VIDA BCHS 3304: Exam 1

Tuesday 2/5; SR1 116; 1PM-2:20PM

40 multiple choice questions;
possibly two bonus point questions
covers chapters 1-5; 5 is partial, does
not include protein purification
you need a pencil(s), eraser, and
calculator

Chapter 1

Atmosphere
CH4

Water vapor

Electrode
NH

H2

Condenser

Cooled water
containing
organic
molecules

H2O
sea
Sample for
chemical analysis

Cold
water

Representative Prokaryotes

Animal Cell

Units of Measurement
LENGTH

standard in science is the meter, m

common unit in (bio)chemistry is the Angstrom,

1 = 10-10 m = 0.1 nm
10 = 10-9 m or 1 nm
100 = 10-8 m or 10 nm
1000 = 10-7 m or 100 nm
10000 = 10-6 m or 1000 nm or 1 m
9
You must know and be comfortable using these units

The Laws of Energy Transformation

Thermodynamics is the study of energy
transformations
A closed system, such as that approximated
by liquid in a thermos, is isolated from its
surroundings
In an open system, energy and matter can
be transferred between the system and its
surroundings
Organisms are open systems

Thermodynamics First Law

The First Law of Thermodynamics
Energy (U) is conserved it can be neither
created nor destroyed
Most biological processes take place under constant
pressure (P) and variable volume (V)
The Enthalpy (H) of a process is defined as follows:
H = U + PV
H = U + PV (under constant pressure, the
volume will change like the expansion of a gas)
The volume changes in biological processes are
practically negligible so
H U

The Second Law of

Thermodynamics
During every energy transfer or
transformation, some energy is unusable,
and is often lost as heat
According to the second law of
thermodynamics:

Every energy transfer or

transformation increases the
entropy (disorder) of the universe

G = Gproducts - Greactants

Gibbs Free Energy (G)

The Free Energy (G) change of a
spontaneous process is negative
Free energy is defined as follows: G = H TS
Normally, we are interested in the change in
free energy so the following equation is more
useful: G = H TS
For a spontaneous process, G < 0.
If the G is < 0, the process is called
exergonic
If the G is > 0, the process is called
endergonic
If the 0, the process is called equilibrium
14

Equilibrium Constants

Relationships between concentration and free energy

G0 = -RT ln Keq, where G0 is the free energy
change in the standard state, R is the gas constant
8.3145 J/K-mol (gas constant will be on the exam)

aA bB cC dD
c [ D ]d

[
C
]
G G 0 RT ln
a
b
[
A
]
[
B
]

At equilibrium, G=0 so G0 = -RT ln Keq

K eq

d
[C ] ceq[ D]eq
a [ B]b
[ A]eq
eq

e G

/ RT

Chapter 2

A hydrogen-bond between two water

molecules

Water of Hydration
Hydration - to be surrounded by H2O
A polar molecule is hydrated by the partial charge interaction
of the water molecule
Multiple hydrogen-bonds increase solubility
Hydrophilic molecules are those that love to be in water
Hydrophobic molecules are those that hate to be in water
(remember oil and water dont mix, although they can form
some very nice emulsions (salad dressings))
19

 water molecules
form hydrogenbonds with organic
functional groups
water can act as
both a hydrogenbond acceptor and
donor (even
simultaneously)

20

Hydrophobic effect
Hydrophobic effect: The tendency for water to minimize its
contacts with hydrophobic molecules
It is driven by the ordering of water molecules around the
hydrophobic molecule, as stated above, to minimize its contact
Therefore, water is more ordered around hydrophobic
molecules and thus this process is entropically disfavored

non-polar molecules are

hydrated in a different
way (i.e. NOT via
hydrogen-bonds to the
molecule but rather by
forming cage-like
structures)
this results in the
hydrophobic effect
non-polar molecules
tend to congregate in
these water cages

Aggregation of non-polar molecules in

water

23

Hypotonic solution
H2O

Isotonic solution
H2 O

H2O

Hypertonic solution
H2O

(a) Animal

cell
Lysed
H2 O

Normal

Shriveled
H2O

H2O

H2O

(b) Plant

cell
Turgid (normal)

Flaccid

Plasmolyzed

Ionization of Water
H2O

H+ + HO-

H+ (proton), HO- (hydroxide), H3O+ (hydronium ion)

HO -

H 2 O

Recall that K is an dissociation constant, and [A] represent the

concentration of species A
Recall also that [H2O] is 55.5M by definition but we ignore it
since it remains constant, so the equation simplifies to:

Kw H

HO
-

25

Ionization of Water
H2O

H+ + HO-

pure water has equal concentrations of H+ and HO [H+] = [HO-] = (Kw)1/2 = 10-7 M for a neutral solution
Therefore, KW = 10-14 M
If [H+] > 10-7 M, then the solution is acidic
If [H+] < 10-7 M, then the solution is basic

!!!!! pH = -log[H+] !!!!!

26

Acid-Base Chemistry
HA

H+ + A-

H A

K[H O]

Ka

HA

pK -logK

27

Charge of acid/base as function of pH

Acid:
If pH < pKa, neutral (0)
If pH = pKa, (50% ionized, -0.5)
If pH > pKa, charged (-1)
Base:
If pH < pKa, charged (+1)
If pH = pKa, (50% ionized, +0.5)
If pH > pKa, neutral (0)
28

Henderson-Hasselbalch Equation

HA

H K
A -

HendersonHasselbalch equation

A -

pH -logK log
HA

A -

pH pK log
HA

you MUST know this equation

used to compute the pH of a solution of a weak acid

(HA) and its conjugate

base (A-)
29

Buffers
a substance when in solution will resists changes in
pH when only small quantities of a strong acid or
strong base are added
any weak acid can act as a buffer if the pH of the
solution is near the pK midpoint for the compound
(i.e. BY DEFINITION, pH = pK at the midpoint of the
titration curve)
addition of small quantities of a strong acid or base
has little effect on the pH of the solution

read about the blood buffering system, Bb

Chapter 3

Nucleotides, Nucleic Acids,

and Genetic Information
know:
structure of purines and pyrimidines
structure of nucleotides, nucleosides
understand how tautomerization
affects base pairing
structure of DNA and RNA

Tautomers and Tautomerization

tautomers are structural isomers
migration of a hydrogen atom or proton, accompanied
by a switch of a single bond and adjacent double
bond
tautomers are in equilibrium with one another
solvents, pH, and temperature can influence which
form is more stable
http://en.wikipedia.org/wiki/Tautomer

Tautomers and Tautomerization

http://en.wikipedia.org/wiki/Tautomer

Chapter 4

General properties
The backbone of individual amino acids are
zwitterionic (i.e. has both a positively charged and a
negatively charged group)
In addition, some amino acids have ionizable (i.e.,
charged) side chains
Because of these ionizable groups (backbone and
some side chains), amino acids can have a number of
different charge states
The R group in an amino acid is called the side chain
An amino acid is often called a residue (i.e., an
amino acid residue)
There are 20 standard amino acids - they all differ in
R

Peptide bonds
As mentioned previously,
amino acids can be
connected together (i.e.
condensed) to form a
bigger molecule, now
containing two amino
acids
The bond formed is a
peptide bond and the
molecule is a dipeptide.
If we add another amino
acid, then we would
have a tripeptide

Classification
Non-polar
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine
(Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline (Pro,
P), Phenylalanine (Phe, F), Tryptophan (Trp, W)
Polar
Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N),
Glutamine (Gln, Q), Tyrosine (Tyr, Y), Cysteine (Cys, C)
Charged
Aspartic acid (Asp, D, -1); Glutamic acid (Glu, E, -1)
Lysine (Lys, K, +1); Arginine (Arg, R, +1), Histidine (His, H,
+1)

Classification

43

44

45

46

47

Non-standard amino acids

Post-translationally
modified amino acids
These transformations
are made after the
amino acids are
already incorporated
into a protein
Typical alterations
include: hydroxylation,
methylation,
acetylation,
carboxylation, and
phosphorylation
Addition of PO32- to a
Ser, Thr, or Tyr is a
common theme in
signal transduction

48

Chapter 5

Four levels of protein structure

1. Primary structure
1 = Amino acid sequence of the peptide chain(s), the
linear order of AAs.
Remember from the N-terminus to the C-terminus
Above all else this dictates the structure and function
of the protein.
2. Secondary structure
2 = Local spatial alignment of amino acids without
regard to side chains.
Usually repeated structures
Examples: -helix, -sheets, random coil, or -turns
50

3. Tertiary Structure
3 = the 3-dimensional structure of an entire peptide (e.g.
folding of secondary structural elements against one
another).
Great in detail but vague to generalize. Can reveal the
detailed chemical mechanisms of an enzyme.
4. Quaternary Structure
4 two or more peptide chains associated with a protein.
Spatial arrangements of subunits.

51

Cleavage of disulfide bonds

Permits separation of polypeptide chains
Prevents refolding back to native structure
Performic acid oxidation
Cystine (-S-S-) or cysteine (-SH) to Cysteic acid (-SO 3-)
Methionine to Methionine sulfone, Trp destroyed
2-Mercaptoethanol, dithiothreitol, or dithioerythritol
Keeps the equilibrium toward the reduced form

54

55

This chart will be on the exam!

Rn-1 O
NH CH

Rn

NH CH

Scissile Bond

56

Edman degradation with Phenyl isothiocyanate, PITC

Edman degradation used to

automatically sequence the <50
AA peptide fragments
Sequentially degrades inward
from the N-terminus
PTH-amino acid is then
identified by signature TLC,
HPLC, MS, gel electrophoresis,
GLC, etc.

57

Specific chemical cleavage reagents

Cyanogen Bromide Rn-1 = M
Cleave the large protein using i.e., trypsin (Rn-1=Lys, Arg), separate
fragments and sequence all of them. (We do not know the order of the
fragments!!)
Cleave with a different reagent i.e., Cyanogen Bromide (Rn-1= M),
separate the fragments and sequence all of them. Align the fragments
with overlapping sequence to get the overall sequence.

58

How to assemble a protein

sequence
1. Write a blank line for each amino acid in the
sequence starting with the N-terminus.
2. Follow logically each clue and fill in the
blanks.
3. Identify overlapping fragments and place in
sequence blanks accordingly.
4. Make sure that all your amino acids fit into the
logical design of the experiment.
5. Double check your work.
59

1
2
3
4
5
6
7
H3N-_-_-_-_-_-_-_-_-_-_-_-_-_-_-COO

10

11

12

13

14

K
F - A- M - K
K - F - A- M
Q-M-K
D-I-K-Q-M
G-M-D-I-K
Y-R-G-M
Y-R

Cyanogen Bromide (CN Br)

Cleaves after Met i.e M X
D-I-K-Q-M
K
K-F-A-M
Y-R-G-M

Trypsin cleaves after K or R

(positively charged amino acids)
Q-M-K
G-M-D-I-K
F-A-M-K
Y-R
60

DNA and Proteins as Tape Measures

of Evolution
The linear sequences of nucleotides in DNA
molecules are passed from parents to
offspring
Two closely related species are more similar
in DNA and protein sequence than are more
distantly related species
Molecular biology can be used to assess
evolutionary kinship