biochem exam 1

amino acids

protein monomer

glucose

carbohydrate monomer (most common)

fatty acids

lipid monomer

nucleotide

- nucleic acid monomer

- nitrogenous base + 5C sugar (ribose) + phosphate

nucleoside

nitrogenous base + 5C sugar (ribose)

purines

- bicyclic structure

- adenine and guanine

pyrimidines

- unicyclic structure

- uracil, thymine, and cytosine

phosphate or phosphoryl group

a functional group common to both lipids and nucleic acids

thymine

pyrimidine that pairs with adenine in DNA

uracil

pyrimidine that pairs with adenine in RNA

cytosine

pyrimidine that pairs with guanine in DNA and RNA

guanine

purine that pairs with cytosine in DNA and RNA

adenine

purine that pairs with thymine in DNA and uracil in RNA

nitrogenous bases

adenine, guanine, cytosine, thymine, uracil

rotation around a single bond

> double bond > triple bond

bulk elements

gram quantities

trace elements

milligram or micrograms

carbonyl (aldehyde and ketone)

carbohydrate functional groups

imidazole

histidine functional group

carboxylate

fatty acid functional group

disulfide

cystine functional group

sulfhydryl

cysteine functional group

thioester

acetyl CoA functional group

thioether

methionine functional group

phosphoanhydride

ATP functional group

stereoisomers

have different physical properties

geometric isomers

- have different physical and chemical properties

- cis vs trans

cis isomers

similar substituents or functional groups on the same side of the double bonded carbon atoms

ex: maleic acid

trans isomers

substituents diagonally opposite to the double bonded carbon atoms

ex: fumaric acid

enantiomers

- mirror images

- have identical physical properties (except w regard to polarized light) and react identically with achiral molecules

diastereomers

- isomers that are not mirror images

- have different physical and chemical properties

chiral center

asymmetric carbon with 4 different substituents

stereospecific

binding of chiral biomolecules

second law of thermodynamics

- entropy of the universe always increases

- ultimate driving force of cell chemical and physical processes is the tendency for entropy of universe to be maximized

entropy

disorder/randomness in a system

free energy (G)

energy capable of doing work under conditions of constant temperature and pressure

actual free energy changes

depend on reactant and product concentrations (supply and demand)

additive

standard free energy changes

application of free energy

allows the prediction of the direction and the equilibrium position of chemical reactions

endergonic

input of energy

exergonic

generation (release) of energy

endothermic

absorbs heat

exothermic reaction

releases heat

more entropic

disorder of system increases

less entropic

disorder of system decreases

ΔG

free energy change

+ΔG

endergonic

unfavorable/non-spontaneous

-ΔG

exergonic

favorable/spontaneous

ΔH

heat change

+ = endothermic

- = exothermic

ΔS

entropy change

+ = more entropic

- = less entropic

ΔG =

ΔH - TΔS

ΔG'°

- standard free energy change

- a constant

- is the difference between the free energy content of the products and reactants under standard condition

[products]/[reactants]

K'eq =

reaction proceeds forward (spontaneuous, more products)

K'eq is > 1 and ΔG'° is negative

reaction is at equilibrium

K'eq = 1 and ΔG'° is zero

reaction proceeds in reverse (not spontaneous, more reactants)

K'eq is < 1 and ΔG'° is positive

chemical coupling

- (of exergonic and endergonic reactions) allows otherwise unfavorable reactions to be favorable

- ΔG'° is additive

high energy phosphorylated biomolecules

- phosphoenolpyruvate (PEP)

- phosphocreatine

- 1,3-bisphosphoglycerate (1,3-BPG)

phosphate groups donated to ADP to make ATP

ATP

adenosine triphosphate

nitrogenous base

- adenine : purine

sugar

- pentose (5C): ribose

3 phosphate groups

- 2 high energy phosphoanhydride linkages

classified as a nucleotide

catabolic pathways

- breaking down

- exergonic

- generate ATP

anabolic pathways

- building up

- endergonic

- consume ATP

hydrolysis

breaking bonds by adding water

high energy of hydrolysis

- charge repulsion

- resonance stabilization

- ionization

oxidation

losing electrons (hydrogen)

reduction

gaining electrons (hydrogen)

oxidation is losing, reduction is gaining (electrons)

OIL RIG

glucose (sugars)

- oxidized by all human cells to generate energy

- partially oxidized (in the absence of O2) of completely oxidized (with O2)

palmitate (fats)

- complete oxidation generates more energy

- more energy, more reduced

how to speed reactions up (used by living organisms)

- change the reaction by coupling to a fast one

- lower activation barrier by catalysts

catalysts

- increases the rate of a chemical reaction

- lowers the activation free energy

- does not alter free energy

metabolic pathway

produces energy or useful byproducts

signal transduction pathway

- transmits information

- hormones

feedback/end product inhibition

pathways are controlled in order to regulate levels of metabolites

ex: product of enzyme 5 inhibits enzyme 1

complementarity of DNA

allows for replication with near-perfect fidelity

central dogma of biochemistry

DNA → RNA → protein

transcription

DNA to RNA

translation

RNA to protein

ribozymes

catalytic RNA molecules that function as enzymes and can splice RNA (reverse transcription)

water molecule structure

- 4 electron pairs around an oxygen

- two pairs covalently link two H to a central O2

- remaining two pairs nonbonding (lone)

- distorted tetrahedron

- net dipole movement

- H donor and acceptor due to dipole nature

- high BP

- high MP

- large surface tension

up to 4 H-bonds per water molecule gives water its...

H donor

H acceptor

water can serve as both

covalent bonds

strong bonds found in biomolecules

non-covalent bonds

weaker bonds, contribute to structure, stability, and functions of biomolecules

directionality of H bonds

linear = strong

bent = weak

entropy of water

increases as ordered crystal lattice is dissolved

high dielectric constant of water

reduces attraction between oppositely charged ions in a salt crystal

ionic (coloumbic) interactions

electrostatic interactions between permanently charged species, or between the ion and a permanent dipole

dipole interactions

electrostatic interactions between uncharged, but polar molecules

van der Waals interactions

- weak interactions between all atoms, regardless of polarity

- attractive (dispersion) and repulsive (steric) component

- weak individually

- universal

- stacking of bases in DNA

hydrophobic effect

- complex phenomenon associated with the ordering of water molecules around nonpolar substances

- refers to the association or folding of nonpolar moolecules in an aqueous solution

- does NOT arise due to attractive force between two nonpolar molecules

attractive force (london dispersion)

- depends on the polarizability

- dominates at longer distances (0.4-0.7 nm)

repulsive force (steric repulsion)

- depends on the size of atoms

- dominates at very short distances

Importance of van der waals interactions

- determines steric complementarity

- stabilizes biological macromolecules (stacking in DNA)

- facilitates binding of polarizable ligands

water as a good solvent

charged and polar substances

- amino acids/peptides

- small alcohols

- carbohydrates

water as a poor solvent

nonpolar substances

- nonpolar gases

- aromatic moieties

- aliphatic chains

bulk water

little order

high entropy

water near a hydrophobic solute

highly ordered

low entropy

low entropy

thermodynamically unfavorable, thus hydrophobic solutes have low solubility

amphipathic lipids

polar/hydrophilic head

nonpolar/hydrophobic tail

amphipathic lipids in water

- lipid molecules disperse in solution

- nonpolar tail surrounded by ordered water molecules

- entropy decreases