Biochemistry Exam Review

Biochemistry Exam Review

Organic Molecules and Elements

• Organic molecules are composed primarily of carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur.

Covalent Bonds

• Covalent bonds involve the sharing of electrons between atoms.
• Electronegativity: A measure of an atom's ability to attract electrons in a covalent bond.
  • Polar Covalent Bonds: Unequal sharing of electrons due to differences in electronegativity, resulting in partial charges (δ+ and δ-).
  • Non-polar Covalent Bonds: Equal sharing of electrons due to similar electronegativity.

Polar Molecules

• Polar molecules have an uneven distribution of charge.
• Determination of polarity:
  • Bonds: Presence of polar bonds.
  • Symmetry: Molecular shape and symmetry can cancel out bond dipoles, resulting in a non-polar molecule, even with polar bonds.

Intermolecular Forces

• Forces of attraction between molecules.
  • Hydrogen Bonds: Attraction between a hydrogen atom bonded to a highly electronegative atom (O, N, F) and another electronegative atom.
    • Responsible for many unique properties of water.

Properties of Water

• Cohesion: Attraction between water molecules due to hydrogen bonds.
• Adhesion: Attraction between water molecules and other substances.
• Surface Tension: Measure of how difficult it is to stretch or break the surface of a liquid; high in water due to cohesive forces.
• High Heat Capacity: Water's ability to absorb a large amount of heat without a significant change in temperature.
• Density: Water is less dense as a solid (ice) than as a liquid.

Importance in Biology

• Cohesion and adhesion are important for water transport in plants.
• High heat capacity helps moderate temperature in living organisms and environments.
• Lower density of ice allows aquatic life to survive in freezing temperatures.

Structure/Shape of Water

• Bent shape and polar bonds (due to oxygen's high electronegativity) result in an overall polar molecule, enabling hydrogen bonding.

Functional Groups

• Specific groups of atoms attached to carbon skeletons that confer characteristic properties.

Examples

• Hydroxyl (-OH): polar, increases solubility
• Carbonyl (C=O): polar
• Carboxyl (-COOH): acidic
• Amino (-NH2): basic
• Sulfhydryl (-SH): can form disulfide bridges
• Phosphate (-PO4): negatively charged, involved in energy transfer (ATP)
• Methyl (-CH3): non-polar, affects gene expression

Characteristics

• Influence polarity, forces of attraction, and solubility of molecules.

Types of Reactions

• Dehydration (Condensation): Removal of water to form a bond (e.g., monomer to polymer).
  • glucose + glucose \rightarrow maltose + H_2O
• Hydrolysis: Addition of water to break a bond (e.g., polymer to monomer).
  • starch + H_2O \rightarrow individual \ glucose \ molecules
• Neutralization: Reaction between an acid and a base to form water and a salt.
• Redox (Reduction-Oxidation): Transfer of electrons.
  • Oxidation: Loss of electrons.
  • Reduction: Gain of electrons.

Macromolecules

Carbohydrates

• Monomers: Monosaccharides (e.g., glucose, fructose, galactose).
  • Basic Structure: (CH2O)n, where n is typically 3 to 7.
• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., maltose, sucrose, lactose).
  • Formation: Dehydration synthesis (e.g., glucose + fructose → sucrose).
• Polysaccharides: Polymers of monosaccharides.
  • Starch: Energy storage in plants; found in roots and seeds.
    • Amylose: Linear structure.
    • Amylopectin: Branched structure.
  • Glycogen: Energy storage in animals; found in liver and muscles.
    • Highly branched structure.
  • Cellulose: Structural component of plant cell walls; most abundant organic compound on Earth.
    • Linear structure with beta linkages; humans cannot digest it.
  • Chitin: Structural component in exoskeletons of arthropods and cell walls of fungi.

Proteins

• Monomer: Amino acids.
  • Basic Structure: Central carbon atom bonded to an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom (-H), and an R group.
• Amino Acid Linkage: Peptide bonds between the carboxyl group of one amino acid and the amino group of another.
• R Group Differences: Provide unique chemical properties to each amino acid (e.g., polarity, charge, size).
  • Determine the protein's structure and function.
• Levels of Protein Structure:
  • Primary: Sequence of amino acids.
  • Secondary: Localized folding (alpha-helices and beta-pleated sheets) stabilized by hydrogen bonds.
  • Tertiary: Overall 3D shape stabilized by interactions between R groups (e.g., hydrophobic interactions, hydrogen bonds, disulfide bridges).
  • Quaternary: Association of two or more polypeptide chains.
• Protein Denaturation: Loss of protein's native structure due to disruption of chemical bonds (e.g., by heat, pH, chemicals).
• Functions of Proteins: Enzymes, structural components, transport, defense, hormones, receptors, etc.

Enzymes

• Biological catalysts that speed up chemical reactions by lowering activation energy.
• Substrate: Reactant that an enzyme acts on.
• Active Site: Region of enzyme where substrate binds.
  • Lock and Key Model: Substrate fits perfectly into the active site.
  • Induced-Fit Model: Enzyme changes shape slightly to better fit the substrate.
• Optimal pH and Temperature: Conditions for maximum enzyme activity.
• Allosteric Regulation: Regulation of enzyme activity by binding of a molecule to a site other than the active site.
  • Allosteric Activation: Activator molecule stabilizes the active form of the enzyme.
  • Allosteric Inhibition: Inhibitor molecule stabilizes the inactive form of the enzyme.
• Feedback Inhibition: End product of a metabolic pathway inhibits an enzyme early in the pathway.

Lipids

• Hydrophobic molecules (insoluble in water).
• Functions: Energy storage, insulation, structural components of cell membranes, hormones.
• Triglycerides: Glycerol molecule + 3 fatty acids.
  • Saturated Fatty Acids: No double bonds; solid at room temperature.
  • Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature.
• Phospholipids: Glycerol + 2 fatty acids + phosphate group.
  • Location: Primary component of cell membranes.
  • Structure: Phosphate head (polar, hydrophilic), fatty acid tails (nonpolar, hydrophobic).
  • Formation: Form a bilayer in water, with hydrophilic heads facing outward and hydrophobic tails facing inward.
• Sterols (Steroids): Four fused carbon rings.
  • Examples: Cholesterol, testosterone, estrogen.
  • Functions: Hormones, membrane components.
• Waxes: Esters of long-chain fatty acids and long-chain alcohols.
  • Functions: Waterproofing, protection.

Metabolic Processes

Cellular Respiration

• Process by which cells generate energy (ATP) by breaking down organic molecules.
• Balanced Chemical Reaction: C6H{12}O6 + 6O2 → 6CO2 + 6H2O + ATP
• Glycolysis: Occurs in the cytoplasm; breaks down glucose into pyruvate.
  • Products: 2 ATP (net), 2 NADH, 2 pyruvate.
• Pyruvate Oxidation (Transition Reaction): Occurs in the mitochondrial matrix; converts pyruvate to acetyl CoA.
  • Products: 2 Acetyl CoA, 2 NADH, 2 CO2.
• Krebs Cycle (Citric Acid Cycle): Occurs in the mitochondrial matrix; oxidizes acetyl CoA.
  • Products: 2 ATP, 6 NADH, 2 FADH2, 4 CO2.
• Electron Transport Chain (ETC): Occurs in the inner mitochondrial membrane; uses NADH and FADH2 to generate a proton gradient, which drives ATP synthesis.
  • NADH & FADH2: High-energy electron carriers.
  • Final Electron Acceptor: Oxygen.
• ATP Production:
  • Substrate-level phosphorylation: ATP produced directly during glycolysis and Krebs cycle.
  • Oxidative phosphorylation: ATP produced via ETC and chemiosmosis.
• Anaerobic Respiration: Occurs in the absence of oxygen.
  • Lactate Fermentation: Pyruvate is reduced to lactate.
  • Ethanol Fermentation: Pyruvate is converted to ethanol and CO2.

Photosynthesis

• Process by which plants and other organisms convert light energy into chemical energy.
• Balanced Chemical Reaction: 6CO2 + 6H2O + \text{Light Energy} → C6H{12}O6 + 6O2
• Leaf and Chloroplast Structure:
  • Stomata: Pores in leaves that allow for gas exchange (CO2 in, O2 out).
  • Chloroplasts: Organelles where photosynthesis occurs; contain thylakoids (internal membranes) and stroma (fluid-filled space).
• Chlorophyll and Other Pigments:
  • Absorb specific wavelengths of light; chlorophyll absorbs red and blue light, reflects green light.
• Light-Dependent Reactions: Occur in the thylakoid membranes.
  • PSII and PSI: Photosystems that capture light energy and transfer electrons.
  • Electron Pathway: Electrons move through an ETC, releasing energy to pump protons (H+) into the thylakoid space.
  • ATP Production: ATP is synthesized via chemiosmosis, using the proton gradient.
  • NADPH production: NADP+ is reduced to NADPH
  • Photolysis: Water is split to provide electrons, releasing O2.
  • Final Electron Acceptor: NADP+.
  • Proton Gradient: Drives ATP synthesis via ATP synthase.
  • Cyclic vs. Non-Cyclic Electron Flow: Cyclic electron flow uses only PSI and produces ATP but not NADPH; non-cyclic electron flow uses both PSII and PSI and produces both ATP and NADPH.
• Light-Independent Reactions (Calvin Cycle): Occur in the stroma.
  • Requirements: ATP and NADPH from the light-dependent reactions, CO2.
  • Process: CO2 is fixed, reduced, and converted into glucose.

Photorespiration

• Occurs when RUBISCO binds to O2 instead of CO2.
• Decreases photosynthetic efficiency.
• C4 and CAM Plants: Adaptations to minimize photorespiration in hot, dry environments.
  • Examples of C4 plants: corn, sugarcane.
  • Examples of CAM plants: cacti, succulents.
  • Transpiration: Water loss from plants.
  • C4 Cycle: CO2 is initially fixed into a 4-carbon compound in mesophyll cells, then transported to bundle sheath cells where the Calvin cycle occurs.
  • CAM Cycle: CO2 is fixed at night and stored as an acid; during the day, the acid is broken down and CO2 is released to the Calvin cycle.

Comparison

• Photosynthesis and Cellular Respiration: Interdependent processes; products of one are reactants of the other.
• Mitochondria and Chloroplasts: Both involved in energy production; contain electron transport chains and generate ATP via chemiosmosis.

Molecular Genetics

DNA and RNA Structure

DNA Replication

• Strand separation, building complementary strands, dealing with errors

Transcription

• mRNA, initiation, elongation, termination, modification (introns/exons/cap and tail)

Mutations

• point mutations (substitutions, deletion, insertion), silent/nonsense/missense/frameshift mutations, large scale mutations, causes of mutations (spontaneous vs. induced)

Translation

• structure/function of tRNA, wobble hypothesis, ribosome binding sites, phases of translation (initiation, elongation, termination

Controlling Gene Expression

• lac operon and trp operon in prokaryotes

Recombinant DNA

PCR, gel electrophoresis

DNA profiling

Homeostasis

• Define homeostasis
• List different levels that the body must maintain/control (ex: pH)
• Describe and illustrate positive and negative feedback loops. Use the terms sensor, control center and effector.
• Describe a specific positive (ex: oxytocin) and a specific negative feedback loop (ex: blood glucose levels)

Nervous System

• Describe the divisions of the nervous system: CNS vs PNS
  • Afferent vs. efferent
  • Somatic vs. autonomic
  • Sympathetic vs. parasymphathetic
• Describe various physiological responses the sympathetic and parasympathetic nervous systems promote or inhibit.
• Describe the 2 different types of nerve cells and the 3 types of neurons
• Describe and label the structural features of a typical neuron
• Describe nerve signals and how they are passed along the neuron
  • Chemical vs. electrical synapse
  • Resting membrane potential of the plasma membrane (what ion is outside, what ion is inside)
  • Describe the action potential in stages (ex: excitation, depolarization, repolarization, hyperpolarization)
  • What role does the sodium potassium pump play in restoring the resting membrane potential?
  • Reaching the threshold and the All-or-None Principle – describe
• Describe synaptic transmissions: what is a synapse, how do neurotransmitters help send signals from one neuron to the next
  • Describe the role that calcium ions play
  • Excitatory vs. inhibitory
  • Examples of neurotransmitters
  • Drugs and how they can mimic/interfere with neurotransmitters

Endocrine System

• Describe how hormones move around the body and how they are received at cells
• 2 classes of hormones – steroid hormones vs. protein hormones
• How do hormones act on the cell? (differences between steroid and protein)
• Parts of the endocrine system (ex: hypothalamus, pituitary gland, etc.)
• What does the pituitary gland control in our bodies? (numerous examples)
• Describe how the thyroid gland, the adrenal gland, and the pancreas help to regulate our body with their respective hormone responses
  • Be able to describe how thyroid levels are maintained and how blood glucose levels are maintained
• Describe various glands, hormones, targets, and effects on body (from chart)
• Choose one gland and describe the hormone feedback loops associated with the gland of choice.