Foundations of Biochemistry

distinguishing features of living organisms

high degree of chemical complexity and microscopic organization

systems for extracting, transforming, and using energy from the environment

defined functions for each of an organism’s components and regulated interactions among them

mechanisms for sensing and responding to alterations in their surroundings

capacity for precise self-replication and self-assembly

capacity to change over time by gradual evolution

ribosomes and proteasomes

supramolecular site of protein synthesis and degradation

metabolites

hundreds of small organic molecules that are intermediates in biosynthetic and degradation pathways

coenzymes

compounds essential to many enzyme-catalyzed reactions

nucleoid or nucleus

stores genome and complete set of genes composed of DNA

membranes

plasma membrane

cytoplasm/cytosol

eukaryotes have double membrane

nuclear envelope

yes - eukaryotes (part of double membrane)

no - prokaryotes

size and diffusion

cellular dimensions are limited by division

ratio of surface area to volume is large, but size is small

increasing size decreases the ratio

bacteria

inhabit soils, surface waters, and tissues of other living or decaying organisms

archaea

inhabit extreme environments like salt lakes, hot springs, highly acidic bogs, and ocean depths

eukarya more closely related to archaea than bacteria

aerobic

habitats with plenty of oxygen and organisms derive energy from the transfer of electrons from fuel molecules to oxygen within the cell

anaerobic

devoid of oxygen

adapted to environment to obtain energy by transferring electrons to nitrate, sulfate, or CO2

obligate anaerobes: die when exposed to oxygen

facultative anaerobes: able to live with or without oxygen

prototrophs

trap and use sunlight

chemotrophs

derive energy from oxidation of a chemical fuel

inorganic sometimes

autotroph

synthesize all biomolecules directly from CO2

heterotroph

require performed organic nutrients made by other organisms

archaea vs. bacteria

similar plasma membranes, specific specialization of envelopes, plasmids and unique physical and metabolic specializations, smaller sizes

archaea: different lipids, peptidoglycan on envelope

bacteria: envelope gram stain (- = outer membrane with lipid bilayer which are inserted lipopolysaccharides and proteins), social behaviors with cells

ER and Golgi

synthesis and processing of lipids and membrane proteins

peroxisomes

long fatty acid chains are oxidized

lysosomes

digestive enzymes to degrade unneeded cellular debris

plants have

vacuoles, chloroplasts, and mitochondria, cell wall and membrane

animals = only mitochondria, just membrane

learn of features through cell fractionation

cytoskeleton

actin filaments - motion of organelles/cell

microtubules - motion of organelles/cell

intermediate filaments

constant disassembly and reassembly; locations change and can be regulated

endomembrane system

segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reaction occur

endo and exo cytosis (secretion and uptake between cytoskeletons and organelles; reversible in response to intra and extra cellular activities

in vitro vs in vivo

in glass vs. in intact living cell

in vivo could be interference

can observe differently depending on method

all cells have

plasma membrane

metabolites

coenzymes

inorganic ions

enzymes

genes in nucleoid or nucleus

source of energy for cellular work

some cytoskeleton

1 Da

1/12 of Carbon-12

secondary metabolites

small molecules which play roles specific to plant life

charactertistic scents, colors, compounds from plants

metabolome

entire collection of small molecules in a given cell under a specific set of conditions

metabolomics

systematic characterization of the metabolome under very specific conditions (such as following administration of a drug or a biological signal such as insulin)

oligomers

shorter polymers

proteome

sum of all proteins in a cell

makes up most of cell mass

proteomics

systematic characterization of this protein complement under a specific set of conditions

glycome

all of cell’s carbohydrate-containing molecules in a cell

lipidome

all of fat’s containing molecules in a cell

informational macromolecules

proteins and nucleic acids

stereoisomers

molecules with same covalent bond and same chemical formula but different configuration

stereospecific = certain combinations

geometric/cis-trans isomers

differ in arrangment of their substituent groups with respect to the nonrotating double bonds

cis = same side

trans = across/opposite side

chiral centers

asymmetric molecule with asymmetric carbons

1 chiral carbo = 2 stereoisomers

2^n for more than one chirality center

enantiomers

mirror images

diastereomers

not mirror images

racemic mixture

50:50 of each enantiomer

found through plane-polarized light - no optical rotation

no chirality center = no rotating

naming

R = clockwise = D

S = counter-clockwise = L

typically only occur as one of these forms in nature - opposite won’t have complementary fit

conformation

spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of rotation about single bonds

universe

system and surroundings

isolated vs. closed vs. open

no exchange of matter or energy

exchange of energy but not matter

exchange matter and energy

obtaining energy

chemotrophs: oxidizing energy-rich products of photosynthesis from plants and pass on electrons to O2 to form CO2

autotrophs and heterotrophs: global cycles of O2 and CO2

redox

endergonic vs. exergonic

energy-requiring reactions (sum = +); coupling

free energy (sum = -); ATP to ADP and Pi or AMP and PPi

equilibrium

rate of product formation = rate of product conversion to reactant

no net change in concentration, temperature, or pressure

Keq

big = reaction proceeds until reactants are almost completely converted to product (favors right)

small favors left

delta G equations

G = H - TS

G = G initial + RTln(concentration prod/concentration react)

transition state

bonds created of higher free energy than either reactant or product

highest point

activation energy

difference in energy between the reactant in its ground state and in its transition state

catabolism

energy released to drive next reaction

ATP, NADH, NADPH production to donate electrons and drive pathway steps

delta G is large and negative

anabolism

require input of energy

catabolism and anabolism = metabolism

native conformation

precise 3D structure for protein

start of living organisms

UV, radiation, volcanoes

simulated these conditions in lab and amino acids and organosulfur compounds formed over time

RNA and polypeptide formation possible under these conditions too

RNA as first gene and catalyst on simple metabolic pathways on hot vents in the ocean floor

used sulfur instead of oxygen - anaerobes

aerobic advantage later on

synthesize DNA to make synthetic cell

start of eukaryotes

DNA and specialized proteins to make DNA-protein complexes

system of intracellular membranes (double membrane)

incapable of photosynthesis - endosymbionts - mitochondria / plastids/chloroplasts for plants

endosymbiosis

bacteria engulfed and multiplied

move to nucleus and become mitochondria, carrying out aerobic catabolism

paralogs

2 homologous genes occur in the same species

orthologs

2 homologous genes occur in different species

annotated genome

DNA sequence and description of the likely function of each gene product, deduced from comparisons with other genomic sequences and established protein functions

water properties

polar and dissolves polar

high BP and heat of vaporization

cohesion/adhesion

H - bonds (when one breaks, another forms; can make bridges, binding sites, chains for larger molecules)

104.5 degree tetrahedron

electronegative O makes for 2 electric dipoles

low bond dissociation energy

lattice - crystalline as solid ice

ice has lower density than water

lose heat and evaporate sweat

universal solvent

h - bond orientation

right next to each other

gives way to 3D structures

loss of enthalpy when polar added to water, gain of enthalpy when nonpolar added to water and decrease of entropy

electrostatic

water can detect electrostatic interactions 

F = charge1xcharge2 / er²

r = distance

e = constan

clathrates

crystalline compounds of nonpolar solutes and water

amphipathic

compounds that have regions that are polar and nonpolar

micelles and phospholipids - hydrophilic heads and hydrophobic tails

clustering shows hydrophobic interactions

van der Waals interactions

transient electric dipole with opposite electric dipole in nearby atom weakly attract each other

electron clouds repel

contact when closest

van der Waals radius: how close an atom will allow another to approach

covalent bonds

strongest but other types of bonding can sum to one of these

colligative properties

effect of solutes on vapor pressure, boiling point, melting point, and osmotic pressure mean the concentration of water is lower in solutions than in water

solute concentration is independent, only depends on number of solute particles

water moves high to low

osmotic pressure

osmotic pressure = icRT

i = factor (number of particles)

c = concentration

ic = osmolarity (ic1+ic2+…)

polysaccharides prevent enormous increase in pressure compared to simple sugars

isotonic vs. hypertonic vs. hypotonic

solutions equal

outside concentration higher than inside (shrink)

inside concentration higher than outside (swell)

slight ionization of water

2 H2O —> H3O+ + OH-

fast

pH

scale of 14

-log(H+)

dyes sensitive to H+ not other ions

affects structures, activity, etc.

acidosis

blood below pH of 7.4

alkalosis

blood above pH of 7.4

pKa

stronger acid = lower pKa; strong base = higher pKa

Ka = (H+)(A-)/HA

pKa = -log(Ka)

lose H over course of titration

weaker acids reach equivalence point latest or at a higher pH

buffer

aqueous systems that resist changes to pH when small amounts of acid or base are added

made of weak acid and conjugate base

buffering region = midpoint when pH =. pKa

decrease in one region is balanced by an increase in another

Henderson-Hasselbalch equation

pH = pKa + log(A-/HA)

weak acids

pH optimum

maximal catalytic activity at a characteristic pH

condensation reaction

elements of water are eliminated

ex. ATP from ADP and inorganic phosphate

endergonic

hydrolysis reaction

addition of elements of water

ex. depolymerization of proteins, carbohydrates, nucleic acids

exergonic

hydrolases

enzymes of hydrolysis

exergonic

amino acid residue

loss of water

amino acid structure

carboxyl group, amino group, R group, hydrogen atom, central carbon

glycine - R is another H

carbon is a chiral center

2 stereoisomers for each - mainly L in proteins because active sites are asymmetric so this is stereospecific

polarity

tendency to interact with water at biological pH of 7

beer’s law

A = ecl

A = transmittance or absorbance

e = molar extinction coefficient in liters/mol cm

c = concentration

l = path length

A is directly proportional to the concentration

amino acid main ideas

important functions

can act as acid or base and have different acid-base properties

carboxyl and amino groups titrated (removal of H from COO before NH2)

ampholytes

can be acid or base electrolytes

zwitterion

isoelectric

no net electric charge (0)

pI = 1/2(pK1+pK2)

oligopeptide

a few amino acids linked

polypeptide for many

N-terminal amino residue and C-terminal carboxyl residue - do not ionize - only R groups

multisubunit

two or more polypeptides associated noncovalently

oligomeric

two proteins of a subunit are identical - protomers

average amino acid weight

110 Da

conjugated proteins

proteins permanently associated with chemical components in addition to amino acids

ex.  lipoproteins, glycoproteins, metalloproteins

prosthetic group

non-amino acid part of a conjugated protein

protein separation and purification

crude extract

extracts to separate fractions - fractionation

column, ion-exchange (pH), size exclusion (size), cation-exchange, affinity (binding), high performance liquid (pressure) chromatography

electrophoresis shape = charge/frictional coefficient (2D combines SDS and isoelectric) - mass or change

assays

activity

number of total units of enzyme in a solution

specific activity (per milligram)

primary structure

link between structure and function

polymorphic = variants

Edman degredation

labels and removes only amino-terminal residues

reacted with phenylisothiocynate - PTC adduct

derived amino acid is extracted with organic solvent and treated with aqueous acid and identified

first basic then acidic

porteases

catalyze the hydrolytic cleavage of peptide bonds