Comprehensive Biology 1 Study Guide (by Abdullah Sultan)

Biology Finals Study Guide

UNIT 1: BIOLOGICAL MACROMOLECULES

Functional Groups

Macromolecules Overview

Polymerization and Depolymerization

• Dehydration Synthesis (Condensation): Monomers join, releasing water (H₂O)

  • Builds polymers (anabolic)

  • Requires energy

• Hydrolysis: Polymers break down by adding water

  • Breaks down polymers (catabolic)

  • Releases energy

Carbohydrates

• Formula: (CH₂O)ₙ - carbon, hydrogen, oxygen in 1:2:1 ratio

• Monosaccharides: Simple sugars (glucose, fructose, galactose)

• Disaccharides: Two monosaccharides (sucrose = glucose + fructose)

• Polysaccharides: Many monosaccharides

  • Starch/Glycogen: Energy storage in plants/animals

  • Cellulose/Chitin: Structural components in plants/insects

Lipids

• Hydrophobic molecules - insoluble in water

• Triglycerides: 3 fatty acids + glycerol backbone

  • Saturated: No double bonds, solid at room temp

  • Unsaturated: Contains double bonds, liquid at room temp

• Phospholipids: 2 fatty acids + phosphate group - form cell membranes

• Steroids: 4 fused carbon rings (cholesterol)

• Waxes: Long-chain fatty acids + alcohols

Nucleic Acids

• Nucleotide structure: Sugar + phosphate + nitrogenous base

• DNA: Deoxyribose sugar, double helix, A-T and G-C base pairs

• RNA: Ribose sugar, single strand, A-U and G-C base pairs

• Function: Genetic information storage and transfer

UNIT 2: PROTEINS & ENZYMES

Amino Acids

• 20 different types with same backbone (NH₂-C-COOH) but different R groups

• Classified by properties of R group:

  • Nonpolar/Hydrophobic: Alanine, valine, leucine, isoleucine, etc.

  • Polar/Hydrophilic: Serine, threonine, cysteine, etc.

  • Acidic: Aspartic acid, glutamic acid

  • Basic: Lysine, arginine, histidine

Protein Structure

1. Primary: Amino acid sequence linked by peptide bonds

2. Secondary: Regular patterns formed by hydrogen bonds

   • α-helix: Spiral structure

   • β-sheet: Pleated structure

3. Tertiary: Overall 3D shape due to R group interactions

   • Hydrophobic interactions

   • Ionic bonds

   • Hydrogen bonds

   • Disulfide bridges (between cysteine residues)

4. Quaternary: Multiple polypeptide chains together

Protein Denaturation

• Loss of structure and function due to:

  • Temperature changes

  • pH changes

  • Salt concentration changes

• Primary structure remains intact

• Higher levels of structure are disrupted

Enzymes

• Biological catalysts that speed up reactions

• Lower activation energy required for reactions

• Substrate specificity: Active site binds only specific substrates

• Enzyme-substrate complex: Temporary structure during catalysis

• Induced fit model: Active site shape adjusts to fit substrate

Enzyme Kinetics

• Factors affecting enzyme rate:

  1. Enzyme concentration: Linear relationship until substrate limiting

  2. Substrate concentration: Hyperbolic curve leading to saturation

  3. Temperature: Rate increases until optimum, then decreases (denaturation)

  4. pH: Each enzyme has optimal pH range

  5. Inhibitors: Substances that reduce enzyme activity

Enzyme Inhibition

• Competitive inhibition: Inhibitor resembles substrate, competes for active site

• Non-competitive inhibition: Inhibitor binds elsewhere, changes enzyme shape

UNIT 3: DNA/GENE EXPRESSION & REGULATION

DNA Structure

• Double helix of two antiparallel strands

• Nucleotide: Deoxyribose sugar + phosphate + nitrogenous base (A, T, G, C)

• Base pairing: A-T (2 hydrogen bonds), G-C (3 hydrogen bonds)

• Sugar-phosphate backbone: Alternating sugar and phosphate groups

• Chargaff's rule: A=T and G=C

DNA Packaging

• DNA wound around histones to form nucleosomes

• Nucleosomes coil into chromatin fibers

• Chromatin condenses into chromosomes during cell division

• Humans have 23 pairs of chromosomes

The Central Dogma

• DNA → RNA → Protein

• Transcription: DNA → RNA

• Translation: RNA → Protein

Transcription

1. Initiation: RNA polymerase binds to promoter with help of transcription factors

2. Elongation: RNA polymerase synthesizes RNA (using DNA template strand)

3. Termination: RNA polymerase reaches termination sequence and detaches

RNA Processing (Eukaryotes)

• 5' cap and 3' poly-A tail added

• Introns (non-coding regions) removed

• Exons (coding regions) spliced together

• Alternative splicing: Different arrangements of exons create different proteins

Translation

1. Initiation: Ribosome assembles at start codon (AUG)

2. Elongation: tRNAs bring amino acids; peptide bonds form

3. Termination: Stop codon (UAA, UAG, UGA) reached, polypeptide released

The Genetic Code

• Codon: 3 nucleotides code for 1 amino acid

• Degenerate: Multiple codons can code for same amino acid

• Universal: Same in most organisms

Gene Regulation in Prokaryotes: Operons

• Operon: Cluster of genes with related functions controlled together

• Lac Operon: Activated when lactose present, glucose absent

  • Repressor: Binds to operator when lactose absent

  • Inducer: Lactose binds to repressor, prevents operator binding

• Trp Operon: Repressed when tryptophan present

  • Repressor: Inactive until it binds tryptophan

  • Co-repressor: Tryptophan activates repressor

Genetic Engineering

• Recombinant DNA: DNA from different sources combined

• Plasmids: Small circular DNA molecules in bacteria

  • Origin of replication: Allows plasmid replication

  • Selectable marker: Often antibiotic resistance gene

  • Cloning site: Where new genes can be inserted

• Bacterial transformation: Introduction of foreign DNA into bacteria

Mutations

• Point mutations: Change in single nucleotide

  • Silent: No change in amino acid

  • Missense: Different amino acid coded

  • Nonsense: Creates premature stop codon

• Frameshift mutations: Insertion or deletion shifts reading frame

  • Often more severe than point mutations

UNIT 4: PHOTOSYNTHESIS & CELLULAR RESPIRATION

Photosynthesis Overview

• Equation: 6CO₂ + 6H₂O + light energy → C₆H₁₂O₆ + 6O₂

• Location: Chloroplasts in plant cells

• Two main stages:

  1. Light-dependent reactions

  2. Calvin cycle (light-independent reactions)

Light-Dependent Reactions

• Location: Thylakoid membrane

• Process:

  1. Light energy absorbed by chlorophyll

  2. Water molecules split (photolysis): 2H₂O → 4H⁺ + 4e⁻ + O₂

  3. Electrons move through electron transport chain

  4. ATP produced by chemiosmosis (ATP synthase)

  5. NADP⁺ reduced to NADPH

• Products: ATP, NADPH, O₂

Calvin Cycle (Light-Independent Reactions)

• Location: Stroma

• Process:

  1. Carbon fixation: CO₂ combines with RuBP (catalyzed by Rubisco)

  2. Reduction: ATP and NADPH from light reactions used to form G3P

  3. Regeneration of RuBP using ATP

• Products: Glucose, other organic compounds

Cellular Respiration Overview

• Equation: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + ATP

• Stages:

  1. Glycolysis

  2. Pyruvate processing

  3. Krebs cycle (Citric Acid Cycle)

  4. Electron Transport Chain & Oxidative Phosphorylation

Glycolysis

• Location: Cytoplasm

• Process: Glucose (6C) split into 2 pyruvate (3C) molecules

• Net products (per glucose):

  • 2 ATP

  • 2 NADH

  • 2 Pyruvate

• Anaerobic: No oxygen required

Pyruvate Processing

• Location: Mitochondrial matrix

• Process: Pyruvate (3C) → Acetyl-CoA (2C) + CO₂

• Products (per pyruvate):

  • 1 NADH

  • 1 CO₂

  • 1 Acetyl-CoA

Krebs Cycle

• Location: Mitochondrial matrix

• Process: Acetyl-CoA enters cycle, regenerates starting compound

• Products (per acetyl-CoA):

  • 3 NADH

  • 1 FADH₂

  • 1 ATP (GTP)

  • 2 CO₂

Electron Transport Chain & Oxidative Phosphorylation

• Location: Inner mitochondrial membrane

• Process: Electrons from NADH and FADH₂ move through proteins

  • Energy used to pump H⁺ into intermembrane space

  • H⁺ gradient powers ATP synthase (chemiosmosis)

• Final electron acceptor: O₂, forming H₂O

• Products: ~34 ATP (total from all stages)

ATP Yield Summary

• Glycolysis: 2 ATP + 2 NADH (→ ~4 ATP) = ~6 ATP

• Pyruvate processing: 2 NADH (→ ~6 ATP)

• Krebs cycle: 2 ATP + 6 NADH (→ ~18 ATP) + 2 FADH₂ (→ ~4 ATP) = ~24 ATP

• Total: ~36 ATP per glucose molecule

Environmental Connections

• Photosynthesis and CO₂ levels:

  • Plants absorb CO₂ during photosynthesis

  • Rising atmospheric CO₂ leads to ocean acidification

  • Ocean pH decreases as more CO₂ dissolves in water

• Cellular respiration and metabolism:

  • Tissues with high energy needs (muscle, nerve) have more mitochondria

  • Other energy sources: Lipids and proteins can enter respiratory pathways