Unit 3: Biochemistry

Organic compound

• all contain carbon/hydrogen

• produced by/occur naturally in organisms

Six most common elements found in organic compounds

CHONPS

*carbon is the most important

Hydrocarbon

basic organic molecule (made of carbon and hydrogen chains)

Substituted hydrocarbon

one or more “H” are replaced by a functional group in a hydrocarbon

• biological macromolecules are substituted hydrogen

Biological macromolecules

large, complex substituted organic molecules with specific roles in organisms

Monomers (train car)

single unit building blocks of larger molecules

Polymer (train)

long chains of monomers; large molecules

Four major groups of biological macromolecules

• carbohydrates

• proteins

• lipids

• nucleic acids

Carbohydrates

• composed of carbon, hydrogen, and oxygen

• used primarily as a source of energy in cellular respiration

Monosaccharides

• simplest carbohydrates, monomers

• single-ringed

Isomers

two molecules that share the same molecular formula but different structural formulas

Disaccharides

• double-ringed sugar

• form through dehydration synthesis

Dehydration synthesis

formation of a bond between monomers caused by the removal of water

Hydrolysis

breaking of a bond between monomers by adding water

• lysis means “to break”

Polysaccharides

• complex carbohydrates/polymers

• made up of chains of monosaccharides (>12 mono. linked)

Starch

• molecule in which plants store excess sugar in roots, stems, and leaves

• easily digested

Cellulose

• tough, structural polysaccharide found in plant cell walls

• cannot be digested

Glycogen

• molecules used by animals to store excess sugar in the liver

• animal starch (highly branched)

Chitin

tough, structural polysaccharide found in the exoskeleton of insects, spiders, and crustaceans

*fungal cell walls are also made of chitin

Proteins

• contain CHONS

• found in hair, nails, skin, muscle, and feathers (structure)

• perform functions: hormones, antibodies, and enzymes

*enzymes speed up chemical reactions

Amino acids

• monomers of proteins

• 20 different types

Replacement group

differs between each specific amino acid, ex: glycine & alanine

Polypeptides

• polymers; long chains of amino acids

• range in size from 50-100,000 amino acids

Dipeptide

two linked amino acids

Peptide bond

special bond that holds together a chain of amino acids

Protein

one or more polypeptides folded into a specific shape

Fibrous proteins

• structural

• long, straight chains

location: nails, skin, muscles, bones, horns, shells, feathers, fins

Globular proteins

• chemical reactions

• chains folded into 3D shape

location: hormones, antibodies (attack germs), enzymes (promote chemical reactions)

Enzymes

• organic catalysts

• names end in -ase; Lipase (breaks down lipids), Catalase, Amylase (digests carbohydrates)

• react only with a substrate that matches its unique 3D shape

Catalyst

a substance that speeds up chemical reactions without being changed/destroyed itself

Substrate

• the specific substance(s) undergoing a chemical reaction

• enzyme termporarily bonds to the substrate(s)

Lock and Key Theory

describes how enzymes promote reactions

Catabolic and anabolic

larger reactions

Denaturation

• destruction of the normal shape of the protein; no longer matches shape of the substrate

• caused by changes in pH and high temperature

Reaction coordinate

displays the progress of a chemical reaction

Activation energy

energy needed to start a chemical reaction

Chemical equation

symbolic representation of a chemical reaction

Law of Conservation of Matter/Mass

states that matter cannot be created or destroyed during a reaction; balanced reaction represents this law

Law of Conservation of Energy

states that energy cannot be created or destroyed during a reaction; total energy is equal before and after reaction

Endergonic reaction

the total amount of P.C.B.E. in the reactants is less than is contained in the products; reaction appears cold/dark as energy is absorbed from the environment into the products

Exergonic reaction

the total amount of P.C.B.E. in the reactants is more than can be contained in the products; reaction appears light/hot as energy is released to the environment from the reactants

Lipids

• contain CHO

• insoluble in water (hydrophobic/non-polar)

• reserve energy in animals

• includes triglycerides (fats & oils), waxes, and steroids

Triglycerides

• large lipid polymers found in fat/oils

• made of 3 fatty acids and 1 glycerol

Fats

• solids

• no double bonds

• saturated with hydrogen

• less healthy (coagulate in bloodstream - change to a solid/semisolid state)

• source: animals, ex: bacon, butter

Oils

• liquid

• one or more double bonds

• unsaturated; not as much hydrogen

• more healthy (easier to digest)

• source: plants, ex: peanut, soybean, and olive oil

Waxes

• structural lipid, not a triglyceride

• beeswax, ear wax (cerumin)

Steroids

• 4 fused rings of carbon to which many different groups of elements are attached

• cholesterol, testosterone

Phospholipid

• special type of triglyceride found within cell membranes

• both polar and nonpolar

Nucleic acids

contain the code which stores hereditary information

Monomer of nucleic acids

nucleotide

Nucleotide is composed of

• 5 carbon sugar

• phosphate group

• nitrogen base

DNA nucleotide

• contains deoxyribose sugar

• possible bases: thymine, guanine, cytosine, adenine

RNA nucleotide

• contains ribose sugar

• possible bases: uracil, guanine, cytosine, adenine

Polymers of nucleic acids

• DNA (Deoxyribonucleic acid)

• RNA (Ribonucleic acid)

DNA function

• copied during cell divison

• found only in the nucleus

• stores the genetic code; determines protein structure

• thymine=adenine

RNA function

• temporary copy of genetic code

• found in nucleus, ribosome, cytoplasm of the cell

• directly used in protein synthesis

• uracil=adenine

Water is

polar

Polar molecule

a molecule with two oppositely charged regions

Hydrogen bonding

attraction between the oppositely charged regions of two neighboring polar molecules

Water properties

• temperature stabilization

• capillarity

• density

• solubility

Temperature stabilization

• water resists dramatic temperature changes

• allows cells (which contain a lot of water) to more easily maintain a stable internal environment (homeostasis)

Capillarity

rise of water in a narrow tube due to:

• adhesion - force of attraction between water molecules and molecules of the narrow tube

• cohesion - attraction between water molecules themselves

Density

• water is less dense as a solid

• ice floats on top

• water freezes from top down

Solubility

• water dissolves other polar or ionic substances easily

• water does not easily combine with nonpolar substances

Hydrophobic substances

• “water-fearing;” non-polar substances

• do not dissolve easily in water, ex: lipids like oil

Hydrophilic substances

• “water-loving;” polar substances

• dissolve easily in water, ex: alcohol

Solutions

• a homogeneous mixture of two or more substances

• one substance (solute) is dissolved in another (solvent), ex: air, soda, vinegar

Aqueous solution (Aq)

solution in which a substance (solute) is dissolved in water (solvent)

Acids/bases

special types of aqueous solutions

Acids

• form when hydrogen ions mix with water

• have a low pH (lower pH = stronger acid)

• tend to taste sour

• ex: HCl acid formation

Bases

• form when hydroxide ions mix with water

• have a high pH (higher pH = stronger base)

• tend to taste bitter

• ex: NaOH base formation

Indicator

types of substances that turn different colors in different pH solutions to indicate pH

• ex: Litmus paper, pHydrion paper, phenolphthalein

Neutralization reaction

acid + base → salt + water

• ex: HCl + NaOH → NaCl + H₂O

pH scale

used to measure acidity or alkalinity of aqueous solutions

Buffer

a chemical that purposely neutralizes an acid or base

Chemical reactions in our bodies often

depend on the correct pH

Homeostasis must be maintained otherwise

organic molecules face damage