Biochem 3461 Exam 1

Phylogenetic trees

- show evolutionary relationships

- nodes represent a common ancestor

- branch length represents time (longer branch = more time passed)

Prokaryotic cells
size
number of membrane layer

whats in it

small

unicellular

single membrane

no nucleus or organelles

eukaryotic cells

size

multi single or both

how many layer membrane

what are present

1000-10000 times larger

single or multi-celled

bi-layer membrane

nucleus and organelles present

what are the 3 domains?

eukarya, archaea, and bacteria

what is special about archaea

they live in extreme conditions

what are the 2 types of archaea?

thermoacidophiles (heat and acid)

halophiles (salt)

what atoms make up 99% of the human body?

Hydrogen, oxygen, carbon, and nitrogen

what are the trace elements?

- Elements necessary for life in small amounts

- manganese, iron, cobalt, nickel, copper, zinc, iodine, and selenium

Why do C, H, O and N make such good atoms in making up the human body?

they form covalent bonds that are very strong

how many covalent bonds in hydrogen?

1

how many covalent bonds in oxygen?

2

how many covalent bonds in nitrogen?

3

how many covalent bonds in carbon?

4

what are the major functional groups in biomolecules?

hydroxyl

carbonyl

carboxyl

amino

imino

thiol

phosphate

thioether

hierarchy of life

inorganic precursors -> metabolites -> building blocks -> macromolecules -> supra molecule complexes -> organelles

what do amino acids build?

proteins

what do sugars build?

polysaccarides

what do nucleotides build?

nucleic acids

properties of biomolecules

- directionality (N terminus to C terminus)

- informational

- 3-D architecture

- weak forces

- condensation reaction (dehydration)

what kind of bonds do macromolecules have?

weak bonds which allow for movement

when at the same distance, which type of bond has the weakest interaction?

hydrogen bonds

ionic interactions

- forces between oppositely charged ions

- charges may depend on pH

- strength depends on charge and distance

van der Waals interactions

- induced interactions between transient positively charged nuclei and the electron shell of a nearby atom

- strength increases as the distance between them decreases

if the energy is positive, it's in or out of system

being put into the system

if energy is negative, it's

being released, more spontaneous and favorable

hydrogen bonds
what do they occur between?
what kind of bonds
what is strength dependent on

-occur between a hydrogen atom that is covalently bonded to an electronegative atom (donor) and a second electronegative atom (acceptor)

- strength depends on polarity donor and acceptor atoms

properties of water

- high boiling point

- melting and freezing point are both 32 degrees

- low density at solid state

- bent structure = polar

- non-tetrahedral bond angles (not 109 degrees)

- H-bond donor and acceptor

cooperative H-bonding

bind of 1 hydrogen atom leads to the binding of others

What's the density of the 3 states of matter for water? (least to most)

gas < solid <liquid

what does an open lattice cause?

low density at a solid state due to open space

hydrogen bonds in ice

how many? whats the speed?

what is the h-bond lifetime

4 (slow)

H-bond lifetime is about 10 microseconds

hydrogen bonds in water

2.3 (constantly moving)

H-bond lifetime is about 10 picoseconds

water is a universal solvent because

-it forms H bonds with polar solutes (salt)

- forms a hydration shell around ionic solutes

dielectric constant

- how well something can dissolve

- ability to separate charges

what water ionizes it forms what?

H+ and OH-

when H+ hydrates it forms

H3O+

eq means

rate of forward reaction

Keq means

ratio of products to reactants (equal reverse and forward rxn)

in equilibrium

forward rxn = reverse rxn

pH increases when

H+ decreases or OH- increases

dissociation of strong acids and bases

completely dissociate to form ions like NaCl and HCl

what are the 4 properties to determine what acid is more favorable?

atom electronegativity/size

resonance

induction

orbital types

what are the trends seen in the periodic table in relation to size and electronegativity?

- electronegativity increases going from the left to the right of the table

- size increases from up to down

if Ka is large, this means

it dissociates very well

if Keq is moderate or small, this means

it doesn't dissociate very well

Ka equals

[H+][A-]/[HA]. Use this when dissociation is lower than 5%

Concentration of M

- High M means it's highly dissociated and therefore is probably a strong acid

- low M means it's lowly dissociated and therefore is a weak acid (more protonated)

- equal to moles/L

if dissociation is higher than 5%, what must you use to solve?

quadratic equation

If Ka is higher, this means

dissociation is higher, so the acid is stronger

pKa

concentration of acid and conjugate base

pKa is the pH at which acid = conjugate base

important formulas for calculating pH

- pH = -log10[H+]

- pKw = pH + pOH = 14

- Ka = [H+][A-]/[HA]

- pH = pKa + log10[A-]/[HA]

titration curves

used to determine the total amount of acid in a solution

when OH- neutralizes an equal amount of H+,

this shifts the equilibrium to the right

what is the inflection point in a titration curve?

the equivalence point of the titration (pKa)

Polyprotic acids

when multiple protons are being given off

system

portion of the universe

isolated system

cannot exchange matter or energy

closed system

can exchange only energy

open system

can exchange both matter and energy

first law of thermodynamics

Energy cannot be created or destroyed

total energy of an isolated system is

conserved

how is energy exchanged?

heat and work

E2-E1=q-w

if q is positive, this means

heat is absorbed (endothermic)

if q is negative, this means

heat is released (exothermic)

if work is positive, this means

work BY a system

if work is negative, this means

work ON a system

when volume is constant

work is 0

when pressure is constant

work will be very high

what is ∆H?

enthalpy change

heat transferred in constant pressure

what is ∆E?

heat transferred in constant volume

why is ∆H usually equivalent to ∆E?

most biochemical systems have small V changes and constant P

second law of thermodynamics

entropy (S)

systems tend toward disorder and randomness

order is low S

disorder is high S

S= klnW

Boltzmann's constant

k = 1.38 x 10^-23 J/K

what is W in the entropy formula?

number of equal energy arrangements in a system

Entropy per mole (what are the formulas and gas constant)

S=2.303RlogW (S=RlnW) or (S=kNlnW)

R=8.314 J/(Kmol) (8.134)

entropy-driven process

a reaction that cannot be reversed

(mixing mio into water)

Gibbs free energy
what does it let us know
what is the formula

quantity that allows us to asses whether reactions will occur or not

G= H-TS

what's true regarding pressure in biological and biochemical processes?

pressure is constant

if ∆G is 0

reaction is at equilibrium

if ∆G is negative then the reaction is

reaction is favorable (exergonic)

if ∆G is positive

reaction is unfavorable (endergonic)

what is enthalpy?

The heat content of a system at constant pressure

what's an example of a reaction that favors both enthalpy and entropy?

fermentation of glucose to ethanol (both values are negative)

what's an example of a reaction that favors only enthalpy?

combustion of ethanol (only enthalpy value is negative)

what's an example of a reaction that favors only entropy?

decomposition of nitrogen pentoxide (only entropy value is negative)

chemical potential

substance's contribution to free energy of the system

(refer to slide 13 of lecture 4)

temperature is always in

Kelvin

what is the equation for Keq?

Keq= e^(∆G/RT)

what happens when concentration is NOT 1 M?

∆G changes

what is the pH at the standard state in biochemical systems?

pH=7

what is the one exception where 1 M isn't the standard state?

protons

what does a superscript signify?

standard state

when H+ is produced

∆G + RTln[H+]

when H+ is consumed

∆G - RTln[H+]

when pressure and temperature are constant

∆G = ∆H - T∆S

(refer to slide 21 of lecture 4)

when plotting lnKeq v. 1/T, what is the formula?

lnKeq= - (∆H/R)(1/T) + (∆S/R)

coupling

how reactions with negative ∆G' can occur

high energy phosphate compounds

- phosphoenolpyruvate (PEP)

- 1,3-bisphosphoglycerate (CP)

- phosphocreatine (ATP)

reduced coenzymes

NADH and FADH2

(NADH gives more energy)

overall ∆G' is the

sum of the two ∆G' values of individual reactions