BIOCHEMISTRY

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I. Bonding Properties of 10. Anhydride – dako ug bakante
Carbon
 Biochemistry – study of life at the
molecular level; focus on compounds
with living organism
11. Phenyl – presence of benzene ring
 Carbon with 4 valence electrons
(electrons on the outermost shell) can
bond as many as four of the same or
different atoms/group
 Carbon can be linear, branched,
cyclic or tetrahedral
II. Carbon atoms in 2 different
 Optical special arrangement between
compounds may have 4 the
the reacting molecules is needed for
same constituents bound to
biochemical reactions to occur.
them yet different in the
Ex. Oxygen + oxygen = no reaction
arrangement of constituent
Oxygen + carbon = reaction occur
 Stereochemistry – study of interaction
of molecules in 3 dimension
 Isomers – same chemical formula,
 R – summary or shortcut of CH
same element but different
CH = R – defines properties,
bonding
components, characteristics, and
abilities.

Functional Groups
1. Hydroxyl – hydrogen + oxygen

OH – al alcohol (eg. Ethanol)

2. Carbonyl – carbon and oxygen

3. Carboxyl – carbonyl + hydroxyl

Ex. Acetic Acid III. 3 Dimensional Models

4. Ester – carbonyl + Oxygen + R  Ball and Stick Model
group Atoms = spheres
Bonding = stick
 Cahn-Ingold Prelog System
Ex. Phosphatide chaline R path and S path
5. Amino – NH2 attach to R group Steps:
- Rank elements according to
atomic number
6. Amido – Carbonyl + NH2 - Heaviest elements will be
number 1
- And hydrogen always naa sa
likod
7. Thiol – SH S path – counterclockwise; R path
8. Disulfide – S-S ; two sulfide Clockwise
9. Phospho
 Fischer Projection – used to
repeated carbohydrates; place the
most oxidized
D – Dextro ; L – Levo
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L – OH on the left side
D – OH on the right side

Can be determined from the

second to the last hydroxyl; away
from the cabronyl

PROTEIN COMPOSITION AND

STRUCTURE
What is protein?
 Protein – performs their work
within cells
- Building blocks: amino acids
– consist of an alpha/ central
carbon atom linked to an
amino group, carboxyl group,
hydrogen atom and a side
chain
- Defined sequences of amino
acids linked through peptide
bonds to perform polymers

 Peptide – molecule formed by

linking together a small number of
amino acids (2 – dozen) through
peptide bonds
 Peptide bond – biochemical
reaction that extracts water
molecule as it joins the amino
group of one amino acid to the
carboxyl group of a neighboring
amino acid
Free amine group – N-terminal
residue
Free carboxyl group – C-terminal
residue

Structure of Amino Acids

Amino acids contain a central
carbon called alpha carbon (a carbon;
chiral center) bound to 4 substituents
- Amine group NH2
- Carboxylic group COOH
- Hydrogen atom H
- R group (side chain) – varies
from other amino acid
Carbons of R group are labeled
with Greek letters starting with B for the
first carbon attached to the central
carbon.
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 B alanine, a B amino acid is a
building block of pantothenic acid,
which is one of the structural units
of coenzyme
 Y-aminobutyric acid (GABA) – a y
amino acid involve in the
transmission of nerve pulses
 a carbon – chiral center
3 Different types of Side chain/ R
group
1. Nonpolar Side Chains
- Hydrophobic + repel water
- Side chains: long carbon
chain/ carbon rings making
them bulky
Ex. Glycine, alanine, valine,
leucine, isoleucine,
phenylalanine, proline,
tryptophan, methionine
GAVLIPPPT
2. Charged Polar Chains
- Forms an ionic bond
Negative Charged: aspartate,
glutamate
Positive Charged: lysine,
arginine, histidine
3. Uncharged Polar Side Chains
- Can form multiple hydrogen
bonds
- Prefer to project into the
aqueous phase
Ex. Serine, threonine, tyrosine,
cysteine, aspargine, glutamine
Chemical Properties of Amino Acid
 Chemical properties of an
individual amino acids are
influenced by chemical properties
of their r group
 Amino acid become ionized at a
specific PH in the body and is
determined by the number of
ionizable groups it possesses in
an amino acid
 Amino acids can be classified
based on their side chain’s
functional group and chemical
characteristics.
Classifications:
1. Aliphatic Amino Acids
- Characterized by Aliphatic
(non-benzene related) side
chains
Glycine and alanine – smallest
side chains; can fit into tight
spaces
Valine, leucine, Isoleucine –
branched chain amino acid; have
extended aliphatic side chains
causing them to cluster in
formations that allow them to
repel water
2. Aromatic Amino Acids
- Benzene related/with ring
- Feature an aromatic group
connected to carbon through
a methylene (CH2) group / R
group
- Phenylalanine, tyrosine,
tryptophan
Phenylalanine and Tryptophan –
hydrophobic
Hydroxyl group present in
tyrosine enhances its
hydrophicility and makes it more
chemically reactive compared to
phenylalanine.
4. Sulfur – containing Amino Acids
- Cysteine and methionine – 2
primary amino acids
containing sulfur, hydrphobic
in nature
Cysteine  oxidation  cystine
- Creation of disulfide bonds –
connect 2 separate peptide
chains or link different
cysteine residues within the
same peptide
- Serine and threonine –
hydrophilic and chemically
reactive properties
- Proline’s structure is unique
because the nitrogen from
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the alpha-amine group is part
of the side chain, restricting
the molecules’ rotation
around the C-N bond.
- Aspartate and Glutamate, the
acidic amino acids, are
dicarboxylic and monobasic
- Asparagine and glutamate
amino acids with an amide
group on side chains –
positively charged
- Histidine – imidazole ring –
uncharged
Ionization of Amino Acids
 Every amino acid possesses at
least 2 ionizable groups: alpha
carboxylic and alpha-amine group
 The proteins total charge is
established by the charge present
in the amino acid side chains (R
group) and charge on the proteins
N-terminal and C-terminal.
 2.35 pKA – COOH looses proton -
-1charge
 9.69 pKa – NH2 becomes
protonated - +1charge
 Amino acid lacking ionizable side
chains will posses a +1 charge
and a -1 charge. Consequently, its
overall charge is neutral
(zwitterion – isoelectric point of a
compound is the PH at which it
exists as a zwitterion), totalling
zero.
LEVELS OF PROTEIN STRUCTURE
1. Primary Structure
- Sequence and number of
amino acids linked by peptide
bonds
- Peptide bond is rigid and
plantar
2. Secondary Structure
- Localized shape of a protein
- Intro and intramolecular
hydrogen bonding
 a (alpha) helix – rod-
like structure ; 3.6
amino acids per turn;
intra
 B (beta) pleated sheet
– secondary structure
of silk; inter
 Collagen Triple Helix –
abundant structural
proteins found on
vertebrates; 3.3 amino
acids per turn
3. Tertiary Structure
- Interactions between amino
acid side chains of each the
residues
 Van der Waals Forces
 Ionic Bond
 Hydrophobic bond
 Hydrogen bond
4. Quaternary
- Composed of more than 1
polypeptide shade
DETERMINING AMINO ACID
COMPOSITION
 In the first stage, all peptide bonds
are hydrolyzed by an acid or base
 In the second stage of determining
the amino acid, the hydrolyzed
amino acids separated, identified
and quantified.
 Next will be the determination of
the structure includes identifying
the N-terminal residue and C
terminal residue...
 Edman Degradation – identifying
an entire sequence of amino acids
in a protein by successively
releasing individual N terminal,
residues.
DISSOCIATION OF PROTEIN
SUBUNITS
 Denaturation – process of treating
a protein with heat or chemical
reagents to break it down into its
constituent subunits
IDENTIFICATION, SEPARSTION, AND
CHARACTERIZATION OF PROTEINS
 Spectroscopy – identifying and
quantitating unknown molecules
by virtue of their interaction with
light
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 Ultracentrifugation – proteins
according to size (centrifugal
force)
 Svedberg (S) unit, measure of the
sedimentation coefficient of a
particle is equal to 10‐¹³ second
 Gel filtration chromatography –
packing inert porous beads into a
column with pore size
corresponding to molecular
weight.
 Ion exchange chromatography –
separates protein based on their
ion.
 Affinity chromatography –
separates protein that bind
specifically with certain chemical
groups
 Electrophoresis – exposure to
electric field
 Isoelectric focusing – separates
proteins on the basis of their
isoelectric point.

DETERMINATION OF HIGHER
LEVELS OF PROTEIN STRUCTURE

 X-ray diffraction
 Nuclear magnetic resonance
spectroscopy provides structural
and functional information about
an environment of a particular
protein
 Mass spectroscopy – can
determine the structure of very
small quantities of protein.
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