FI Unit 1: Biochemistry

Properties of water

adhesion, cohesion, surface tension, specific heat

polar

Hydroxyl group

nonpolar

Methyl group

polar

carbonyl group

charged and acidic

carboxyl group

charged and basic

amino group

charged and acidic

Phosphate group

polar

sulfhydryl group

Proteins structure

amino acid sequences + environment determine shape, diverse chemical identities due to R-group

Carbohydrates structure

made of sugars, long chains, hydrophilic

Nucleic Acids structure

made of nucleotides, mostly hydrophilic, helical in shape

Lipid structure

made of fatty acids (1. fats 2. phospholipids 3. steroids), mostly hydrophobic

Protein Function

“workers” of life, enzymes, hormones, receptors, transporters, antibodies

Forward reactions

Endergonic (requires energy), Dehydration synthesis (removal of water), Anabolic (builds larger molecule)

Peptide bonds

bond amino acids together, polar covalent, nitrogen and carbon bond together

N-terminus

Side of polypeptide chain with amine group

C-terminus

Side of polypeptide with carbonyl group

Primary proteins

sequence of amino acids

Secondary structure

interactions of nearby amino acids

Tertiary structure

3-D shape of protein

Quaternary structure

interactions of protein subunits

Alpha helix

secondary structure, carbonyl group forms hydrogen bonds with amine group 4 units away

Beta sheets

secondary structure, carbonyl groups form hydrogen bonds with amide groups in different parts of polypeptide

Steric hindrance

determined by R-groups, molecules repel if take up same space, if R-groups too big, stabilization via hydrogen bonds cannot occur

Tertiary structure

Determined by R-groups that interact during backbone folding

Disulfide bonds

between 2 cysteines, very strong and cannot be broken by heat

Ionic bonds

Between acidic and basic R-groups

How proteins interact with oil

Fold in on themselves to interact with each other and not nonpolar oil

How proteins interact with salt/acid

Ions get in the way of R-group bonding and disrupt protein folding

Sugars function

energy, structure, biological specificity

Backwards reactions

Exergonic (lose energy), hydrolysis (break up water), catabolic (break down molecules)

How carbs used for structure

cell walls, exoskeleton, backbone of nucleic acid

Carbohydrates biological specificity

glycoproteins, glycolipids, on outside of molecules

Types of polysaccharides

starch + glycogen (alpha-helices), cellulose and chitin (beta-linkages)

Starting amino acid

Methionine

How do enzymes accelerate reactions

1. bonding to substrate + holding them in proper conformation + making different exchanges of electrons possible

2. Creating intermediate steps

Stabilize transition state allowing more reactions to happen over a period of time

cofactors

vitamins/divalent cations, helps substrate fold and holds it in place

coupled reactions

energy release of 1 reaction drives another reaction

Nucleic acid function

information storage (DNA/RNA) and utilization (mRNA, tRNA, rRNA), metabolism (ribozymes)

Nucleotide function

cell energetics (ATP) and cell signaling (cAMP)

DNA structure

3 phosphate groups (acidic), ribose sugar (polar), nitrogenous base

DNA vs RNA

RNA has OH on 2’C DNA has H on 2’C making RNA more polar and prone to interactions/reactions

pyrimidines

1 ring, Thymine (DNA), cytosine (both), uracil (RNA)

Purines

2 rings, adenine (both), guanine (both)

Bond holding nucleotides together

phosphodiester bond, between phosphate group and 3’ C

mRNA

carries info from DNA to make proteins, single-stranded

tRNA

translator between language of nucleic acids and language of proteins + builds primary structure of protein, double-stranded,

rRNA

part of ribosomes, enzyme that forms peptide bonds, double-stranded

Lipid function

cell energetics (triglycerides, fats and oils), cell membranes (phospholipids, steroids), signaling (steroids, fatty acids)

Saturated fatty acids

single bonds only, pack closely together and strong hydrophobic interactions so more energetically favorable

Unsaturated fatty acids

contain double bonds, kinked and rigid so cannot pack closely, more movement

Why do nonpolar bonds have more energy

electrons further away from nucleus have more energy —> electrons equally shared in nonpolar bonds so further from both nuclei creating more potential energy

Phospholipids

made up of unique polar phosphate heads and nonpolar fatty acid tails, spontaneously assemble in water

Steroids

Hydrocarbon rings + polar functional groups, can pass through cell membrane but polar functional groups make this process slower