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QuickStudy - Biochemistry
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WORLD’S #1
ACADEMIC OUTLINE
BIOCHEMICAL PERIODIC TABLE
1
H
Key Elements in the Body
1. Hydrogen
3. Lithium
6. Carbon
7. Nitrogen
8. Oxygen
9. Fluorine
11. Sodium
12. Magnesium
13. Aluminum
14. Silicon
15. Phosphorus
16. Sulphur
17. Chlorine
19. Potassium
20. Calcium
22. Titanium
25. Manganese
26. Iron
27. Cobalt
28. Nickel
29. Copper
30. Zinc
32. Germanium
33. Arsenic
34. Selenium
35. Bromine
50. Tin
53. Iodine
Hydrogen
3
6
7
8
9
Li
C
N
O
F
Lithium
Carbon
Nitrogen
Oxygen
Fluorine
11
12
13
14
15
16
17
Na
Mg
Al
Si
P
S
Cl
Sodium
Magnesium
Aluminum
Silicon
Phosphorus
Sulfur
Chlorine
19
20
22
25
26
27
28
29
30
32
33
34
35
K
Ca
Ti
Mn
Fe
Co
Ni
Cu
Zn
Ge
As
Se
Br
Potassium
Calcium
Titanium
Manganese
Iron
Cobalt
Nickel
Copper
Zinc
Germanium
Arsenic
Selenium
Bromine
50
53
Sn
I
Tin
Iodine
GLUCOSE
BROADER CHEMICAL PRINCIPLES
A.
Intermolecular Forces
1.
Electrostatic:
Strong
interaction between ions; for
charges
q
1
and
q
2
; separated by
r
12
,
and solvent dielectric constant, e;
water has
large
e; stabilizes
zwitterion formation
2.
Polarizability,
a
:
Measures
distortion of electron cloud by other
nuclei and electrons
3.
Dipole moment,
µ
:
Asymmetric
electron distribution gives partial
charge to atoms
4.
London forces (dispersion):
Attraction due to induced dipole
moments; force increases with µ
5.
Dipole-dipole interaction:
The
positive end of one dipole is attracted
to the negative end of another dipole;
strength increases with µ
6.
Hydrogen bonding:
Enhanced
dipole interaction
between bonded
H
and
the lone-pair of
neighboring
O
,
N
or
S
;
gives “structure” to
liquid water; solubilizes
alcohols, fatty acids,
amines, sugars, and
amino acids
B.
Types of Chemical
Groups
1.
Hydrophobic =
Lipophilic:
Repelled
by polar group; insoluble in water; affinity for
non-polar
Examples:
alkane, arene, alkene
Energy =
e
q
1
.
q
2
r
12
2.
Hydrophilic = Lipophobic:
Affinity for polar
group; soluble in water, repelled by nonpolar
Examples:
alcohol, amine, carboxylic acid
3.
Amphipatic:
Polar and nonpolar functionality;
common for most biochemical molecules: fatty
acids, amino acids and nucleotides
C.
Behavior of Solutions
1.
Miscible:
2 or more substances form 1 phase;
occurs for polar + polar or non-polar + non-polar
2.
Immiscible:
2 liquids form aqueous and organic
layers; compounds are partitioned between the
layers based on chemical properties (acid/base,
polar, nonpolar, ionic)
3.
Physical principles:
a.
Colligative
properties depend on solvent identity
and concentration of solute; a solution has a higher
boiling point, lower freezing point and lower vapor
pressure than the pure solvent
b.
Biochemical example: Osmotic pressure -
Water
diffuses through a semi-permeable membrane from a
hypotonic to a hypertonic region; the flow produces
a force, the osmotic pressure, on the hypertonic side
H
O
H
Polarizability
H
C
R
C
C
O
d
-
R
R-O
d
-
R
H
d
-
DNA
N
R
R
Dipole
Interaction
+- + -
stable
TRIGLYCERIDE
+ - - +
H
H
H
H
H
less stable
H
C
C
H
C
C
H
Osmotic Pressure
P
= iMRT
P
:
Osmotic pressure (in atm)
i:
Van’t Hoff factor = # of ions per solute molecule
M:
Solution molarity (moles/L)
R:
Gas constant = 0.082 L atm mol
–1
K
–1
T:
Absolute temperature (in Kelvin)
C
H
H
H
H
C
Hydrogen Bonding
H
H
H
C
H
H
H
d
-
N
H
C
H
H
C
H
C
H
H
H
d
+
H
H
C
H
H
C
H
C
H
Ammonia
H
C
H
C
H
H
H
C
H
d
-
O
R
H
C
H
4.
Solutions of gases
a.
Henry’s Law:
The amount of gas dissolved in a
liquid is proportional to the partial pressure of the gas
b. Carbon dioxide dissolves in water to form carbonic acid
c. Oxygen is carried by hemoglobin in the blood
d.Pollutants and toxins dissolve in bodily fluids; react
with tissue and interfere with reactions
Examples:
Sulfur oxides and nitrogen oxides yield
acids; ozone oxidizes lung tissue; hydrogen cyanide
disables the oxidation of glucose
H
C
C
H
C
H
C
O
d
-
...
H
d
+
H
d
+
H
Water
H
H
H
H
C
H
H
d
+
C
C
H
H
Alcohol
H
O
H
H
C
H
C
H
H
H
C
d
-
N
H
C
H
O
H
C
C
C
R
R
R
C
O
H
H
C
H
H
Amine
H
H
H
C
H
H
H
O
C
C
H
C
C
H
H
C
C
C
O
H
H
O
H
H
BONDS & STRUCTURE IN
ORGANIC COMPOUNDS
REACTIONS, ENERGY & EQUILIBRIUM
A.
Mechanisms
1. Biochemical reactions involve a
number of simple steps that together
form a
mechanism
2. Some steps may establish
equilibria
,
since reactions can go forward, as well
as backward; the slowest step in the
mechanism, the
rate-determining
step
, limits the overall reaction rate
and product formation
3. Each step passes through an energy
barrier, the
free energy of activation
(E
a
)
, characterized by an unstable
configuration termed the
transition
state (TS)
;
E
a
has an
enthalpy and
entropy
component
DG > 0
endergonic
not spontaneous small K
eq
DG = –RT ln(K
eq
) – connection with
equilibrium
D.
Standard-Free Energy of
Formation,
D
G
0
:
1. D
G
= S prod DG
0
– S react DG
0
2.
For coupled reactions: Hess’s Law:
3. Combine reactions, add DG, DH, DS
4. An exergonic step can overcome an
endergonic step
Example: ATP/ADT/AMP
reactions
are exothermic and exergonic; these
provide the energy and driving force
to complete less spontaneous
biochemical reactions;
Example:
ATP + H
2
O => ADP + energy
E.
Equilibrium
1.
LeChatlier’s Principle
a.Equilibrium shifts to relieve the stress
due to changes in reaction conditions
b. K
eq
increases: Shift equilibrium to the
product side
c.K
eq
decreases: Shift equilibrium to the
reactant side
2.
Equilibrium and temperature
changes
a.For an exothermic process, heat is a
product; a decrease in temperature
increases K
eq
b.For an endothermic process, heat is a
reactant; an increase in
temperature increases K
eq
3.
Entropy and Enthalpy factors
DG = DH – TDS
a.DH < 0 promotes spontaneity
b.DS > 0 promotes spontaneity
c.If DS > 0, increasing T promotes
spontaneity
d.If DS < 0, decreasing T lessens
spontaneity
Note: T is always in Kelvin;
K = ºC + 273.15
A.
Bonding Principles
1. Most bonds are
polar covalent
; the more
electronegative atom is the “
–
” end of the bond
Example:
For
>C=O
,
O
is negative,
C
is positive
2.
Simplest Model: Lewis Structure:
Assign
valence electrons as bonding electrons and non-
bonding lone-pairs; more accurate bonding models include
valence-
bonds
,
molecular orbitals
and
molecular modeling
3.
Resonance:
The average of several Lewis structures describes the
bonding
Example:
The peptide bond has some
>C=N<
character
B.
Molecular Structure
Resonance
O
O
-
C
C
<=>
N
N
+
Typical Behavior of C, N & O
Atom
sp
3
sp
2
sp
C 4 e
–
4 bonds
-C-C-
>C=C<
-C ºC-
N 5 e
–
3 bonds, 1 lone pair
>N-
R=N-
-CºN
Endothermic
Exothermic
O 6 e
–
2 bonds, 2 lone pairs
-O-
>R=O
P
Transition state
E
a
E
a
R
1.
Geometries of valence electron hybrids:
sp
2
- planar, sp
3
- tetrahedral, sp - linear
2.
Isomers and structure
a.
Isomers: same
formula,
different
bonds
b.
Stereoisomers:
same formula
and
bonds,
different
spatial
arrangement
c.
Chiral = optically active:
Produces + or –
rotation of plane-polarized light
d.
D:
Denotes dextrorotary based on clockwise
rotation for glyceraldehyde
e.
L:
Denotes levorotary based on counter-clockwise
rotation for glyceraldehyde;
insert
(
–
)
or
(
+
)
to
denote actual polarimeter results
f.
D/L
denotes
structural
similarity with
D
or
L
glyceraldehyde
g.
Chiral:
Not identical with mirror image
h.
Achiral:
Has a plane of symmetry
i.
Racemic:
50/50 mixture of stereoisomers is
optically inactive;
+
and
–
effects cancel
j.
R/S notation:
The four groups attached
to the chiral atom are ranked a,b,c,d by
molar mass
• The lowest (
d
) is directed away from
the viewer and the sequence of a-b-c
produces clockwise (
R
) or counter-
clockwise (
S
) configurations
• This notation is less ambiguous than
D/L
; works for molecules with
>1
chiral centers
k.
Nomenclature:
Use
D/L
(or
R/S
) and
+/–
in the compound name:
Example: D
(
–
) lactic acid
l.
Fisher-projection:
Diagram for chiral compound
m.
Molecular conformation:
All
molecules exhibit structural variation
due to free rotation about
C-C
single
bond; depict using a
Newman
-
diagram
n.
Alkene: cis
and
trans isomers
;
>C=C<
does not rotate; common in
fatty acid side chains
C.
Common Organic Terminology
1.
Saturated:
Maximum # of
Hs
(all
C-C
)
2.
Unsaturated:
At least one
>C=C<
3.
Nucleophile:
Lewis base; attracted to the
+
charge of a nucleus or cation
4.
Electrophile:
Lewis acid; attracted to the electrons in a bond or lone pair
D
H
H
O
D
H
P
R
C
R
P
Reactants
Reaction progress
Products
H
C
OH
H
C
OH
B.
Key Thermodynamic Variables
1. Standard conditions: 25ºC, 1 atm,
solutions = 1 M
2.
Enthalpy (H):
DH = heat-absorbed or
produced
DH < 0 exothermic
DH > 0 endothermic
C.
Standard Enthalpy of Formation,
D
H
0
1. D
H
= S prod
DH
0
– S react
DH
0
2.
Entropy (S):
DS = change in disorder
3.
Standard Entropy, S
0
:
DS = S prod S
0
– S react S
0
4.
Gibbs-Free Energy (G):
DG = DH – TDS; the capacity to
complete a reaction
DG = 0 at equilibrium
steady state
H
D
(+) -
Glyceraldehyde
H
O
C
HO
C
H
H
C
OH
H
L
(–) -
Glyceraldehyde
C
H
3
CH
3
Br
C
H
Br
H
=
K
eq
= 1
C
Br
H
Br
DG < 0
exergonic
spontaneous
H
large K
eq
CH
3
CH
3
Three-
dimensional
Fischer
projection
KINETICS: RATES OF REACTIONS
Alkene
A.
Determination of Rate
For a generic reaction, A + B => C:
1.
Reaction rate:
The rate of producing
C (or consuming A or B)
2.
Rate-law:
The mathematical dependence
of the rate on [A], [B] and [C]
3.
Multiple-step reaction:
Focus on
rate-determining step
- the slowest
step in the mechanism controls the
overall rate
B.
Simple Kinetics
1. First-order: Rate = k
1
[A]
Examples:
stabilized complex; the enzyme
reaction may be 10
3
-10
15
times faster
than the uncatalyzed process
2.
Mechanism:
Step 1.
E + S = k
1
=> ES
Step 2.
ES = k
2
=> E + S
Step 3.
ES = k
3
=> products + E
[E] = total enzyme concentration,
[S] = total substrate concentration,
[ES] = enzyme-substrate complex
concentration, k
1
- rate ES
formation, k
2
- reverse of step 1,
k
3
- rate of product formation
3.
Data analysis:
Examine steady
state of [ES]; rate
of ES formation
equal rate of
disappearance
K
m
= (k
2
+ k
3
)/k
1
(Michaelis constant)
v – reaction speed = k
3
[ES]
V
max
= k
3
[E]
H
H
H
Me
C
C
C
C
Me
Me
Me
H
Cis
Trans
Chain Positions
R
C C C C CC C
d
g
b
a
b
g
d
SN1, E1, aldose
Michaelis-Menten
Equation:
rearrangements
2. Second order: Rate = k
2
[A]
2
or
k
2
[A][B]
Examples:
SN2, E2, acid-base,
hydrolysis, condensation
C.
Enzyme Kinetics
1. An enzyme catalyzes the reaction of a
substrate to a product by forming a
Carbon-chain Prefixes
v
=
V
max
[S]
K
m
+ [S]
1 meth-
2 eth-
3 prop-
4 but-
5 pent-
6 hex-
7 hept-
8 oct-
9 non-
10 dec-
11 undec-
12 dodec-
13 tridec-
14 tetradec-
15 pentadec-
16 hexadec-
17 heptadec-
18 octadec-
19 nonadec-
20 eicos-
22 docos-
24 tetracos-
26 hexacos-
28 octacos-
2
4.
Practical solution:
Lineweaver-Burk approach:
1/v=K
m
/V
max
(1/[S])+1/V
max
The plot “1/v vs. 1/[S]” is
linear
Slope = K
m
/V
max
,
y - intercept = 1/V
max
x - intercept = –1/ K
m
Calculate K
m
from the data
D.
Changing Rate Constant (k)
1. Temperature increases the rate constant:
Arrhenius Law: k = Ae
–Ea/RT
• Determining E
a
: Graph “ln(k) vs. 1/T”; calculate
E
a
from the slope
2.
Catalyst:
Lowers the activation energy; reaction
occurs at a lower temperature
3.
Enzymes
a. Natural protein catalysts; form substrate-enzyme
complex that creates a lower energy path to the product
b. In addition, the enzyme decreases the
Free Energy of
Activation
, allowing the product to more easily form
c.Enzyme mechanism is very specific and selective;
the ES complex is viewed as an “induced fit”
lock-key model since the formation of the
complex modifies each component
1
v
ORGANIC ACIDS & BASES
1
V
max
Acid
Base
6.
Pyrimidine:
Nucleic acid
component: cytosine (4-amino-
2-hydroxypyrimidine), uracil
(2,4-dihydroxypyrimidine) &
thymine (5-methyluracil)
D.
Buffers
1. A combination of a weak acid and salt of a weak
acid; equilibrium between an acid and a base that
can shift to
consume excess acid
or
base
2. Buffer can also be made from a weak base and salt
of weak base
3. The
pH of a buffer
is roughly equal to the pK
a
of
the acid, or pK
b
of the base, for comparable
amounts of acid/salt or base/salt
4. Buffer pH is approximated by the
Henderson
Hasselbalch
equation
Note: This is for an acid/salt buffer
H
C
1
K
m
Arrhenius
aqueous H
3
O
+
aqueous OH
–
N
4
CH
K
m
V
max
3
2
5
6
slope =
Brønsted
-
Lowry
proton donor
proton acceptor
CH
1
[s]
HC
1
N
Lewis
electron-pr acceptor electron-pr donor
electrophile
Lineweaver-Burke
nucleophile
Pyrimidine
A.
Amphoteric
1. A substance that can react as an
acid or a base
2. The molecule has acid and base functional
groups;
Example:
amino acids
3. This characteristic also allows amphoteric
compounds to function as
single-component buffers for
biological studies
B.
Acids
1. K
a
= [A
–
][H
+
]/[HA]
pK
a
= –log
10
(K
a
)
2.
Strong acid:
Full dissociation: HCl, H
2
SO
4
and HNO
3
: Phosphoric acid
3.
Weak acid:
K
a
<< 1, large pK
a
4. Key organic acid:
RCOOH
Examples:
Fatty acid: R group is a long
hydrocarbon chain; Vitamin C is abscorbic acid;
nucleic acids contain acid phosphate groups
OH
O
P OH
OH
Phosphoric acid
Henderson Hasselbalch Equation:
pH = pK
a
+ log (salt/acid)
Common Buffers
Buffer composition
Enzyme + Substrate
Enzyme/Substrate
complex
Enzyme + Product
approx. pH
Active
site
Common Acids & pK
a
acetic acid + acetate salt
4.8
ammonia + ammonium salt
9.3
Acid
pK
a
Acid
pK
a
Enzyme
Enzyme
Enzyme
Acetic
4.75
Formic
3.75
carbonate + bicarbonate
6.3
E + S
E/S complex
E + P
Carbonic
6.35
Bicarbonate
10.33
diacid phosphate + monoacid phosphate
7.2
E.
Energetic Features of Cellular Processes
1.
Metabolism:
The cellular processes that use
nutrients to produce energy and chemicals
needed by the organism
a.
Catabolism:
Reactions which break molecules apart;
these processes tend to be
exergonic
and
oxidative
b.
Anabolism:
Reactions which assemble larger
molecules; biosynthesis; these processes tend to
be
endergonic
and
reductive
2. Anabolism is coupled with catabolism by ATP,
NADPH and related high-energy chemicals
3.
Limitations on biochemical reactions
a. All required chemicals must either be in the diet or be
made by the body from chemicals in the diet; harmful
waste products must be detoxified or excreted
b.
Cyclic
processes are common, since all reagents
must be made from chemicals in the body
c.
Temperature
is fixed; activation energy and
enthalpy changes cannot be too large; enzyme
catalysts play key roles
H
2
PO
4
–
7.21
HPO
4
2–
12.32
E.
Amino Acids
1.
Amino acids
have amine (base)
and carboxylic acid functionality;
the varied chemistry arises from
the chemical nature of the R- group
•
Essential amino acids:
Must be
provided to mammals in the diet
2.
Polymers of amino acids
form
proteins and peptides
• Natural amino acids adopt the L
configuration
3.
Zwitterion
; self-ionization; the
“acid” donates a proton to the “base”
•
Isoelectric point
, pI: pH that produces balanced
charges in the
Zwitterion
COOH
H
3
PO
4
2.16
NH
4
+
9.25
H
2
N
C
H
C.
Organic Bases
1. K
b
=[OH
–
][B
+
]/[BOH]
pK
b
= –log
10
(K
b
)
2.
Strong base:
Full
dissociation: NaOH, KOH
3.
Weak base:
K
b
<< 1,
large pK
b
4.
Organic: Amines & derivatives
Examples:
NH
3
(pK
b
= 4.74), hydroxylamine
(pK
b
=7.97) and pyridine (pK
b
= 5.25)
5.
Purine:
Nucleic acid component:
adenine (6-aminopurine) &
guanine (2-amino-6-hydroxypurine)
H
C
R
N
L Amino acid
6
C
N
7
1
2
5
8
CH
HC
4
C
9
3
N
H
N
COO
-
Purine
H
3
N
+
C
H
R
Zwitterion
TYPES OF ORGANIC COMPOUNDS
MAJOR TYPES OF
BIOCHEMICAL REACTIONS
Type of Compound
Examples
Alkane
C C
ethane C
2
H
6,
methyl (Me) -CH
3,
ethyl (Et) -C
2
H
5
Addition
Add to a
>C=C<
Hydrogenate
Alkene
>C=C<
ethene C
2
H
4,
unsaturated fatty acids
Nucleophilic:
Nucleophile attacks
Hydrate
Aromatic ring
-C
6
H
5
benzene - C6H6, phenylalanine
Electrophilic: >C=O
Hydroxylate
Substitution
Replace a group
Amination
Alcohol
R-OH
methanol Me-OH, diol = glycol (2 -OH), glycerol ( 3 -OH)
Nucleophilic:
on alkane (OH, NH
2
)
of
R-OH
Ether
R”-O-R’
ethoxyethane Et-O-Et, or diethyl ether
SN1 or SN2
deamination
Aldehyde
O
methanal H
2
CO or formaldehyde, aldose sugars
Elimination:
Reverse of addition,
Dehydrogenate
R-C-H
E1 and E2
produce
>C=C<
Dehydrate
Ketone
O
Me-CO-Me 2-propanone or acetone ketose sugars
Isomerization
Change in bond
aldose =>
R-C-R’
connectivity
pyranose
Carboxylic acid
O
Me-COOH ethanoic acid or acetic acid
Oxidation
-
Biochemical:
Oxidize:
ROH
to
>C=O
RC-OH
Me-COO
-
Acetate ion
loss of e-
Add
O
or remove
H
Reduction-
Reduce: Reverse of
Hydrogenate
Ester
O
Me-CO-OEth, ethyl acetate, Lactone: cyclic ester, Triglycerides
gain of e- oxidize
fatty acid
RC-OR’
Coupled Metals: Change
Processes valence
Water breaks a bond, Hydrolyze
Amine
N-RR’R”
H
3
C-NH
2
, methyl amine, R-NH
2
(1
º
) - primary, RR'NH (2
º
) - secondary,
RR'R"N (3
º
) - tertiary
Amide
O
H
3
C-CO-NH
2
, acetamide Peptide bonds
Hydrolysis
add
-H
and
-OH
to
peptide, sucrose
form new molecules
triglyceride
R-C-NRR'
Condensation
R-NH
or
R-OH
Form peptide
combine via bridging or amylose
O
or
N
Cyclic Ethers:
O
O
Pyran Furan
3
BIOCHEMICAL COMPOUNDS
A.
Carbohydrates: Polymers of Monosaccharides
1.
Carbohydrates
have the general formula
(CH
2
O)
n
2.
Monosaccharides
: Simple sugars; building
blocks for polysaccharides
e.
Disaccharides
• 2 units
• Lactose (b-galactose + b-glucose) b (1,4) link
• Sucrose (a-glucose + b-fructose) a, b (1,2) link
• Maltose (a-glucose + a-glucose) a (1,4) link
Disaccharide
M-OH + M-OH
Æ
M-O-M
Common Fatty Acids
Common
Name
Systematic
Formula
Acetic acid ethanoic
CH
3
COOH
Butyric
butanoic
C
3
H
7
COOH
Common Sugars
CH
2
OH
CH
2
OH
Valeric
pentanoic
C
4
H
9
COOH
Triose
3 carbon
glyceraldehyde
O
O
Myristic
tetradecanoic
C
13
H
27
COOH
H
H
H
H
H
H
Pentose
5 carbon
ribose, deoxyribose
Palmitic
hexadecanoic
C
15
H
31
COOH
Hexose
6 carbon
glucose, galactose, fructose
O
Stearic
octadecanoic
C
17
H
35
COOH
HO
OH
H
OH
H
OH
a.
Aldose:
Aldehyde
type structure:
H-CO-R
b.
Ketose:
Ketone type
structure:
R-CO-R
c.
Ribose and
deoxyribose:
Key component in
nucleic acids and
AT P
CHO
CH
2
OH
C
C H
Oleic
cis-9-octadecenoic
C
17
H
33
COOH
OH
Maltose - Linked
a
D Glucopyronose
OH
H
H
C
C H
OH
O
Linoleic
cis, cis-9, 12
C
17
H
31
COOH
HO
HO
octadecadienoic
H
C OH
H
C
OH
f.
Oligosaccharides
• 2-10 units
• May be linked to proteins (glycoproteins) or
fats (glycolipids)
•
Examples of functions:
cellular structure,
enzymes, hormones
g.
Polysaccharides
• >10 units
Examples:
-
Starch:
Produced by plans for storage
-
Amylose:
Unbranched polymer of a (1,4)
linked glucose; forms compact helices
-
Amylpectin:
Branched amylose using
a (1,6) linkage
-
Glycogen:
Used by animals for storage;
highly branched polymer of a (1,4) linked
glucose; branches use a (1,6) linkage
-
Cellulose:
Structural role in plant cell wall;
polymer of b (1,4) linked glucose
-
Chitin:
Structural role in animals; polymer of
b (1,4) linked N-acetylglucoamine
3.
Carbohydrate Reactions
a.Form polysaccharide via condensation
b.Form glycoside: Pyranose or furanose + alcohol
c.Hydrolysis of polysaccharide
d.Linear forms are reducing agents; the aldehyde
can be oxidized
e.Terminal -CH
2
-OH can be oxidized to
carboxylic acid (uronic acid)
f. Cyclize acidic sugar to a lactone (cyclic ester)
g.Phosphorylation: Phosphate ester of ribose in
nucleotides
h.Amination: Amino replaces hydroxyl to form
amino sugars
i. Replace hydroxyl with hydrogen to form deoxy
sugars (deoxyribose)
B.
Fats and Lipids
1.
Lipid:
Non-polar compound,
insoluble in water
Examples:
steroids, fatty acids,
triglycerides
2.
Fatty acid: R-COOH
Essential fatty acids
cannot be synthesized by
the body: linoleic, linolenic and arachidonic
3.
Properties and structure of fatty acids:
a.
Saturated:
Side chain is an
alkane
b.
Unsaturated:
Side chain has at least one
>C=C<
; the name must include the position #
and denote cis or trans isomer
c.
Solubility in water:
<6 C soluble, >7 insoluble;
form micelles
d.
Melting points:
Saturated fats have higher melting
points; cis- unsaturated have lower melting points
Linolenic
9, 12, 15-
C
17
H
29
COOH
octadecatrienoic (all cis)
Arachidonic 5, 8, 11, 14-
H
C OH
H
C
OH
CH
2
OH
CH
2
OH
C
19
H
31
COOH
eicosatetranoic (all trans)
Aldose
D Glucose
Ketose
D Fructose
O
OH
O
OH
C
C
CH
2
OH
O
CH
2
OH
O
H
H
H
H
H
OH
H
H
H
OH
OH
OH
OH
H
Ribose
Deoxyribose
d.Monosaccharides cyclize to ring structures in water
• 5-member ring:
Furanose
(ala furan)
• 6-member ring:
Pyranose
(ala pyran)
•The ring closing creates two possible
structures: a and b forms
• The carbonyl carbon becomes another chiral
center (termed
anomeric
)
• a: -OH on #1 below the ring; b: OH on #1
above the ring
• Haworth figures and Fischer projections are
used to depict these structures (see figure for
glucose below)
Saturated
Stearic Acid
Unsaturated
Oleic Acid
4.
Common fatty acid compounds
a.
Triglyceride or
triacylglycerol:
Three
fatty acids bond via
ester linkage to glycerol
b.
Phospholipids:
A
phosphate group bonds
to one of three positions of fatty acid/glycerol;
R-PO
4
-
or HPO
4
-
group
5.
Examples of other lipids
a.
Steroids:
Cholesterol and hormones
Examples:
testosterone, estrogen
R1
CO
O
CH2
R2
CO
O
CH
R3
O
Triglyceride
CO
CH2
Fischer Projection
Haworth Figure
R = Nearly always methyl
R' = Usually methyl
R'' = Various groups
R''
R
12
17
11
13
16
H
C OH
6
CH
2
OH
H
5
O
R
14
15
1
9
H
C
OH
H
H
H
H
2
10
8
H
HO
C
H
O
4
1
3
5
7
HO
OH
H
OH
Fatty Acid
4
H
6
H
C
OH
Generic Steroid
R
2
3
H
C
H
OH
C
O
b.
Fat-soluble vitamins:
• Vitamin A: polyunsaturated hydrocarbon, all trans
• Vitamins D, E, K
6.
Lipid reactions
a.Triglyceride:
Three - step
process:
dehydration
reaction of fatty acid and glycerol
b.The reverse of this reaction is hydrolysis of the
triglyceride
c.Phosphorylation: Fatty acid + acid phosphate
produces phospholipid
d.Lipase (enzyme) breaks the ester linkage of
triglyceride
CH
2
OH
HO
a
-D-Glucopyronose
3 Fatty Acids + Glycerol
2.
Polysaccharides
a.Glucose and fructose form polysaccharides
b.Monosaccharides in the pyranose and furanose
forms are linked to from polysaccharides;
dehydration reaction creates a bridging oxygen
c.Free anomeric carbon reacts with
-OH
on
opposite side of the ring
d.Notation specifies form of monosaccharide
and the location of the linkage; termed a
glycosidic
bond
R1
CO
OH
HO
CH2
R2
CO
OH
HO
HO
CH
R3
CO
OH
CH2
4
H
BIOCHEMICAL COMPOUNDS
continued
C.
Proteins and Peptides - Amino Acid
Polymers
1.Peptides are
formed by
linking amino
acids; a l l
natural peptides
contain L-amino acids
a.
Dipeptide:
Two linked amino acids
b.
Polypeptide:
Numerous linked amino acids
c.The
peptide bond
is
the linkage that
connects a pair of
amino acids using a
dehydration reaction;
the N-H of one amino
acid reacting with the -
OH of another => -N- bridge
d.The dehydration reaction links the two units;
each amino acid retains a reactive site
2. The nature of the peptide varies with amino
acids since each R- group has a distinct
chemical character
a.R- groups end up on alternating sides of the
polymer chain
b.Of the
20 common amino acids
: 15 have neutral
side chains (7 polar, 8 hydrophobic), 2 acidic and
3 basic; the variation in R- explains the diversity
of peptide chemistry
(see table, pg. 6)
3.
Proteins
are polypeptides made up of
hundreds of amino acids
a.Each serves a specific function in the organism
b.The structure is determined by the interactions
of various amino acids with water, other
molecules in the cell and other amino acids in
the protein
4.
Types of proteins:
a.
Fibrous:
Composed of regular, repeating
helices or sheets; typically serve a structural
function
Examples:
keratin, collagen, silk
b.
Globular:
Tend to be compact, roughly
spherical; participates in a specific process:
Examples:
enzyme, globin
c.
Oligomer:
Protein containing several subunit
proteins
d.
Quaternary structure:
The conformation of
protein subunits in an oligomer
6.
Chemical reactions of proteins:
a.Synthesis of proteins by DNA and RNA
b.Peptides are dismantled by a hydrolysis reaction
breaking the peptide bond
c.
Denaturation:
The protein structure is
disrupted, destroying the unique chemical
features of the material
d.
Agents of denaturation:
Temperature, acid,
base, chemical reaction, physical disturbance
7.
Enzymes
a.Enzymes are proteins that function as
biological catalysts
b.
Nomenclature:
Substrate +
-
ase
Example:
The enzyme that acts on phosphoryl
groups (R-PO
4
) is called
phosphatase
8. Enzymes are highly selective for specific
reactions and substrates
3.
Cyclic nucleotides
: The
phosphate group attached to
the 3’ position bonds to the
5’ carbon 3’, 5’ cyclic AMP =
cAMP and cGMP
4.
Additional Phosphates
a.A nucleotide can bond to 1 or 2 additional
phosphate groups
b.AMP + P => ADP - Adenosine diphosphate
ADP + P => ATP - Adenosine triphosphate
c.ADP and ATP function as key biochemical
energy-storage compounds
5.
Glycosidic bond
: Linkage between the sugar and
base involve the anomeric carbon (carbon #1)
>C-OH (sugar) + >NH (base) => linked sugar
- base
6.
Linking Nucleotides
: The
polymer forms as each
phosphate links two sugars; #5
position of first sugar and #3
position of neighboring sugar
7.
Types of nucleic acids
:
Double - stranded
DNA
(deoxyribonucleic acid) and
single - stranded
Phosphate
O
H
R2
Sugar Base
Nucleotide
C
OH
N
C
COOH
H
H
H
2
N
C
R1
H
+
2 Amino acids
H
R2
O
N
C
COOH
H
C
H
2
NH
C
R1
Dipeptide
B
S
Six Classes of Enzymes
(Enzyme Commission)
Type Reaction
1. Oxidoreductase
Oxidation-reduction
Examples: oxidize CH-OH, >C=O or CH-CH;
Oxygen acceptors: NAD, NADP
2. Tranferase
Functional group transfer
Examples: transfer methyl, acyl- or amine group
3. Hydrolase
Hydrolysis reaction
Examples: cleave carboxylic or phosphoric ester
4. Lysase
Addition reaction
Examples: add to >C=C<, >C=O, aldehyde
5. Isomerase
Isomerization
Example: modify carbohydrate, cis-trans fat
6. Ligase
Bond formation, via ATP
Examples: form C-O, C-S or C-C
P
S
B
P
S
B
RNA
Linking
Nucleotides
(ribonucleic acid)
8.
Components of a nucleotide
: sugar, base and
phosphate
a.Sugar:
ribose
(RNA) or
deoxyribose
(DNA)
b.
Bases
:
purine
(adenine and guanine) and
pyrimidine
(cytosine, uracil (RNA) and
thymine
(DNA))
9. In DNA, the polymer strands pair to form a
double helix;
this process is tied to base
pairing
10.
Chargaff’s Rule for DNA:
a.Adenine pairs with thymine
(A: T) and guanine pairs with
cytosine (C: G)
b.Hydrogen bonds connect the base
pairs and supports the helix
c.The sequence of base pairs along
the DNA strands serves as
genetic information for
reproduction and cellular control
11.
DNA vs RNA:
DNA uses deoxyribose, RNA
uses ribose; DNA uses the pyrimidine thymine,
RNA uses uracil
12.
Role of DNA & RNA in protein synthesis
a.DNA remains in the nucleus
b.
Messenger-RNA
(m-RNA): Enters the nucleus
and copies a three-base sequence from DNA,
termed a
codon
.
m-RNA
then passes from the
nucleus into the cell and directs the synthesis of
a required protein on a ribosome
c.
Transfer-RNA
(t-RNA): Carries a specific
amino acid to the
ribosomal-RNA
(r-RNA) and
aligns with the m-RNA codon
d.Each codon specifies an amino acid, STOP or
START; a protein is synthesized as different
amino-acids are delivered to the ribosome by t-
RNA, oriented by m-RNA and r-RNA, then
chemically connected by enzymes
9. An enzyme may require a
cofactor
Examples:
Metal cations (Mg
2+
, Zn
2+
or
Cu
2+
); vitamins (called
coenzymes
)
10.
Inhibition:
An interference with the enzyme
structure or ES formation will
inhibit
or block
the reaction
11.
Holoenzyme:
Fully functional enzyme plus
the cofactors
12.
Apoenzyme:
The polypeptide component
D.
Nucleic Acids: Polymers of Nucleotides
1.
Nucleotide:
A phosphate group and organic
base (pyrimidine or purine) attached to a sugar
(ribose or deoxyribose)
• Name derived from the base name
•
Example:
Adenylic acid = adenosine-5’-
monophosphate = 5’ AMP or AMP
2. Nucleoside: The base attached to the sugar
• Nomenclature: Base name + idine (pyrimidine)
or + osine (purine)
•
Example:
adenine riboside = adenosine;
adenine deoxyriboside = deoxyadenosine
P P
S-T...A-S
P P
S-C...G-S
P P
S-G...C-S
P P
Chargaff’s
Rule
Common Protein
Examples
Mol Wt
Function
fibrinogen
450,000
Physical structures
hemoglobin
68,000
Binds O
2
insulin
5,500
Glucose metabolism
ribonuclease
13,700
Hydrolysis of RNA
trypsin
23,800
Protein digestion
5.
Peptide Structure:
a.
Primary
structure:
The linear sequence of
amino acids connected by peptide bonds
• Ala-Ala-Cys-Leu or A-A-C-L denotes a
peptide formed from 2 alanines, a cysteine and
1 leucine
• The order is important since this denotes the
connectivity of the amino acids in the protein
b.
Secondary structure:
Describes how the
polymer takes shape
Example:
Helix or pleated sheet
•
Factors:
H-bonding, hydrophobic interactions,
disulfide bridges (cysteine), ionic interactions
c.
Tertiary structure:
The overall 3-dimensional
conformation
Primary Structure
Ala-Ala-Cys-Leu
Nucleic Acid Components
Base
Nucleoside
Nucleotide
adenine
Adenosine Adenylic acid, AMP
Deoxyadenosine dAMP
guanine
Guanasine Guanylic acid, GMP
Deoxyguanisine dGMP
cytosine
Cytidine
Cytidylic acid, CMP
Deoxycytidine
dCMP
uracil
Uridine
Uridylic acid, UMP
thymine
Thymidine
Thymidylic acid, dTMP
5
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