i s t r y I

o c h e m
B i e r s o n
P a t t g e
J i m C ol l e
e a t t l e s
o r t h S C a r d
N F l a s h
x a m 1
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1.What are the atoms
involved in biochemistry?
C, N, O, H, P, S
1.What entropy correlated to something
that is complex vs. simple? How does
this relate to Gibbs free energy
equation?
If complex low entropy (-S)
If simple  high entropy (+S)
Entropy is a component in Gibbs free
energy equation G= H – TS
1.Review functional groups: alcohol,
amine, aldehyde, ketone, carboxylic
acid, ester, phosphate, amide, thiol
• Alcohol  OH
• Amine  NH2
• Aldehyde HCOR
• Ketone RCOR
• Carboxylic Acid COOH
• Ester RCOOR
• Phosphate PO43-, Double bond to one
O
• Amide CON, Carbon double bonded to
O, single bonded to N and C
• Thiol SH
1.What’s G and its equation?
G= H – TS
G= Gibbs free energy= a calculation for
spontaneity of reactions
If G  (-), then the reaction is spontaneous
and does NOT need input of energy
1.Define enthalpy? Define entropy?
 Enthalpy (H) = energy of the bonds in the molecules
- If H is (-)  Reaction is exothermic (it releases heat), thus
product bonds are more stable/ stronger, they’re happier bonds,
with less energy!
- If H is (+)  Reaction is endothermic (requires energy), thus
product bonds are weaker, the reactant bonds are stronger!
 
Entropy (S) = Measure of order/disorder/randomness
- If S is (-)  molecules or reaction is more entropic/ more
disordered system/ less complex/ more freedom
- If S is (+)  molecules or reaction is more ordered/structured
1.What does it mean if H is (-) or (+)?
If H is (-)  Reaction is exothermic (it releases heat),
thus product bonds are more stable/ stronger, they’re
happier bonds, with less energy!
If H is (+)  Reaction is endothermic (requires
energy), thus product bonds are weaker, the reactant
bonds are stronger!
1.What does it mean if S is (-) or (+)?
If S is (-)  molecules or reaction is more
entropic/ more disordered system/ less complex/
more freedom
If S is (+)  molecules or reaction is more
ordered/structured
1.When is a reaction spontaneous?
When G is (-), thus does NOT need an input of energy
1.How is G related to the equilibrium constant?
Keq= [C][D]/[A][B]
G= -RTlnKeq
1.If K is large what way will the reaction go?
If Keq is large it means the
reaction will favor the products!
1.What are 2 questions you want to ask of a reaction?
- Is the reaction worthwhile? aka, will there be
better bonds or a better molecule?
- How long will the reaction take? What’s the
G of activation?
Know the equation G= H-TS and G= -RT lnK
1.Be able to calculate/predict the Equilibrium
constant of a reaction (K) using the G
equations if the constant ‘R’ value is given to
you.
1.Be able to predict relative values of H and S
as you did on the thermodynamic worksheet.
1.What determines a proteins function?
Shape of molecules & how it folds
determines a proteins function!
1.What is water? Describe some properties?
Water is the biological solvent! Its small,
polar, and contains hydrogen bonds!
1.What are intermolecular forces?
The forces between molecules,
which can be strong or weak!
1.Describe covalent bonds?
C-C, or C-O, or C-H, which are strong
bonds at ~400kJ/ mole
1.Describe ionic interactions?
Full charges, always a (+) to (-)
interaction, ~ 90kJ/ mole
1.Describe hydrogen bonds?
Partial (+) and partial (-) interaction, so not
the full charge, hydrogen bonds contain
most -OH, and -NH
1.Describe dipole-dipole interactions?
Also, a partial (+) and partial (-) interaction BUT
partial (+) is buried and hard to get to! ~9 kJ/mole
1.Describe London forces?
Induced dipole!
1.Define hydrophobic, hydrophilic, & amphiphilic?
Hydrophobic avoids water, non-polar molecules
Hydrophilic loves water, polar molecules, soluble in
water!
Amphiphilic contains both polar, and non-polar regions!
- Ex: Amphiphilic molecule is a fatty acid, which contains
a polar carboxylate end, and non-polar hydrocarbon tail
1.What the equation for acid with its
conjugate base?
HA  H+ & A-
A- is the conjugate base to the acid
1.How is acidity measured?
Ka and pKa both measure the same
thing, which is how many protons are
in solution!
1.What’s the equation for Ka and pKa?
Ka= [H+][A-]/ [HA]
pKa= -log(Ka)
1.Describe acidity correlation with small and
large pKa? Include number ranges!
Large Ka strong acid! (lots of H+)
Small pKa strong acid!
Small Ka weak acid
Large pKa weak acid
 
Strong Acid – pKa between -10 to 2
Weak Acid – pKa between 3 to 10
Non acidic – pKa > 10
1.What range of pKa are biological acids and why?
Biological acids are all weak acids because if
they were strong, they would destroy body cells!
Biological acids have a pKa from about 4 to 7
1.Describe the 3 types of biological acids?
Acetic Acid (CH3COOH) pKa= 4.75
Phosphoric Acid (H3PO4)  pKa= 6.8
Carbonic Acid (H2CO3)  pKa= 6.4
1.What’s the Henderson-Hasselblach equation?
pH= pKa + log [A-]/[HA]
What this means is if an acid is in a solution where
the pH equals the acids pKa, then there is an equal
amount of acid (HA) and conjugate base (A-)
1.Example problem: What’s the concentration of A-
and HA using acetic acid at pH of 6.75 and pH of
2.75? What do the results mean and why are they
important to us?
1.Describe & interpret the buffer range graph?
Buffer range graph plots weak acids and their effective
buffer range!
Ex: take Acetic acid which has a pKa of 4.75, at that pKa
there is 50/50 ratio of [A-]/[HA]
Add HCl to the solution  you push the graph to the left
and make the pH of solution more acidic, thus CH3COOH
wants to hold onto its H!
Add NaOH to the solution  you increase the pH of
solution, and your products of nearly 100% CH3COO-
which is the deprotonated acetic acid!
1.Describe & interpret the carbonic acid/
bicarbonate buffer system?
Carbonic acid has pKa of 6.4, thus effective
buffer range is 5.4-7.4
1.Equation for CO2-Carbonic Acid-Bicarb
buffer?
CO2 + H2O H2CO3 HCO3- and H+
1.Describe the influence of CO2 concentration on pH?
If [CO2] goes up, then  pH will go down and become
more acidic!
If [CO2] goes down, then  pH will go up and become
more basic/ less acidic because there is less H2CO3
1.How do you maintain a certain pH?
Find a buffer with that specific pKa!
1.Understand the terms of hydrophobic/hydrophilic
and how this relates to structures of organic
molecules?
1.Be able to manipulate the Henderson-
Hasselbalch equation to determine ratios of
acid/base at a given pH?
1.Understand titration curves and where the
effective buffer range will be for a given
buffer system (as in exercise 2 & case study
#1).
1.What are -amino acids?
-amino acids  biological molecules that form peptides
which then build up to make proteins!
1.Describe the components of -amino acids?
• Amino group (-NH2)
• -carbon: chiral carbon, thus you have an
enantiomeric pair/ 2 stereoisomers, D or L
configuration
• H bond
• Carboxylic acid (COOH)
1.Are all types of orientations of amino acids
found?
On earth ONLY the “L” orientation of amino
acids is found!
1.What are some notable amino acids and their
side chain?
• Glycine (Gly)  -H, thus the glycine amino
acid is not chiral!
• Serine (Ser)  -CH2OH
• Cysteine (Cys)  -CH2SH
• Histidine (His)  -CH2C3N2H3 (imidazole
group)
1.What’s a zwitterion?
Zwitterion is a ion having separate (+) and (-)
charged groups, which is found 100% of the time
in the body rather than the neutral form!
1.Describe the names for amino acids as
they get bigger and join together?
Peptides  Protein
1.What type of bond will be formed when 2 amino
acids join? What will be the products?
Peptide bond, which is the amide functional
group (-CONR)
1.Write out a dipeptide of Ala – Cys and vice-versa?
1.Is a peptide bond basic? Why?
1.Describe the geometry of peptide bonds?
 Trans vs. Cis
Amino Acids will always prefer the Trans
form because it reduces steric hinderance!
1.Write of a tetrapeptide of Ser-Ala-Phe-Cys
and vice-versa?
1.What are the 4 things to look for in a peptide?
• N terminus  free amino group on left side of the
amino acid
• C terminus  free acid group on the right side of
the amino acid
• Peptide bond  the trans amide bond
• -carbon  the chiral carbon with side chain
attached!
1.What are the basic side chains?
Lysine (Lys)  -CH2CH2CH2CH2NH3+
Arginine (Arg)  -CH2CH2CH2NHCNH2NH2+
1.What are the acidic side chains?
Aspartic Acid (Asp)  -CH2COOH
Glutamic Acid (Glu)  -CH2CH2COOH
1.What are the polar side chains?
Serine (Ser)  -CH2OH
Cysteine (Cys)  -CH2SH
1.What are the non-polar side chains?
Phenylalanine (Phe)  -CH2 and benzene ring
Alanine (Ala)  -CH3
1.Why is Cysteine (Cys) a unique amino acid?
Is can easily undergo oxidation and reduction
reactions as well as made a disulfide bond with
other cysteine amino acids!
If oxidation  disulfide bond
If reduction  2 cysteine molecules
1.Describe the 1o, 2o, 3o, 4o structure of peptides?
1o – order of amino acids from N to C terminus
2o – 3D shape that forms along the 1o structure and
determined by intramolecular forces of the amino
acid
3o – overall globular shape, which is the
summation of all 2o structures
4o – multiple proteins coming together
1.How do you determine protein structure?
- Edman Degradation
- Endopeptidase
- Trypsin
1.Define & describe Edman Degradation?
Edman Degradation  biological mechanisms
which cleaves the protein at the N-terminus, 1
amino acid at a time to view amino acid
structure.
1.Define & describe Endopeptidase?
Endopeptidase  an enzyme that causes
hydrolysis from the middle of the peptide
chain
1.Define & describe Trypsin?
Trypsin  cleaves the carbon side of Lys/Arg
1.Can we protonate aromatic electrons?
No! They are the ones that aid in the
aromaticity of the bond!
The only electrons we can protonate are the
ones that do not aid in aromaticity
1.Know how the protease trypsin cleaves peptide
chains (similar to problem #8 in exercise 2)?
1.What are native structure of a protein and what
are they determined by?
Native structure of a protein  is the tertiary overall
shape, aka the lowest energy conformation!

Native structure is determined the summation of…

- Hydrophobic effect
- Hydrogen bonding
- Ion pair/ salt bridges
- Disulfide bond
- Metal ions
1.Explain the hydrophobic effect?
Hydrophobic effect when non-polar groups avoid
water and those non-polar regions go “inside” the
protein because the outside is surrounded by H2O

Hydrophobic effect is the most important factor

determining the overall shape and lowest energy
conformation!
1.Explain Hydrogen Bonding?
Happens between the amide peptide bond as
well as O-----H partial charges!
1.Explain and give an example of ion pair/ salt
bridges?
Ion pair/ salt bridges are (+) to (-) interactions
and happen between the free acid terminus and
free amine terminus on 2 different amino acids
Ex: Arginine and Lysine
1.Explain the disulfide bond?
Happens between 2 Cysteine amino acids
1.Explain relation between metal ions and
amino acids?
Metal ions like Zn2+, Mg2+, and Fe2+ bind to
amino acids and aid in having a structural
function
1.Explain the result of putting an amino acid into
a solution with a pH higher AND lower than
that of the pKa of its R group?
• Putting an amino acid into a solution with a pH
lower than the pKa of its R group  you will
keep the R group protonated!
• Amino acid into a solution with a pH higher
than the pKa of its R group  deprotonated
form of R-group!
1.Define and describe denaturation and the
components that effect it?
Denaturation= unfolding/ changing the native state of
a protein, thus changing the conformation! Affected
by…
- Adjusting the pH, remember that if you increase
the pH, you can break ion bridges like the example
with Lysine and Glutamine
- Temperature G= H-TS
1.Define & Describe Invariant Residue’s,
Conservative substitution, and Hypervariability
when it comes to Protein Structure?
All the components are important for maintaining protein
structure!
• Invariant residue  a residue that is critical for the
function of the enzyme/ protein and must be a specific
amino acid, usually reoccurs at certain loci
• Conservative substitution  must be close in
structure/ size/ polarity
• Hypervariable  any amino acid will work
1.Explain an -helix?
A type of secondary structure which are 
helices wrapping around each other like a cable
or rope
Ex: collagen which is tough because of its triple
helix!
1.Explain -pleated sheets?
A type of secondary structure which  orients
polypeptides in an antiparallel fashion of its N and
C terminus!
1.What is the hydropathy scale – what is it used for?
Hydropathy scale is the scale for side chain polarity!
(+) numbers on the hydropathy scale typically
correlate to  non-polar R groups, which will give
rise to the hydrophobic effect by wiggling inside the
protein to hide!
(-) numbers on the hydropathy scale typically
correlate to  polar R groups, which are hydrophilic
and whose side chain will be found outside of the
protein!
1.Be able to draw the structure of a peptide from
the abbreviated name (example: ala-gly) and
vice-versa as in question #7 of exercise 2.
1.How do you note where the N, C terminus, and
amide/peptide bond are?
To determine the N & C terminus, you have to 1 ST
identify the -carbon…

If the amine group is towards the left from the -

carbon  left side is the N-terminus and right side is
the C-terminus, and vise-versa!

Amide/ Peptide Bond: -RCON

1.Be able to recognize secondary structures of a
protein and identify where hydrogen bonding
would occur (Eg: fig 6-7 pg 133, 6-9 pg 134).
1.What is the significance of the torsion angles—
where are they on a peptide chain?
1.What are the factors that determine the tertiary
structure of a protein (section 4A pg 157)?
1.What is myoglobin & what is it composed of?
Myoglobin= an O2 carrying protein, composed
of a Heme group, metal Iron (Fe2+), and O2
Primary structure 153 amino acids
Secondary structure 8 -helices!
1.What is a Heme group? What is it composed of?
Heme group 4 pyrrole rings ionically bonded and
linked to a center Iron (Fe2+)
1.Where does O2 bind on the Heme group?
O2 binds to the amino acid Histidine, which binds
to Fe2+
Fe2+ and O2 do NOT directly react!
1.What are specific amino acid residues that are
essential to lock O2 in place?
Histidine (His E7) which binds to O2 on “top”
Histidine (His F8) which binds to Fe2+ on “bottom”
Val D11 & Phe D1 both  hold O2 in place!
1.Which equation can describe the binding of
O2 to myoglobin?
Dissociation Constant (K)=
Numerator unbound O2 and the myoglobin protein
Denominator bound O2
1.Describe the dissociation constant (K) for
O2 and myoglobin?
 (K)=
If large K?  large numerator, thus weak binder b/c
there's more O2 unbound to the myoglobin molecule

Small K?  strong binding of myoglobin, thus high

affinity for O2!
1.What is the fractional saturation (YO2)?
Fractional Saturation (YO2)  the % of Mb that is bound!

YO2= or YO2=

Numerator bound O2
Denominator bound O2 + total myoglobin proteins
1.Describe the oxygen binding curve for
myoglobin? What does it mean?
Oxygen binding curve for Myoglobin distinguished as 
hyperbolic curve!
Hyperbolic curve is a steep curve indicative of good binding!
YO2=

If pO2=K, then 50% of O2 is

bound to myoglobin!
The smaller the K means the
better binder, which according
to the equation, means that
YO2 will be closer to 100%
1.What is hemoglobin?
Hemoglobin  O2 carrier in blood, NOT in muscle like with
myoglobin! Hemoglobin is composed of 4 protein Heme units, thus 4 O2
carriers!

O2 binding curve for Hemoglobin distinguished by  sigmoidal curve

& portrays cooperative binding of O2!
- Cooperative Binding= as some O2 starts binding, it allows and makes
it easier for other O2 to bind!
1.Explain the oxygen binding curve for hemoglobin?
O2 binding curve for Hemoglobin distinguished by 
sigmoidal curve & portrays cooperative binding of O2!
- Cooperative Binding= as some O2 starts binding, it
allows and makes it easier for other O2 to bind!
1.Define R and T States for Hemoglobin?
Hemoglobin has 2 conformational states: T & R States
dependent upon bound or unbound O2!
- T-State (terrible state)  is the conformation without
O2 bound (“deoxy”) state, thus it correlates to a large
K making the T-state a poor binder of O2! T-state has
puckered Heme groups!

- R-State  “oxy” conformation w/ O2 bound, thus

correlates to a small K with high affinity for O2. R-state
has flat Heme groups!
1.What’s the Bohr Effect?
Bohr Effect: how pH affects hemoglobin’s (Hb) ability to bind O2

- T-state is less acidic b/c  the C-terminus forms ionic bridges

between Asp + His
- R-state is more acidic b/c  the Asp/His ionic bridge bond is
broken as Asp + His move too far apart, thus the Histidine is in
it’s protonated form
1.Explain R and T States of Hemoglobin?
T-state is less acidic b/c  the C-terminus forms ionic
bridges between Asp + His

R-state is more acidic b/c  the Asp/His ionic bridge

bond is broken as Asp + His move too far apart, thus the
Histidine is in it’s protonated form
1.How does pH affect T and R States
of Hemoglobin?
 O2 + T R + H+

If you lower pH?  you increase H+ ions & the R-state Hb

will drop off O2, “pucker up”, form ionic bridge, and make
the solution more basic by transforming to the T-state.

If you increase pH?  you decrease H+ ions & the T-state

Hb will pick up O2, “de-pucker”, break the ionic bridge
bond and make the solution more acidic via conformational
change into the R-state.
1.What is the role of His E7, Val E11, Phe CD1 and
His F8 in myoglobin?
1.Understand the read the oxygen binding curves
for myoglobin and hemoglobin. Know and
recognize hyperbolic and sigmoidal curves.
1.Memorize the dissociate constant K (7-1 pg 179)
and fractional saturation YO2 (7-6 pg 180).
 K=
YO2= or YO2=
1.Know terms cooperative binding, non-
cooperative binding, allosteric interactions
Cooperative Binding: Hemoglobin exhibits cooperative binding, as
O2 binding increases the affinity of hemoglobin for more O2.
Hemoglobin exhibits cooperative binding b/c of the 4 units on its
protein!

Non-cooperative Binding: Myoglobin exhibits non-cooperative

binding b/c it can only bind one O2 molecule in total, thus we see a
hyperbolic curve b/c one ligand does NOT have an effect on the
binding of another ligand for another protein!

Allosteric Interactions: binding of a small molecule to induce large

conformational shift of a protein
1.How do the T state and R state in Hemoglobin
differ? Under what conditions is one favored over
the other?
T-State & R-State differ in their conformational states, which makes
their state either oxygenated or deoxygenated…

T-State: this conformation is less acidic because an ionic bridge bond

forms between Arg/Lys, it has its iron puckered proximal towards His
F8, and is a poor binder of O2!
- T-State is favored when BPG is present & when pH is low (acidic)!
R-State: more acidic because the ionic bridge bond between Arg/Lys
is broken because the amino acids are too far apart, R-state is the
oxygenated conformation with planar Heme groups, thus increased
affinity for O2!
- R-state is favored when O2 is present & when pH is high (basic)!
1.Know the basic mechanism for how Hemoglobin
binds and releases oxygen?
1. O2 is inspired and enters the lungs... The pO2 is much higher than
the pCO2, thus HbT begins to bind some O2
2. HbT binds enough O2 and undergoes a conformational change to
HbR which travels to the muscle where O2 is needed
3. At the muscles, cellular processes are producing CO2 which
increases the [H+] or pH (acidic), which will cause Hb R to drop off
O2
4. CO2 produced by the cell will bind to the N-terminal of Hb T in the
form of carbamate and travel back to the lungs
5. At the lungs, CO2 will unbind from the N-terminus of Hb T and
CO2 + H2O will be exhaled
1.Know the effect of CO2 on the binding
of Hemoglobin?
High CO2: [H+] thus, pH (acidic) meaning that most Hb will be in T-
state, which has a low affinity for O2

Low CO2: [H+] thus, pH (basic) which increases the affinity of Hb to

O2 so it will pick up O2 via R-state Hb
1.Know the effect of BPG?
Bisphosphoglycerate (BPG): a blood additive produced by RBC’s
to stabilize the T-State of Hb. BPG sits in the central cavity of Hb
and forms ionic bridges in the cavity with His + Lys!

BPG  is an example of an Allosteric Interaction b/c it induces a

conformational change from HbR to  HbT of Hemoglobin!