Biology: Cell Structure, Matter, and Biochemical Principles

Matter

Anything with mass and volume.

States of Matter

Exists in three states: solid, liquid, gas.

Solid

Bone

Liquid

Blood

Gas

Oxygen

Main Elements in Living Organisms

C, H, N, O, P, S

Iron (Fe)

A trace element, essential for oxygen transport via hemoglobin in red blood cells.

Atom

Smallest unit of matter retaining element properties.

Atomic Number

Number of protons.

Atomic Mass Number

Protons + neutrons.

Isotopes

Atoms of the same element with different neutron numbers.

Radioactive Decay

Unstable isotopes break down into stable atoms.

Half-life

Time for half of a radioactive isotope to decay.

Ionic Bonds

Transfer of electrons.

Covalent Bonds

Sharing of electrons.

Polar Molecules

Unequal sharing of electrons → partial charges (+/-).

Nonpolar Molecules

Equal sharing → no partial charges.

Cohesion

Water molecules stick to each other.

Adhesion

Water molecules stick to other polar surfaces.

Monomers of Carbohydrates

Monosaccharides (simple sugars).

Polymers of Carbohydrates

Polysaccharides.

Disaccharides

Formed by dehydration synthesis joining two monosaccharides.

Polysaccharides Examples

Starch (plants), Glycogen (animals), Cellulose (plant cell walls), Chitin (exoskeletons of insects/crustaceans, fungal cell walls).

Monomers of Proteins

Amino acids.

Polymers of Proteins

Polypeptides.

Amino Acid Structure

Components: Amino group (-NH2), Carboxyl group (-COOH), R group (side chain).

Peptide Bonds

Amino acids linked by peptide bonds from dehydration synthesis.

Effects of Mutations

Mutation altering amino acid sequence can affect all structure levels.

Protein Denaturation

Caused by changes in pH, temperature, salt concentration.

Monomers of Nucleic Acids

Nucleotides.

Polymers of Nucleic Acids

Polynucleotides.

Nucleotide Structure

Three parts: Phosphate group, Pentose sugar, Nitrogenous base.

ATP (Adenosine Triphosphate)

Composed of adenine, ribose, and three phosphate groups.

Allosteric activators

Stabilize active conformation → increase activity.

Allosteric inhibitors

Stabilize inactive conformation → decrease activity.

Allosteric inhibition

Noncompetitive inhibition.

Feedback Inhibition

End product of metabolic pathway inhibits an early enzyme.

Example of Feedback Inhibition

Excess isoleucine inhibits first enzyme in its synthesis pathway.

Four features common to all cells

Allow selective passage of substances.

Plasma membrane

Phospholipid bilayer with hydrophilic heads facing outward and hydrophobic tails inward.

Ribosomes

Build proteins based on instructions encoded in DNA.

Prokaryotic cells

Smaller, simpler; lack nucleus.

Eukaryotic cells

Larger, complex; have nucleus and membrane-bound organelles.

Animal vs. Plant cells

Plant cells have cell wall, large central vacuole, chloroplasts; animal cells have centrioles and lysosomes.

Rough ER

Studded with ribosomes; synthesizes proteins destined for secretion, membrane incorporation, or lysosomes.

Smooth ER

Lacks ribosomes; synthesizes lipids (fats, steroids, phospholipids), detoxifies cells.

Golgi apparatus

Modifies and packages proteins.

Lysosomes

Vesicles with hydrolytic enzymes that digest macromolecules, recycle organelles, and participate in apoptosis.

Vacuoles

Large vesicles from ER and Golgi.

Mitochondria

Double membrane: outer membrane, inner membrane with cristae (folds increase surface area).

Cytoskeleton

Network of fibers throughout cytoplasm; functions include support, shape maintenance, organelle anchorage, intracellular transport, cell movement.

Cell wall in plants

Made of cellulose; protects, maintains shape, prevents excess water uptake.

Cell junctions

Communication and interaction between cells.

Integral proteins

Embedded in membrane; amphipathic.

Passive Transport

Does not require energy (ATP).

Diffusion

Net movement of molecules down concentration gradient.

Osmosis

Diffusion of water across selectively permeable membrane.

Active transport

Movement of substances against a concentration gradient (low → high); requires energy (ATP).

Sodium-Potassium Pump

Pumps 3 Na out, 2 K in per ATP hydrolyzed; maintains electrochemical gradient.

First Law of Thermodynamics

Energy can be transferred or transformed but not created or destroyed.

Catabolic reactions

Break down large molecules, release energy, exergonic.

Anabolic reactions

Build larger molecules, require energy, endergonic.

Free Energy (G)

ΔG = G_final - G_initial.

ATP Structure

Three phosphate groups, negatively charged and repelling.

Oxidative Phosphorylation

Process where ATP is produced using energy from electron transport.

Electron Transport Chain (ETC)

Series of protein complexes that transfer electrons and pump protons.

Location of ETC

Inner mitochondrial membrane.

Final Electron Acceptor

Oxygen, which forms H2O.

ATP Synthase

Enzyme that synthesizes ATP as protons flow back into the matrix.

Chemiosmosis

Process of ATP production driven by a proton gradient.

Decoupling

Process where uncoupling proteins allow protons to bypass ATP synthase.

Fermentation

Anaerobic process that regenerates NAD and produces ATP.

Alcohol Fermentation

Conversion of pyruvate to ethanol and CO2.

Lactic Acid Fermentation

Conversion of pyruvate to lactate.

Anaerobic Respiration

Respiration using electron acceptors other than O2.

Photosynthesis

Process that converts CO2 and water into glucose and oxygen.

Equation of Photosynthesis

6 CO2 + 6 H2O + light → C6H12O6 + 6O2.

Chlorophyll a

Main pigment that absorbs blue and red light.

Light Reactions

Phase of photosynthesis that produces ATP and NADPH.

Calvin Cycle

Phase of photosynthesis that fixes CO2 into sugars.

Carbon Fixation

Process of fixing CO2 to RuBP by rubisco.

G1 Phase

Cell growth and organelle duplication.

M Phase

Phase where mitosis occurs.

Cytokinesis

Division of the cytoplasm to form two daughter cells.

Binary Fission

Cell division process in prokaryotes.

G1 Checkpoint

Checks cell size, nutrients, and DNA integrity.

p53

Tumor suppressor gene that inhibits cell division.

Proto-oncogenes

Genes that promote cell division.

Cyclins

Proteins that regulate the cell cycle.

G-Protein Linked Receptor (GPCR)

Receptor that activates intracellular signaling pathways.

Secondary Messengers

Small molecules that relay signals within cells.

Juxtacrine Signaling

Direct contact signaling between adjacent cells.

Autocrine Signaling

Cell signals to itself via secreted ligands.

Paracrine Signaling

Signal affects nearby cells via diffusion.

Endocrine Signaling

Long-distance signaling via hormones in the bloodstream.