Brooker Biology Chapter 3

Organic chemistry

the science of carbon-containing molecules

Organic molecules

carbon containing molecules found in all forms of life

Hydrocarbons

molecules with largely H-C bonds; hydrophobic (poorly water soluble)/nonpolar

Isomers

two molecules with an identical chemical formula but different structures and characteristics

Structural isomers

contain same atoms but in different bonding relationships

Stereoisomers

identical bonding but spatially different

Cis

hydrogen is bonded on on the same side of carbon

Trans

hydrogen is bonded on opposite sides of carbon

Enantiomers

pair of molecules that are mirror images; d (sugars) and l (amino acids)

Enzymes

molecules that are catalyzers; typically recognize one version of an enantiomer

Macromolecules

large, complex molecules; composed of monomers (smaller molecules); synonymous with polymers; formed by dehydration

hydrolysis reaction

polymer is broken down into monomers; water added back; enzyme catalyzed

carbohydrates

Hydrated carbon-containing compounds; essentially in the formula Cn(H2O)n

Monosaccharide

monomer, simplest sugar, very water-soluble; ex. fructose (pent), glucose (hex)

Disaccharide

dimer, two sugars; two monosaccharides combined by dehydration; ex. sucrose, lactose

Glycosidic bond

bond formed by dehydration reaction linking two monosaccharides by removal of a hydroxyl (-OH) group from one mono and a H from the other, forming a water

Polysaccharides

many sugars; monosaccharides linked together to form polymers

Starch

store energy in plant cells; less branched and water soluble

Glycogen

in animal cells; more branched and water soluble; polysaccharide

Cellulose

store energy in plant cells; used in formation of rigid cell-wall structure; known as fiber when undigestible plant matter; linear/not branched and usually can't be hydrolyzed because enzymes don't recognize shape of polymer formed

Chitin

forms exoskeleton of insects and crustaceans as well as cell walls of fungi

Glycosaminoglycan

large polysaccharide that plays a structural role in animals such as in cartilage

Lipids

hydrophobic molecules composed mainly of H, C, some O; nonpolar; insoluble in water

Triglycerides (fats)

glycerol bonded to three fatty acids

Saturated fatty acid

all carbons are linked by single covalent bonds (stack)

Unsaturated fatty acid

contains at least one C=C double bond (doesn't stack); mono and poly

Trans fat

has double bond and trans stacks

Phospholipids

similar to triglycerides but the third hydroxyl group of the glycerol is bonded to a phosphate group; amphipathic

Steroids

have skeleton of four fused rings of carbon atoms with at least one polar hydroxyl group attached

Proteins

polymers in all cells; composed of more than one polypeptide; critical in nearly all life processes; shape matters

amino acids

monomers-compounds with a carbon atom (α-carbon) linked to amino group (NH2), carboxyl group (COOH), and R group

Lysine, Arginine

polar (charged) amino acid

Serine, Threonine

polar (uncharged) amino acids

Tryptophan, Cysteine

non polar amino acids

peptide bond

covalent; links carboxyl and amino (N and C termini) of separate groups

polypeptide

multiple amino acids joined by peptide bonds (shape/sequence does not matter)

disulfide bridge

amino acid cysteine with sulfhydryl group that reacts with another sulfhyryl group; can stabilize tertiary structure

1. primary structure
2. secondary structure
3. tertiary structure
4. quaternary structure

order of protein structure

primary structure

the amino acid sequence

secondary structure

a repeated folding pattern of amino acids; alpha helix or beta pleated sheet

tertiary structure

the three-dimensional shape of a single polypeptide; can be final structure of protein

quaternary structure

multiple protein subunits (polypeptide chains) combining' multimeric proteins

protein protein interaction

one protein recognizes and binds to the surface of another

domain (protein)

modules within proteins

nucleic acids

responsible for storage, expression, and transmission of genetic information

deoxyribonucleic acid (DNA)

store genetic information coded in the sequence of its monomer blocks; double strand (helix)

ribonucleic acid (RNA)

decode DNA information into instructions for linking amino acids to form polypeptide chain; usually single strand

nucleotide

DNA/RNA monomer

1. phosphate group
2. sugar: deoxyribose
3. nitrogenous base: purine-adenine (A), guanine (G) [fused double rings of C and N]; pyrimidine-cytosine (C), thymine (T) [single ring]

components of DNA nucleotide

2 H-bonds: A-T
3 H-bonds: G-C

base pairs of DNA

1. phosphate group
2. sugar-ribose
3. purine-adenine (A), guanine (G) [fused double rings of C and N]; pyrimidine-cytosine (C), uracil (U) [single ring]

components of RNA nucleotide