Section 1

Question 1

What is biochemistry?

Answer 1

The study of chemical substances and vital processes occurring in a living organism

Interested in how molecules interact with each other and themselves -> aka BONDING

Question 2

What is a biomolecule?

Answer 2

An organic compound normally present as an essential component of living organisms

• 4 types:
  - carbohydrates (sugars, storing energy, cellulose)
  - lipids (membranes, cholesterol [membrane fluidity], energy)
  - nucleic acids (DNA, genetic info, RNA, ATP)
  - proteins (enzymes, structure, transport, receptors, immune function)

Question 3

What 5 elements make up most biomolecules?

Answer 3

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulphur)

Question 4

Characteristics of a covalent bond

Answer 4

sharing of 2 e- between 2 adjacent atoms
About 1 Angstrom (1 x 10^(-10)m)

high bond energy
Short bond width
not easily reversible
Stable and strong interaction (only strong interaction)
NOT electrostatic

Question 5

Carbon with 4 bonds is

Answer 5

tetrahedral
Bond angles 109.5 degrees
free to rotate bonds
Single bonds

Question 6

aromaticity!

Answer 6

Pi conjugated bonding in a planar ring

resonance stabilized

Question 7

Characteristics of a C=C bond

Answer 7

Atoms in single plane

Double bond conformationally restrained BUT atoms attached to C=C-X can rotate even though X

Question 8

Describe an ionic interaction

Answer 8

• 2nd strongest interaction
• electrostatic
• depends on molecule size, solvent and distance
  > interaction of 2 charged atoms based on Coulomb’s Law

Question 9

Coulomb’s Law

Answer 9

F = q1-q2/Er^2

F -> force of interaction
E -> dielectric constant (takes into account medium atoms are in)
Ex.) water has high dielectric constant, surrounds molecules and decreases ionic interaction -> lowers ionic force between 2 charged atoms
q=charge on atom
R = radius between charges on atoms

Question 10

Hydrogen bonding

Answer 10

Hydrogen atom partly unequally shared between 2 electronegative atoms (ELECTROSTATIC, partially ionic (10%))

• H donor (which H is covalently bound to -> electronegative (partly - charged), pulls e- away from H, making it partly + charged)
• H acceptor is also electronegative and develops partial - charge or could be ionically charged
  • needs to have lone pair or charge -> can’t be resonance stabilized

> H+ (partly + charged) attracted to electronegative acceptor and H bond is formed

H BOND DONOR AND ACCEPTOR ARE USUALLY O, N AND S

Question 11

How strong and long are hydrogen bonds?

Answer 11

Strength: 4-13 KJ/mol
Length: 1.5-2.6 Angstroms

0.117nm vs covalent = 0.0965 nm

Question 12

What is one example of a negative type non-covalent interaction?

Answer 12

Electrostatic repulsion of phosphate groups in DNA backbone

• contributes to shape of DNA

Question 13

Examples of H bonds

Answer 13

carbonyl -> O-H
Amino -> O-H
ester -> O-H

Amino-H -> carbonyl
amino-H -> ester
Amino-H -> -N=

complimentary base pairs in DNA

Question 14

Van Der Waal Interactions

Answer 14

• electrostatic interaction of temporary dipoles in any 2 molecules
• attraction lasts until atomic clouds repel eachother
• cause distortion of electron cloud
• occur at Van Der Wall contact distance -> distance of maximal attraction between 2 atoms
  > atoms will start to repel each other if clouds overlap or won’t be close enough to interact if too far

Question 15

How strong is a van Der waal interaction and where can it occur?

Answer 15

• 2-4 kJ/mol
• distance between DNA base pairs is van Der waal contact distance
  
  • maximized intermolecular attraction
  • contributes to the stability

Question 16

Describe the Van Der Waal Graph

Answer 16

as we bring atoms closer they experience attraction past a key distance, then the most attraction at Van Der Waal Radius.

• then repulsion because election clouds repel each other

Question 17

What medium do most biomolecular reactions occur in?

Answer 17

Water

Question 18

What happens as a result of all the H-bonding capability of water?

Answer 18

Very cohesive - forms many H bonds with itself

Question 19

What gives water its H-bonding capability?

Answer 19

Can act as H bond acceptor (x2) and H bond donor (x2) -> bent shape and 2 electron lone pairs

Question 20

Why is water an excellent solvent for polar molecules (hydrophilic)?

Answer 20

Can weaken the electrostatic interactions between polar molecules by H-bonding with them -> competing for their charge against themselves

> reduces the electrostatic interactions up to 80x with high dielectric constant

Question 21

hydrophobic molecules

Answer 21

Water-fearing -> not soluble in water

Question 22

amphipathic

Answer 22

contains both hydrophobic and hydrophilic bits

Question 23

Why is water a double-edged sword?

Answer 23

• can dissolve things

- interferes with electrostatic interactions of molecules (eg. H-bonding or ionic interactions)

Question 24

first law of thermodynamics

Answer 24

the total energy of a system and its surroundings stays constant

energy can’t be created or destroyed but its form can change

Question 25

enthalpy (H)

Answer 25

heat content of the system

Question 26

2nd law of thermodynamics

Answer 26

total energy of a system and its surroundings is always increasing for a spontaneous process

Question 27

entropy (S)

Answer 27

measure of randomness

Question 28

When can the entropy of a local system be acceptably decreased?

Answer 28

When the entropy of the surroundings/universe increases by the same or greater amount eg.) when strands of DNA anneal, heat is released and the entropy of universe increases to counter decreased entropy of annealed strands

Question 29

spontaneity

Answer 29

how likely a reaction is to occur (doesn't tell anything about speed)

Question 30

spontaneity equation

Answer 30

deltaGsys = deltaHsys - T(K) x deltaSsys

Question 31

What is G and why is it important?

Answer 31

Gibbs free energy -> KJ/mol > reactions need to be spontaneous to occur in a cell

Question 32

endergonic reaction

Answer 32

delta G is positive - non-spontaneous

Question 33

exergonic reaction

Answer 33

delta G is negative - spontaneous

Question 34

equilibrium

Answer 34

when delta G is zero

Question 35

What happens where the reaction is exothermic (delta H < 0)

Answer 35

delta G leans towards negative | -reaction becomes more likely to occur

Question 36

What happens when delta S is positive?

Answer 36

reaction is more disordered and leans towards spontaneity

Question 37

hydrophobic effect

Answer 37

- driven by increasing entropy of water - water molecules forced in a smaller SA cage (greater entropy) caused by gathering of nonpolar compounds together (aggregate) - less water in cage -> more random and offsets addition of lipids

Question 38

Buffer

Answer 38

mixture of a weak acid and its conjugate base (with charged/uncharged groups depending on pH) - requires a weak acid that does not completely ionize in water - resists changes in pH in buffering region

Question 39

Kw

Answer 39

ionization constant of waater -> 1 x 10^(-14) = [H+][OH-]

Question 40

What are some qualities of pH scale?

Answer 40

pH = -log[H+] | - goes from 0 (strongly acidic) to 14 (strongly basic)

Question 41

Ka

Answer 41

tells us when [acid]=[conj base] - when acid begins to dissociate (lose its proton) - Ka = [A-][H+]/[HA]

Question 42

pKa

Answer 42

- low pKa is stronger acid | - pKa = -logKa

Question 43

what is the pKa of acetic acid (acetate is conj base)?

Answer 43

4.8

Question 44

Henderson-Hasselbach Equation

Answer 44

pH = pKa + log{A-}/{HA}

Question 45

when pH < pKa when ph = pKa when pH > pKa

Answer 45

- > [HA} > {A-} - > [HA] = [A-] - > [HA] < {A-]

Question 46

normal buffering range of buffer

Answer 46

+/- 1 pH unit on either side

Question 47

When can buffers fail?

Answer 47

When you're outside the buffering region or when there is only acid or conj base

Question 48

3 key buffers in conj base systems

Answer 48

1. carbonate/bicarbonate buffer CO2 + H2O = H2CO3 (carbonic acid) = H+ + HCO3- (bicarbonate) -> pKa => 6.1 2. phosphate buffer H2PO4- (dihydrogen phosphate ion) = H+ + HPO4-2 (monohydrogen phosphate ion) -> pKa => 6.9 3.) free amino acids can use histidine and cysteine

Question 49

what guard systems does the body have for acidosis?

Answer 49

pKa of buffer system is slightly below pH of body to avoid acidosis since there is more conjugate base to soak up acid

Question 50

how does a buffer work?

Answer 50

- if pH is too low, the addition of OH- will affect water instead of the weak acid to steal a proton and be neutralized (H+ + OH- = H2O), and pH rises sharply - when pH is within buffering range, adding H + or OH- will take proton or give proton to acetic acid/acetate, which are in equilibrium with each other - once acetic acid is all used up, it can't give protons to OH- and neutralize it to H2O so pH rises sharply