Lecture Review Notes

Protein bonds and functions

• Question reviewed: what type of bonds hold amino acids together in proteins?
  • Common student responses: ionic peptide, hydrogen, covalent peptide, condensation.
  • Correct answer: peptide bonds.
  • Peptide bonds are covalent bonds that link amino acids together in a polypeptide chain.
  • Covalent bonds generally hold molecules together; ionic bonds hold salts; not typically what sustains living organic molecules in aqueous environments.
• One-word function of proteins (example student prompt):
  • Transport, Structure, Enzymes, Catalysts (examples given in class; refer to slide emphasis for exam prep).

Protein structure levels

• Four levels of protein structure:
  • Primary structure: the sequence of amino acids in the polypeptide chain.
  • Secondary structure: alpha helices and beta sheets formed by backbone interactions and the influence of side-chain properties (hydrophobic/hydrophilic) and bond angles.
  • Tertiary structure: 3D folding of the polypeptide into domains; interaction of alpha helices and beta sheets and other elements into a single chain.
  • Quaternary structure: assembly of multiple polypeptide chains into a functional protein unit (e.g., dimers, larger oligomers).
• Domains:
  • Defined as segments of a polypeptide that can fold independently into compact, stable structures but are still connected within the same polypeptide.
  • Example described: CAP protein with domain 1 (blue) and domain 2 (yellow); each domain folds independently but remains part of the same polypeptide.
  • Important distinction: quaternary structure involves multiple polypeptides, while domains are structural units within a single polypeptide.
• Key mappings:
  • Primary → amino acid sequence
  • Secondary → alpha helix and beta sheet organization
  • Tertiary → overall 3D folding (domains form within a single chain)
  • Quaternary → interaction/assembly of multiple polypeptide chains
• Visual explanation in lecture:
  • Alpha helix and beta sheet shown without side chains in some figures; arrows in beta sheets indicate directionality.
  • In CAP example, domain folding occurs within the same polypeptide; domain 2 folds independently, domain 1 is another folded segment.
• Common exam note:
  • The exam may include diagrams to label or interpret, but not heavy on diagrams; you may draw your own diagram for the written response question if that helps.

Condensation vs hydrolysis (clarification on slides)

• Condensation reactions (dehydration synthesis):
  • Sugar example: Monosaccharide + Monosaccharide → Disaccharide + ext{H}_2 ext{O}
  • Amino acids forming a peptide bond:
    ext{Amino acid}1 + ext{Amino acid}2
    ightarrow ext{Dipeptide} + ext{H}_2 ext{O}
• Hydrolysis reactions (adding water to break bonds):
  • Disaccharide → Monosaccharides + ext{H}_2 ext{O}
  • General note: the slide contains a correction; peptide bond formation is condensation, not hydrolysis. The instructor apologized for the slide error and will repost corrected material on D2L.

Nervous system: synapse and action potential flow

• Action potential propagation basics:
  • Sodium influx depolarizes the cell membrane; inside becomes less negative (more positive relative to outside).
  • Voltage-gated ion channels open/close as the action potential travels along the axon; this propagates the signal toward the nerve terminal.
• Nerve terminal and synaptic transmission:
  • At the presynaptic terminal, the action potential triggers voltage-gated calcium channels to open, allowing Ca²⁺ influx.
  • Calcium influx causes synaptic vesicles containing neurotransmitter to fuse with the presynaptic membrane and release neurotransmitter into the synaptic cleft.
  • Neurotransmitter binds to ligand-gated ion channels on the postsynaptic cell (e.g., sodium channels), allowing Na⁺ influx and continuation of the action potential in the postsynaptic cell.
• Key takeaway: communication between neurons relies on neurotransmitter release and receptor binding rather than direct electrical continuity.

Gel electrophoresis: size-based separation and protein chemistry

• Principle: separation by size (and to some extent charge) under an electric field.
• Procedure overview:
  • Proteins are loaded into wells at the top of a gel; an electric current moves negatively charged samples toward the positive electrode.
  • Smaller molecules migrate faster through the gel than larger ones.
• SDS (sodium dodecyl sulfate) treatment:
  • SDS binds to proteins to give them a uniform negative charge-to-mass ratio, enabling separation primarily by size.
• Beta-mercaptoethanol:
  • Reduces disulfide bonds (R-S-S-R') between cysteine residues, allowing subunits to separate during electrophoresis.
• Example interpretation:
  • A gel showing subunits A and B joined by a disulfide bond will separate into A and B bands after reduction; B (larger) migrates more slowly and appears higher on the gel, while A (smaller) migrates farther down; C remains intact if it has no disulfide bonds or subunits.
• Summary: size is the primary determinant of migration; charge (from SDS) standardizes the charge-to-mass ratio; reduction breaks disulfide-linked subunits.

Amino acid side chains: polarity, hydrophobicity, and charge

• Four types of side chains (and their general behaviors):
  • Nonpolar (hydrophobic): tend to be buried inside proteins unless in transmembrane regions.
  • Polar but uncharged: hydrophilic regions that interact with water.
  • Polar, negatively charged (acidic): hydrophilic; interact with positively charged residues.
  • Polar, positively charged (basic): hydrophilic; interact with negatively charged residues.
• Practical implications:
  • Nonpolar residues are often in the protein interior or within transmembrane regions.
  • Polar residues (including charged ones) tend to be on protein surfaces in contact with water (cytosol or extracellular fluid).
  • Electromagnetic interactions influence protein folding and stability.
• Important reminder: you do not need to memorize exact amino acid identities for each type; focus on the four general categories and how they influence protein structure and interactions.

Cell theory and the basics of cell biology

• Core idea: living organisms are made up of cells; this is the central concept of cell theory.
• Do not require dates or discovery details; focus on the basic concept that cells are the fundamental units of life.
• The lecture emphasized not distinguishing formal categories (prokaryotic vs. eukaryotic) in this particular exam scope, but understanding that cells are the basic units.

Plasma membrane: structure, components, and surface properties

• Composition:
  • Plasma membrane consists of a phospholipid bilayer with cholesterol and various proteins (and associated lipids).
  • In general teaching, the two-layer arrangement includes phospholipids with hydrophilic heads and hydrophobic tails; cholesterol modulates fluidity; proteins function in transport, signaling, and structural roles.
• Outer surface interactions:
  • The outer surface interacts with the extracellular environment; the heads are polar and hydrophilic, facilitating contact with water.
  • The surface is enriched with proteins and polar components that interface with the extracellular milieu.
• Protein mobility in membranes:
  • Proteins embedded in the plasma membrane are not fixed; experiments such as FRAP (fluorescence recovery after photobleaching) and membrane fusion studies show lateral mobility.
  • False statement example from question: once associated with the lipid bilayer, proteins are not necessarily stuck in place; they can move.
• One-word follow-up: aside from phospholipids, the plasma membrane is also made up of proteins (as a major component).
• Membrane morphology reminder:
  • There is a conceptual illustration showing a curved or wavy sheet that can minimize exposure of hydrophobic tails by forming vesicle-like spheres in certain contexts.

Transcription, translation, and rough ER

• Central idea:
  • Transcription: DNA is transcribed into RNA in the nucleus (in eukaryotes); this is the first step in expressing genes.
  • Translation: RNA is translated into an amino acid sequence to form proteins; occurs on ribosomes.
• Rough Endoplasmic Reticulum (RER):
  • RER is characterized by ribosomes attached to its surface, giving it a rough appearance.
  • These ribosomes are the sites of translation of RNA into protein destined for secretion, lysosomes, or the cell membrane.
• Plasma membrane basics touched here:
  • The plasma membrane is a dynamic structure composed of lipids, cholesterol, and proteins, with specific roles in transport and signaling.

Central dogma and related topics from lecture five

• Central dogma (basic concept):
  • DNA stores genetic information; transcription converts DNA to RNA; translation converts RNA to protein.
  • RNA is transcribed from DNA; RNA is translated to protein; the two nucleic-acid language systems are different from the amino acid language.
• Rough ER and protein synthesis:
  • Rough ER is a critical site for translating certain proteins that are secreted or membrane-bound.

Biochemical basics and practical study tips

• “Milk-and-honey” molecules vs functional groups:
  • Oils are lipids and hydrophobic; they do not mix with water and form distinct layers, as in vinaigrettes.
• Condensed reactions and ionic/covalent bonds:
  • polar molecules can arise from covalent bonds with unequal sharing; ionic bonds create charged ions but are not themselves molecules.
• Major bioelements and percentages:
  • Elements forming ~99% of human body atoms: ext{H}, ext{C}, ext{N}, ext{O}
• Factors affecting enzyme-catalyzed reactions:
  • Temperature and pH are key factors that affect reaction rates.
• Lipids and health:
  • Saturated fats vs unsaturated fats: saturated fats are generally more likely to contribute to arterial plaque formation due to straight chains that pack tightly; unsaturated fats have kinks due to double bonds, reducing tight packing.
• Nucleotide vs amino acid components:
  • A false statement example: amino acids are not composed of sugar + phosphate + nitrogenous base; that is a nucleotide structure.
• Carbon-based macromolecules and polarity:
  • Polar/charged residues contribute to hydrophilicity; nonpolar residues contribute to hydrophobic regions.
• Key practice questions from earlier lectures:
  • DNA stores information for amino acid sequence; proteins help replicate DNA; RNA is translated into protein; RNA is transcribed into DNA (central dogma check) – three true statements among given options.
• Differential centrifugation concept (order of pelleting):
  • When separating components by size/density, larger and denser components pellet at lower speeds; smaller components pellet at higher speeds in successive steps. Review slide details for exact ordering (nucleus > mitochondria > fragments of ER > large macromolecules).
• Yeast and domain basics:
  • Yeast are eukaryotes and unicellular; share many genes with humans (homology).
• Practice with Mentimeter during review:
  • Mentimeter codes change per session; you may re-log in to answer again or jot down questions/answers as needed.

Quick recap of key equations and markers

• Peptide bond formation (condensation):
  ext{Amino acid}1 + ext{Amino acid}2
  ightarrow ext{Dipeptide} + ext{H}_2 ext{O}
• Disaccharide formation (condensation):
  ext{Monosaccharide} + ext{Monosaccharide}
  ightarrow ext{Disaccharide} + ext{H}_2 ext{O}
• Polysaccharide breakdown (hydrolysis):
  ext{Disaccharide} + ext{H}_2 ext{O}
  ightarrow ext{Monosaccharide} + ext{Monosaccharide}
• Gel electrophoresis concepts:
  • Separation by size; SDS provides uniform negative charge; β-mercaptoethanol reduces disulfide bonds.
• Membrane components: phospholipid bilayer with cholesterol and proteins; surface polarity governs interactions with water and environment.

Practice tips for exam readiness

• Review levels of protein structure and the concept of domains within tertiary structure.
• Be able to explain why quaternary structure is not associated with domains within a single polypeptide, but with multiple polypeptides.
• Know the basic flow of nerve signaling across a synapse, especially the role of Ca²⁺ in vesicle fusion and the postsynaptic receptor response.
• Be prepared to interpret or label diagrams of protein structure, membranes, and cellular components; you may also draw diagrams for written responses.
• Understand condensation vs hydrolysis concepts in carbs and peptides, and recognize instructor corrections when slides contain errors.
• Remember the core ideas of the central dogma and rough ER’s role in translation.
• Know how SDS-PAGE works and how enzymatic or structural details (e.g., disulfide bonds) affect band formation.
• Be aware of test format notes: 32 MC questions and a 4-part free response; practice with verbal and diagrammatic responses.