Cytoskeleton Components and Functions

• Microtubules: Cell shape, movement, chromosome separation.

• Microfilaments: Cell movement, muscle contraction.

• Intermediate filaments: Structural support.

Ch.5 - Membrane Transport and Cell Signaling

Membrane Structure and Function

Cell membranes are composed of a phospholipid bilayer with embedded proteins.

• Regulate transport of substances in and out of cells.

Active vs. Passive Transport

• Passive transport: No energy required (diffusion, osmosis).

• Active transport: Requires energy (ATP) to move substances against concentration gradients.

Osmosis

• Diffusion of water across a selectively permeable membrane.

Exocytosis/Endocytosis

• Exocytosis: Export of materials via vesicles.

• Endocytosis: Import of materials via vesicles.

Ch.6 - An Introduction to Metabolism

ATP: Structure and Function

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Composed of adenine, ribose, and three phosphate groups.

• Energy released by hydrolysis of phosphate bonds.

• Formula: $\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Enzymes: Structure and Function

• Proteins that catalyze biochemical reactions by lowering activation energy.

• Specificity due to active site structure.

Enzyme Inhibitors

• Competitive inhibitors: Bind to active site, blocking substrate.

• Noncompetitive inhibitors: Bind elsewhere, changing enzyme shape.

Ch.7-8 - Cellular Respiration and Photosynthesis

Overview of Photosynthesis and Cellular Respiration

These processes are essential for energy flow in living organisms.

• Photosynthesis: Converts light energy to chemical energy in plants.

• Cellular Respiration: Breaks down glucose to release energy for cells.

Summary Equations

• Photosynthesis: $6\text{CO}_2 + 6\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2$

• Cellular Respiration: $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{energy}$

Graphing and Data Interpretation

Interpreting Graphs and Error Bars

Graphs are used to visualize data and trends in biology.

• Error bars: Indicate variability or uncertainty in data.

• Understanding types of graphs (bar, line, scatter) is essential for data analysis.

Ch.13 - The Molecular Basis of Inheritance

DNA Structure and Replication

DNA is the hereditary material in cells, composed of nucleotides.

• Nucleotides: Monomers of DNA, each made of a phosphate, deoxyribose sugar, and a nitrogenous base.

• Four types: Adenine (A), Thymine (T), Cytosine (C), Guanine (G).

• Purines: A, G (double ring); Pyrimidines: C, T (single ring).

• Double helix structure with base-pairing rules: A-T, C-G.

DNA Replication

• Semiconservative process: Each new DNA molecule has one old and one new strand.

• Replication fork: Site where DNA is unwound and copied.

• Enzymes involved: Helicase (unwinds), DNA polymerase (synthesizes), Primase (adds RNA primer), Ligase (joins fragments), SSB proteins (stabilize).

• Leading strand: Synthesized continuously; lagging strand: Synthesized in Okazaki fragments.

• Direction: New DNA synthesized 5' to 3'.

• Telomeres: Protective ends of chromosomes.

Ch.14 - Gene Expression: From Gene to Protein

Genotype, Phenotype, and Protein Synthesis

Genotype is the genetic makeup; phenotype is the physical expression.

• One gene-one polypeptide hypothesis: Each gene codes for a single polypeptide.

• Genetic information is coded in DNA as sequences of nucleotides.

Transcription and Translation

• Transcription: DNA to RNA; involves RNA polymerase, promoter, terminator.

• Translation: RNA to protein; involves ribosomes, tRNA, codons, anticodons.

• Codon: Three-nucleotide sequence in mRNA specifying an amino acid.

• AUG: Start codon; stop codons signal end of translation.

• Genetic code is redundant (multiple codons per amino acid) but not ambiguous (each codon specifies only one amino acid).

• Universal genetic code: Shared by all organisms.

mRNA Processing

• G-cap and poly-A tail added for stability and export.

• RNA splicing removes introns, joins exons; alternative splicing allows multiple proteins from one gene.

tRNA and Ribosome Structure

• tRNA: Transfers amino acids to ribosome; has anticodon region.

• Aminoacyl-tRNA synthetase: Attaches correct amino acid to tRNA.

• Ribosome: Composed of rRNA and proteins; has P site (peptidyl), A site (aminoacyl).

Translation Steps

• Initiation: Ribosome assembles on mRNA.

• Elongation: Amino acids added to polypeptide chain.

• Termination: Stop codon reached, polypeptide released.

Mutations

• Base substitutions: Change one nucleotide.

• Insertions/deletions: Add or remove nucleotides; can cause frameshift.

• Missense: Change amino acid; nonsense: Create stop codon.

• Reading frame: Sequence of codons; frameshift alters reading frame.

Gene Study Techniques

• PCR: Amplifies DNA.

• Restriction enzymes: Cut DNA at specific sequences.

• Gel electrophoresis: Separates DNA fragments by size.

Ch.15 - Regulation of Gene Expression

Gene Expression and Control

Gene expression is the process by which information from a gene is used to synthesize a functional product.

• Main control: Regulation of transcription.

• DNA packaging: Chromatin structure affects expression; histones can be modified (acetylation increases expression, methylation decreases).

• Transcription factors: Proteins that regulate transcription (general, activators, inhibitors).

• Post-transcriptional control: RNA interference (miRNA, siRNA) can degrade mRNA or block translation.

Ch.17 - Viruses

Virus Structure and Life Cycles

Viruses are infectious agents composed of genetic material (DNA or RNA) and a protein coat.

• Lytic cycle: Virus replicates and destroys host cell.

• Lysogenic cycle: Viral DNA integrates into host genome, replicates with cell.

• Host specificity: Determined by viral surface proteins.

• Enveloped RNA viruses (e.g., influenza, coronavirus): Enter host, replicate RNA, assemble new viruses.

• DNA viruses: Replicate DNA in host nucleus.

• Retroviruses (e.g., HIV): Use reverse transcriptase to convert RNA to DNA.

• Vaccines: Made of inactivated viruses or viral components; stimulate immune response.

• Emergence of new viral diseases: Mutation, recombination, cross-species transmission.

CRISPR

• Natural function: Bacterial defense against viruses.

• Lab use: Gene editing to knock out or fix genes.

Ch.9-10 - The Cell Cycle, Mitosis, and Meiosis

Cell Division and Its Roles

Cell division is essential for growth, repair, and reproduction.

• Binary fission: Prokaryotic cell division.

• Eukaryotic cell division: Mitosis and meiosis.

Chromatin, Chromosomes, and Chromatids

• Chromatin: DNA and protein complex.

• Chromosomes: Condensed chromatin.

• Sister chromatids: Identical copies joined at centromere.

Phases of the Cell Cycle and Mitosis

• Cell cycle: Interphase (G1, S, G2), M phase (mitosis, cytokinesis).

• Mitosis stages: Prophase, Metaphase, Anaphase, Telophase, Cytokinesis.

• Structures: Mitotic spindle, centrosomes, centrioles, kinetochore.

• Cytokinesis: Animal cells (cleavage furrow), plant cells (cell plate).

Cell Cycle Control and Cancer

• Control: Anchorage dependence, density-dependent inhibition, growth factors.

• Cancer: Uncontrolled cell division; caused by mutations in oncogenes or tumor suppressor genes.

• Benign vs. malignant tumors: Benign do not spread; malignant invade tissues.

Meiosis and Genetic Variation

• Homologous chromosomes: Pairs with same genes.

• Diploid (2n): Two sets; haploid (n): One set.

• Meiosis: Two divisions (meiosis I and II) produce four haploid gametes.

• Genetic variety: Independent assortment, crossing over, random fertilization.

• Alleles: Different versions of a gene.

• Crossing over: Exchange of genetic material during prophase I.

• Spermatogenesis vs. oogenesis: Male vs. female gamete formation.

• Nondisjunction: Failure to separate chromosomes; leads to abnormalities.

Key Terms

• Somatic cell, zygote, locus, synapsis, diploid number, haploid number, gametes.

Ch.11-12 - Mendel and the Gene Idea & The Chromosomal Basis of Inheritance

Genetics and Inheritance

Mendel's principles explain how traits are inherited.

• P generation: Parental generation.

• F1, F2 generations: First and second filial generations.

• Monohybrid cross: One trait; dihybrid cross: Two traits.

• Homozygous: Same alleles; heterozygous: Different alleles.

• Phenotype: Physical traits; genotype: Genetic makeup.

• Dominant/recessive alleles: Dominant masks recessive.

• Connection: Homologous chromosomes carry alleles.

• Punnett squares: Predict offspring ratios.

• Rule of multiplication: Probability of independent events.

• Pedigree: Family tree showing inheritance.

• Carrier: Heterozygous for recessive disorder.

Complex Patterns of Inheritance

• Incomplete dominance: Intermediate phenotype.

• Multiple alleles: More than two alleles (e.g., ABO blood types).

• Codominance: Both alleles expressed (e.g., AB blood type).

• Polygenic inheritance: Multiple genes affect trait (e.g., skin color).

• Epistasis: One gene affects expression of another.

• Sex-linked genes: Located on sex chromosomes; show different inheritance patterns.

• Sex-linked recessive traits: More common in males (e.g., color blindness).

ABO Blood Types Table

Genotype	Phenotype
IAIA, IAi	Type A
IBIB, IBi	Type B
IAIB	Type AB
ii	Type O

Ch.19-21 - Evolution and the Evolution of Populations

Descent with Modification and Natural Selection

Darwin's theory explains how species change over time.

• Descent with modification: Species evolve from common ancestors.

• Natural selection: Favorable traits increase survival and reproduction.

• Homologies: Similarities due to shared ancestry; used in evolutionary trees.

• Convergent evolution: Similar traits in unrelated species due to similar environments.

Classification and Phylogeny

• Scientific name: Genus and species.

• Taxa: Domain, kingdom, phylum, class, order, family, genus, species.

• Phylogenetic trees: Diagrams showing evolutionary relationships.

• Three-domain system: Bacteria, Archaea, Eukarya.

Population Genetics and Microevolution

• Population: Group of individuals of same species.

• Gene pool: All alleles in population.

• Microevolution: Change in gene pool over time.

• Ultimate source of variation: Mutation.

• Hardy-Weinberg equilibrium: No evolution if five conditions met (no mutation, random mating, no gene flow, large population, no selection).

• Agents of microevolution: Genetic drift (bottleneck, founder effect), gene flow, mutation, non-random mating, natural selection (stabilizing, directional, disruptive).

• Evolutionary fitness: Ability to survive and reproduce; relates to selection and drift.