MACROMOLECULES

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Macromolecules
Carbohydrate ? polyhydroxy aldehydes and ketones
sugars
monosaccharides disaccharides
e.g. glucose,
fructose, sucrose, lactose
polysaccharides e.g. starch,
glycogen, cellulose
Lipids ? soluble in nonpolar solvents
fatty acid esters ? steroids ?
prostaglandins ? leukotrienes

Protein ? polymers of amino acids
enzymes ? transporters ? receptors ?
immunoglobulins etc.

Nucleic Acid ? polymers of nucleotides
DNA and RNA

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Macromolecule Functions
Structure ? Make up the substance used to
construct cells and
the extracellular matrix of organs
Energy ? Serves as the fuel for cellular
metabolism Digestion of
macromolecules followed by the oxidation
of the molecular units of
macromolecules provides
cellular energy.
Communication ? molecules involved in the
regulation of cellular
processes. Examples include nerve
transmission
regulation of gene expression, regulation of

metabolism, cell-cell interactions etc.

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Macromolecule Functions
Structure ? Make up the substance is used to
construct cells and
the extracellular matrix of organs
Carbohydrates ? Cellulose ? plant cell
walls Chitin ? insect exoskeletons and
fungal cell walls peptidoglycans ?
bacterial cell walls
Lipids ? Lipid bilayers of cells and
envelopes of some virus particles
Protein ? fibrous proteins e.g. collagen ?
extracellular matrix material
skin, bone, connective tissue
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Macromolecule Functions
Energy ? Serves as the fuel for cellular
metabolism
Nutrition Labels
Total Fat - saturated - trans - cholesterol
Total Carbohydrate ? starch and sugars
dietary fibers ? mostly cellulose (undigestible)
Protein
Na, Ca, Fe, Vitamins A C
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Nutrition Labels peanut butter
Serving size 2Tbs (32g) (35 servings per
container)
Calories 190 calories from fat 130
Total fat 16g (25) saturated fat 3g
(16) trans fat 0g cholesterol 0mg (0)
Sodium 110mg (5)
Total carbohydrate 7g (2) dietary
fiber 2g (12) sugars 3g
Protein 7g (3)
vitamin A 0 vitamin C 0 calcium
0 iron 4
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Body Mass Index - BMI
wt in lbs ht2 in in2
? 730
1 kg 2.23 lbs. 1 in 2.54 cm
underweight lt 18.5 normal 18.5
24.9 overweight 25.0 29.9 obese gt
30.0
Basal metabolic rate (BMR)
Men 66 13.7 ? wt (kg) 5 ? ht (cm) 6.6 ?
age (yrs)
Women 655 9.6 ? wt (kg) 1.8 ? ht (cm) 4.7
? age (yrs)
add 30 for ordinary activity add 50 for regular
exercise
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Macromolecule Functions
Communication

Carbohydrates ? antigenic determinants (e.g.
blood transfusions)
involved in the regulation of metabolism

Lipids ? Steroids ? lipid hormones and
global signaling protaglandins ? internal
tissue signaling leukotirenes ? mediate
immune response and inflammation
Protein ? peptide and protein hormones ?
insulin, glucagon, receptors ? membrane
proteins involved in cell signaling
transcription factors ? regulates gene expression
Nucleic Acid ? DNA determines sequence RNA
RNA determines
sequence of cellular proteins
regulates gene expression

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PROTEINS
Polymers of Amino Acids
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Amino Acid
H H2N - Ca - COOH
R
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L-Alanine nature only makes L amino
acids
D if right
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L-Alanine nature only makes L amino
acids
1
4
2
3
L S except Cys
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Sidechain Categories
Nonpolar hydrocarbon Met (C-S-C)
Acidic carboxylic Acid (-COOH)
Basic Amine (-NH2)
Aromatic Phe, Tyr, Trp
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Henderson Hasselbach Equation
Weak acid HA ? H A-
K H A-/HA
pK - log K -log (H A-/HA)
log xy log x log y
pK - log H - log A-/HA
pK pH - log (b/a) b base a acid
pH pK log (b/a)
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Amino Acid
pK 9.5 see column pK amino on aa handout
H H2N - Ca - COOH
R
pK 2.2 see column pK carboxy on aa handout
pH pK log (b/a)
Acidic and basic side chains may also be ionized
with the fraction ionization determined by the
HH equation. (see column pK side chain on aa
handout)
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pH pK log (b/a)
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Peptide Bond
O H H -N - C - C -
OH R2
O H H H-N - C - C
R1
- OH H
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POLYPEPTIDE CHAIN
Sequence R1-R2-R3-R4 . Etc.
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Sequence YGGFL Listed order of aas
from amino end to carboxyl end
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Sequence ? List of Side Chains in order from
amino end to carboxyl end of polypeptide
chain. Use 3 or 1 Letter abbreviations.
Peptide ? A polymer composed of a small number of
amino acids dipeptide,
tripeptide, oligopeptide, polypeptide Glutathione

gGlu-Cys-Gly Met Enkephalin (neurotransmitter)
YGGFM Aspartame (artificial sweetener)
Asp-Phe-O-CH3
Protein ? A molecule composed of 1 or more folded
polypeptide chains that
performs a biochemical function. Myoglobin
sequence 153 aa 17053 MW GLSDGEWQLV
LNVWGKVEAD IPGHGQEVLI RLFKGHPETL EKFDKFKHLK
SEDEMKASED LKKHGATVLT ALGGILKKKG HHEAEIKPLA
QSHATKHKIP VKYLEFISEC IIQVLQSKHP
GDFGADAQGA MNKALELFRK DMASNYKELG FQG
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Levels of Protein Structure
Primary sequence (translation)
Secondary backbone H-bonds
Tertiary Side Chain interactions
Quaternary 2 polypeptides
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Planarity of Peptide Bond
O C C N C
H
C
N
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FREE ENERGYany spontaneous process must have DG
lt 0
?G ?H - ??S
Melting/freezing Protein folding/unfolding ssDNA/d
sDNA
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A Cell is always striving to achieve a state of
equilibrium, but never succeeding
An organism at equilibrium is a dead organism!
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Bonding Review
covalent bonds (e.g. peptide bond)
ionic bonds (salt bridges) F q1q2/(r2D)
hydrogen bonds (directional)
dispersion forces (hydrophobic interactions)
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Secondary Structure
Due to the formation of H-bonds between the amide
H and the carbonyl O atoms in the backbone of a
polypeptide chain
a-Helix ? coiled every 4th aa is h-bonded
b-Sheet ? extended - must have 2 or more segments
b-Turn ? 4 aa segment reverses direction
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1.5å ca to ca
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alpha helix in cranbin
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3.5å ca to ca
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b-sheet strands are represented as arrows in
protein backbone structure representations.
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Cranbin
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Ramachandran Plot (CPA)
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?
-180
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180
-180
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Myoglobin helices
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Hb Ramachandran Plot
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Bonding Review
covalent bonds ? Sharing of a pair of
electrons between two atoms.
ionic bonds (salt bridges) ? Electrostatic
attraction between opposite charges. F
q1q2/(r2D) ? q charge, r separation distance
D dielectric constant
hydrogen bonds ? d- d
d- Electrostatic bond between X H X
from two molecules where X is an
electronegative atom (O or N in biochemical
molecules) C H can never be part of a
hydrogen bond.
dispersion forces ? temporary dipoles formed
by the uneven distribution of e- in a molecule.
This is the force that causes nonpolar molecule
to avoid water if possible by self association.
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Types of Tertiary Interactions
Disulfide ? A covalent bond between the S
atom from two Cysteine side chains.
H-bonds ? A hydrogen bond between any two
polar (or acidic/basic) side chains
Salt bridge ? An ionic bond between two
oppositely charged side chains. One must be
acidic and the other basic with the pH between
the two pK values.
Hydrophobic interactions ? Dispersion forces
between a group of nonpolar side chains.
Driven by the desire to avoid water causing ?DS.
Water is more ordered when its H-bonding
options are limited by adjacent nonpolar groups.
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TERTIARY STRUCTURE
Disulfide Bond 2 Cys covalent
C-S S-C
H-bond 2 polar
O-H OC
NH2

Salt Bridge Acid/Base
NH3 O-C O
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Nonpolar Groups Fold In to Avoid Water
COO

H3N
CH2 CH2 CH2 CH2 S CH2 CH3 CH2
CH3
CH3 CH-CH3
CH2 OH
CH3
HO
CO NH2
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Hemoglobin (Hb) a2b2
4 subunits
Quaternary structure ? The association of 2 or
more folded polypeptides to form a functional
protein molecule ? held together by H-bonds, salt
bridges, hydrophobic interactions, and
sometimes disulfide bonds.
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WGA Monomer Domains
B
C
A
D
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Denaturing agents ? Cause proteins to unfold
when added to solution in sufficient
concentration. Side chains can form interactions
with solute rather that other side chains.
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Ribonuclease refolds spontaneously into its
correct structure when urea removed. This
requires a small amount of HO-CH2-CH2-SH to
prevent incorrect disulfide bonds.