Bio 130

4 Factors Determining Cell Structure & Function

Matter (builds components), Energy (powers building/function), Organization (protein-protein arrangement), Information (DNA/genes code proteins)

Prokaryote vs Eukaryote nucleus

Prokaryotes lack a membrane-bound nucleus (DNA in nucleoid); eukaryotes have a true membrane-bound nucleus

Pili vs Flagella

Pili = attachment; Flagella = motility

Compartmentalization

Membrane-bound organelles that separate chemical reactions in eukaryotes

Animal vs Plant cell differences

Animal cells have centrioles & lysosomes; plant cells have chloroplasts (photosynthesis), cell wall (structure), and central vacuole (storage/volume)

Genome vs Proteome

Genome = full genetic code, identical in every cell; Proteome = proteins a cell actually makes, determines its function

4 Ways Proteomes Differ

Turning genes on/off, varying protein amounts, alternative splicing, post-translational modifications

Surface area to volume ratio problem

As a cell grows, volume increases faster than surface area, limiting nutrient uptake/waste export

Strategies to maximize SA/V ratio

Staying small, elongating (e.g. neurons), or folding surfaces (e.g. microvilli)

Levels of biological organization

Cells → Tissues (similar cells) → Organs (2+ tissue types) → Organ Systems → Organism

Why carbon forms 4 covalent bonds

4 valence electrons let it bond with C, H, O, N, S in linear, ring, or branched shapes

Nonpolar vs Polar bonds

Nonpolar (C-C, C-H) = hydrophobic; Polar (C-O, C-N) = hydrophilic

Why carbon bonds are stable

Small atomic radius makes bonds short, strong, and stable

Key functional groups & properties

Amino (-NH2, basic), Carboxyl (-COOH, acidic), Hydroxyl (-OH, polar/H-bonds), Methyl (-CH3, nonpolar), Phosphate (-PO4, negatively charged), Sulfhydryl (-SH, forms disulfide bridges)

4 categories of organic macromolecules

Carbohydrates, lipids, proteins, nucleic acids

Carbohydrate functions

Energy (ATP) from sugars, storage/structure from polysaccharides, cell recognition tags

Lipid structure & functions

Nonpolar, not true polymers; used in membranes, energy storage, hormones, insulation

Protein structure (overview)

Polypeptides (amino acid chains) that fold into functional proteins

Nucleic acid structure (overview)

Chains of nucleotides; DNA double-stranded, RNA single-stranded

Pentoses in nucleic acids

Ribose (RNA) and Deoxyribose (DNA)

Glycosidic bond formation & breakdown

Formed by dehydration synthesis (removes water); broken by hydrolysis (adds water)

Disaccharide examples

Sucrose (glucose+fructose), Maltose (glucose+glucose), Lactose (galactose+glucose)

Starch vs Glycogen

Starch = plant storage, less branched; Glycogen = animal storage, highly branched

Cellulose vs Chitin vs Peptidoglycan

Cellulose = plant cell walls; Chitin = fungal walls/exoskeletons; Peptidoglycan = bacterial cell walls

Triglycerides

Glycerol + 3 fatty acids via dehydration; stores 2x more energy per gram than starch

Saturated vs Unsaturated vs Trans fats

Saturated = straight chains, solid at room temp; Unsaturated = kinked, liquid; Trans = artificial straight chain, linked to heart disease

Phospholipids & Amphipathic

Glycerol + 2 fatty acid tails (nonpolar) + phosphate head (polar); amphipathic = both polar and nonpolar regions; forms membrane bilayers

Steroids structure

4 fused carbon rings (cholesterol, estrogen, testosterone)

Peptide bond formation

Links amino acids via dehydration synthesis

Amino acid structure

Alpha-carbon + amino group + carboxyl group + H + R group

Polypeptide vs Protein

Polypeptide = amino acid chain; Protein = 1+ polypeptides folded into functional 3D shape

Protein structure levels

Primary (sequence) → Secondary (H-bond folding, helix/sheet) → Tertiary (3D shape from R-groups) → Quaternary (multiple subunits)

5 forces determining protein structure

Hydrogen bonds, ionic bonds, hydrophobic effect, van der Waals forces, disulfide bridges

Hydrophobic effect in folding

Nonpolar R groups tuck into the center away from water

Denaturation

Protein unfolds and loses function due to heat, pH, or chemicals

Nucleotide structure

Phosphate + pentose sugar + nitrogenous base

DNA vs RNA structure

DNA: double-stranded, deoxyribose, A/G/C/T; RNA: single-stranded, ribose, A/G/C/U

Base pairing

A-T (2 H-bonds, A-U in RNA); G-C (3 H-bonds, stronger)

Chargaff's Rule

%A = %T and %G = %C

Why is RNA single-stranded

Ribose's extra -OH makes it bulkier, preventing a stable double helix; allows folding into functional shapes as a messenger

Passive vs Active transport

Passive = down gradient, no energy; Active = against gradient, requires transport protein + ATP

Simple vs Facilitated diffusion

Simple = direct passage through bilayer; Facilitated = assisted by a channel/transport protein, still no energy needed

Factors affecting bilayer permeability

Size, polarity, charge, concentration

Membrane permeability hierarchy

Gases/small nonpolar > small uncharged polar > large polar (sugars) > charged ions/macromolecules

Chemical vs Electrochemical gradient

Chemical = solute concentration difference; Electrochemical = concentration + charge difference

Osmosis

Water moves across a membrane from lower to higher solute concentration

Isotonic

Equal solute concentration inside/outside; no net water movement

Hypertonic solution effect

Water leaves the cell — animal cells shrink (crenation); plant cells undergo plasmolysis (membrane detaches from wall)

Hypotonic solution effect

Water enters the cell — animal cells may burst (lysis); plant cell wall prevents lysis, maintains turgor pressure

Phospholipid synthesis & flippases

Made on cytosolic leaflet of smooth ER; flippases move them to the other leaflet to balance composition

Lipid transport between membranes

Via lateral diffusion (continuous membranes) or lipid exchange proteins (shuttled through cytosol)

Transmembrane segment

~20 hydrophobic amino acids forming an alpha helix that spans the membrane

Glycosylation & its functions

Attachment of carbs to lipids/proteins; used for cell recognition and protection from degradation

Exocytosis vs Endocytosis

Exocytosis = secretes material out via vesicles; Endocytosis = brings material in via vesicles

Exocytosis steps

Cargo loading → budding/coat formation → coat shedding → fusion with plasma membrane

Types of endocytosis

Receptor-mediated (specific cargo binds receptors), Pinocytosis ("cell drinking," fluid), Phagocytosis ("cell eating," large particles)

3 functions of the cell membrane

Selective barrier, maintains ion/solute differences, mediates communication/attachment

Membrane protein types

Single-pass (crosses once), Multi-pass (crosses multiple times), Lipid-anchored (attached via lipid tail, doesn't span), Peripheral (attached via protein-protein/lipid interactions only)

Why membrane proteins can't flip-flop

Their hydrophilic regions can't pass through the hydrophobic core — energetically unfavorable (but they can move laterally/rotationally)

Lipid rafts & cholesterol's role

Cholesterol-rich microdomains; cholesterol's rigid ring stiffens nearby lipids, creating a less fluid region that corrals certain proteins together

Endoplasmic Reticulum (overview)

Membrane network for membrane synthesis, protein processing, and lipid synthesis

Smooth ER functions

Lipid synthesis, calcium storage, detoxification, glycogen breakdown

Rough ER functions

Ribosome-studded; protein sorting, insertion into membranes, glycosylation, secretion

Nucleus & Nucleolus

Nucleus organizes/expresses genetic material within a nuclear envelope; Nucleolus assembles ribosome subunits

Chromatin

Complex of protein and DNA

Golgi apparatus structure & function

Stack of cisternae; Cis (receives from ER) → Medial (glycosylation) → Trans (packages for secretion); modifies, sorts, and secretes lipids/proteins

Lysosome

Contains acid hydrolases; degrades macromolecules and old cell parts

Peroxisome

Breaks down hydrogen peroxide and harmful molecules

Mitochondrion

Site of ATP synthesis

Centrosome & Cytoskeleton

Centrosome = where microtubules grow; Cytoskeleton = protein filaments providing shape and movement

Endomembrane system

Interconnected network (nuclear envelope, ER, Golgi, lysosomes, plasma membrane) that processes, sorts, and transports molecules

Protein trafficking pathway (ER to lysosome)

Made by ribosomes on rough ER, processed through Golgi, delivered to lysosome via vesicles

Bacterial cell wall composition

Peptidoglycan — mesh of peptides and sugars for shape/support

Membrane permeability examples

High: gases, small nonpolar; Moderate: water, urea; Low: glucose (needs transporter); Very low: ions and charged macromolecules

Channels vs Transporters

Channels = open pore for direct passage; Transporters = bind solute, change shape, release on other side (both can be passive or active depending on protein)

Why ions can't cross membranes alone

Charged molecules can't pass through the hydrophobic bilayer core — always need a transport protein

Sodium-potassium pump

Active transport protein; uses ATP to move Na+ and K+ against their gradients

Semiautonomous organelles

Mitochondria & chloroplasts — grow/divide on their own but rely on host cell cytosol for most components

Mitochondria structure

Outer membrane, inner membrane folded into cristae (more SA for ATP synthesis), intermembrane space, matrix

Chloroplast structure & function

Double membrane; thylakoids (stacked into grana) do light reactions; stroma surrounds them; captures light energy to make glucose

Plastids

Family including chloroplasts (photosynthesis), chromoplasts (pigment storage), leucoplasts/amyloplasts (starch storage, no pigment)

Mitochondrial/chloroplast genomes & division

Each has own circular DNA (like bacteria); divide by binary fission

Endosymbiosis theory

Mitochondria/chloroplasts arose from prokaryotes engulfed by early eukaryotic cells (mitochondria from proteobacteria, chloroplasts from cyanobacteria)

Evidence for endosymbiosis

Circular DNA & bacterial-like ribosomes, similar size/structure to bacteria, binary fission, gene transfer to host nucleus over time

Why do cells need to communicate

To adapt to environmental changes and to share information with other cells across distances

Environmental response examples

Yeast produce enzymes to absorb glucose when present; human skin produces melanin in response to UV light

Direct intercellular signaling

Signals move directly between cells through junctions, such as gap junctions in cardiac muscle cells

Contact-dependent signaling

A membrane-bound signal on one cell binds to a receptor on an adjacent cell, as in immune system recognition

Autocrine signaling

A signal binds to receptors on the secreting cell itself and nearby identical cells, allowing a cell to sense local cell density

Paracrine signaling

Short-lived signals that affect nearby target cells, such as neurotransmitters crossing a synapse

Endocrine signaling

Long-distance signals (hormones) that travel through the blood (animals) or vascular tissue (plants) to reach distant target cells

5 types of cell signaling by distance

Direct intercellular, contact-dependent, autocrine, paracrine, and endocrine

3 stages of cell signaling

Receptor activation (ligand binds, receptor changes shape) → Signal transduction (chain of protein changes inside cell) → Cellular response (target proteins altered)

Cellular response types

Enzymes (changes metabolic activity), Structural proteins (rearranges cytoskeleton for movement), Transcription factors (turns genes on/off)

Cytoskeleton

A network of protein filaments in the cytoplasm that gives cells their shape, provides internal structure, and enables movement

3 main types of cytoskeletal filaments

Microtubules, actin filaments (microfilaments), and intermediate filaments

Microtubules (general role)

Thick, hollow tubes that act as tracks for moving organelles and vesicles, and help separate chromosomes during cell division

Actin filaments (general role)

Thin, flexible filaments that support cell shape, enable cell crawling, and drive muscle contraction

Intermediate filaments (general role)

Rope-like filaments that provide mechanical strength and help anchor organelles like the nucleus in place

How do filaments differ in stability

Microtubules and actin filaments can rapidly assemble and disassemble; intermediate filaments are more stable and permanent