Unit 1: Biochemistry

Isotopes

Same element, different number of neutrons.

Radioisotopes

Unstable isotopes that decay & release radiation.

Valence electrons

Electrons in the outer shell; control bonding.

Ionic bond

Transfer of electrons (NaCl).

Covalent bond

Sharing of electrons (H₂O).

Polar covalent bond

Unequal sharing of electrons (H–O).

Non-polar covalent bond

Equal sharing of electrons (H–H).

Intermolecular bonds

Forces between molecules (e.g., H-bonds).

Intramolecular bonds

Forces inside a molecule (e.g., covalent).

Van der Waals forces

Weak attractions from temporary dipoles.

Hydrogen bond

Weak attraction between H and O/N/F.

Hydrophilic

“Water-loving,” polar, dissolves in water.

Hydrophobic

“Water-fearing,” nonpolar, doesn’t dissolve.

Miscible liquids

Mix completely (water + ethanol).

Immiscible liquids

Don’t mix (oil + water).

Organic compound

Contains C + H (often O, N).

Hydrocarbon

Organic compound with only C + H.

Molecular formula

Actual # of each atom (C₆H₁₂O₆).

Empirical formula

Simplest ratio of atoms (CH₂O).

Monomer

Small building block molecule.

Polymer

Chain of monomers.

Dehydration Synthesis

Joins monomers, removes water.

Hydrolysis

Breaks polymers, adds water.

Monosaccharide

Single sugar unit (glucose).

Disaccharide

2 sugars (maltose, sucrose, lactose).

Polysaccharide

Many sugars (starch, glycogen, cellulose, chitin).

Starch

Plant storage polysaccharide.

Glycogen

Animal storage polysaccharide, highly branched.

Cellulose

Plant cell walls, cannot be dugested. Picks up toxins and food for microbiota

Chitin

Insect exoskeletons, fungi cell walls.

Triglyceride

Glycerol + 3 fatty acids.

Saturated fatty acid

No double bonds, straight chain.

Unsaturated fatty acid

Double bond(s), bent chain.

Phospholipid

Glycerol + 2 fatty acids + phosphate group.

Steroid

Lipid with 4 fused carbon rings (cholesterol, hormones).

Waxes

Waterproof coatings in plants/animals, insoluble

Amino acid

Monomer of proteins (NH₂, COOH, H, R).

Polypeptide

Chain of amino acids.

Peptide bond

Link between amino acids.

Denaturation

Loss of protein shape due to heat/pH.

Enzyme

Protein catalyst, lowers activation energy.

Substrate

Molecule enzyme acts on.

Active site

Region where substrate binds.

• DNA

Double-stranded, bases A, T, G, C.

• RNA

Single-stranded, bases A, U, G, C.

• Purines

A, G 5 memebered ring fused to a 6 membered ring (2 rings).

• Pyrimidines

C, T, U 6 membered ring made up of C and N atoms (1 ring).

• Nucleotide

Sugar + phosphate + base.

• Phospholipid bilayer

2 layers, hydrophobic tails inside, hydrophilic heads outside.

• Integral proteins

Span the membrane (transport).

• Peripheral proteins

Surface proteins (signaling, support).

Cholesterol

• Reduces membrane fluidity

• Hydrophobic with one hydrophilic head

• Allows membranes to function in a wide range of temps

• Helps in the formation of vesicles.

• Membrane protein functions

Transport, signaling, enzymatic activity, recognition.

• Catalyst

Speeds reaction, not used up.

• Activation energy

Energy required to start a reaction.

Glyceraldehyde

Ribose

Fructose

Glucose + Galactose

Phosphodiester Linkage

formed between the phosphate of one nucleodtide and the sugar of the next

Alfa-a helix

helical coil stabilized by h-bonding between every 4th peptide bond. found in filaments proteins

Beta-b pleated sheet

a sheet of antiparellel chains (lysosomes, spidersilk)

Primary Structure

Amino acids joined to form a polypeptide chain, has a unique sequence

Secondary Structure

Regular repeating COILING oof a proteins polypeptide backbone, h-bonding

Tertiary Structure

Irregular contortion of pretin due to bonding between r-groups, important in determining the specificity of enzymes.

Quaternary Structure

Structure thet results from the interaction amond several polypeptides in a single protein (hemoglobin)

Oligosaccharides

Contain small numbers of monosaccrides (3-10)

Structural Isomers

Differ in covalent arrangement of their atoms

Geometric Isomers

Differ in spatial arrangment, subtle difference (swap)

Enantiomers Isomers

Mirror imgaes of eachother. One form can only be biologically active at a time

Metabolism

The sum of all the thousands of different chemical reactions that occur constantly within cells. Anabolic Reaction + Catabolic Reactions

Endergonic Reactions

require energy in order to proceed, products with MORE energy than the reactants ex. photosynthesis

Exergonic Reactions

Release energy, products with LESS energy than the reactants

Exothermic Reaction

More energy is released from the new bonds being made

• Negatve

• Products < Reactants

Endothermic Reactions

More energy is required to break the bonds in the reactant molc

• Heat will show as reactant

• Products > Reactants

Work

Transfer of energy from one body or place to another

Potential Energy

Chemical energy stored in molecular structure

• Gravitational P.E

• Chemical P.E

Kinetic Energy

The energy possessed by moving objects

1. Mechanical Energy

2. Electrical Energy

3. Thermal Energy

4. Electro-magnetic Energy

Entropy

A measure of the randomness or disorder in energy or in a collection of objects.

Coupled Reactions

Endergonic reactions that used free energy released by the exergonic reactions.

• Non Spontaneous rxns use energy released from spontaneous rxns.

The Law of Conservation of Energy

Energy cannot be created or destroyed it can only be converted from one to another.

Law Bioenergetics

Entropy constantly increases with any changes that occurs

Lock and Key Throey

The active site is designed to precisly fit the substrate

The Induced Fit Theory

The enzyme is flexible and only the proper substarte os capable of inducing the proper alignment of the active site.

Cofactor

non-proteins essential for enzyme activity (Ex: ions like K, Mn, Fe)

Coenzymes

non-protein organic molecules bound to enzymes near the active site. Ex: NAD, Niacin, NADP

Competitive Inhibitors

A molecule that blocked the substrate from interecting with the enzyme, dramtically slows down reaction rate. Ex: Cyanide

Non-Competitive Inhibitors

Molecules that bind to a different site on the enzyme, changing the shape of the active site.

Allosteric Regulation

Molecules that naturally regulate enzyme activity, either active or inactive.

Feedback Inhibition

Metabolic control, if too much product accumulates, it will inhibit the action of the first enzyme.

Integral Proteins

Embedded in the bilayer, provide pathways for the selective transfer of certain substances. Have both hydrophobic and hydrophilic regions

Peripheral Proteins

Attached to the outside/inside of membrane, associated with cell shape and mobility.

Passive Transport

No energy is required for the movement of molecules along a concentration gradient (high to low).

Active Transport

Cellus use energy to transport material against a concentration gradient (low to high).

Simple Diffusion

O₂ and CO₂ move from an are of high concentration to low

Osmosis

Refers to the diffusion of water through a membrane of lower solute concentration to higher solute.

Isotonic Solutions

The water and the solute concentration inside the cell equals the concentration outside the cell, balanced movement of water

Hypotonic Solution

More water outside the cell than that inside the cell, water molecules move inside the cell causing it to burst (lysis)

Hypertonic Solution

More water inside the cell than outside, water moved out the cell cause it to shrivel up (plasmolysis)

Hemolysis

Blood serum is diluted, RBC’s will swell and burst.