BIOCHEMISTRY PRELIM REVIEWER: o PROTEINS

o INTEGRAL PROTEINS –
LESSON 1: INTRODUCTION intraverses the whole membrane;
BIOCHEMISTRY has contact; transfers substances
o Deals with the structures, properties and in and out through channels
metabolism of biomolecular compounds and o PERIPHERAL PROTEINS – surface
their interaction with cellular and of the cells; can act as enzymes
physiological systems o CARBOHYDRATES
o Seeks to describe the structure, o CHOLESTEROL
organization and functions of living matter CYTOPLASM
in molecular terms o CYTOSOL
o ORGANELLES
APPLICATION OF BIOCHEMISTRY: o ENDOPLASMIC RETICULUM
o MEDICAL SCIENCE
o CLINICAL CHEMISTRY  ROUGH ER – studded
o PHARMACOLOGY with RIBOSOMES for
o TOXICOLOGY PROTEIN SYNTHESIS
o AGRICULTURE  SMOOTH ER – for LIPID
o NUTRITION SYNTHESIS

THE CELL
o GOLGI APPARATUS – located just
PROKARYOTES (bacteria) after the ROUGH ER and functions
o SIZE: 0.2-5 um in for further modification/processing
of substances from the ROUGH ER
o COMPARTMENT: has no compartments
o DNA CONTAINMENT: DNA is free in the o LYSOSOMES – is membrane
cytoplasm as NUCLEOID bound, serves as the intercellular
o PLOIDY: usually haploid digestive system and are formed in
o REPLICATION: simple division following DNA the GOLGI APPARATUS
replication  SUICIDAL BAG –
o Unicellular with no true nucleus digestive cell & bodies,
bacteria
EUKARYOTES (plants, animals, fungi)
o SIZE: 10-50 um in (larger)  PHAGOCYTOSIS – cell
o COMPARTMENT: several kinds of eating
compartment  PINOCYTOSIS – cell
o DNA CONTAINMENT: in nucleus, condensed drinking
with proteins o PEROXISOMES – OXIDASE
o PLOIDY: diploid ENZYME; capable of self replication
o REPLICATION: MITOSIS (somatic cells) found in the SMOOTH ER and is
MEIOSIS (sex cells) responsible for processing
o Multicellular with true nucleus substances like ALCOHOL

KARYO – nucleus
o SECRETORY VESSICLE – found in
PLOIDY – contents of chromosomes the SMOOTH ER
REPLICATION – simple diffusion o MITOCHONDRIA – POWERHOUSE
PILI – serves as attachment site for prokaryotic OF THE CELL; has 2 lipid
cells membranes( LIPID BILAYER
FLAGELLA – serves for locomotion of MEMBRANE)
prokaryotic cells
 ATP – energy currency of
ORGANIZATION OF CELLS: the cell
2 BASIC PARTS: o FILAMENTS & TUBULAR
o NUCLEUS STRUCTURES
o CYTOPLASM  FILAMENTS – ACTIN &
PROTOPLASM – collective term for the MYOSIN found in the
substances inside the cell muscles
*composed of 70% water
IONS:  MICROTUBULES – CILIA
o POTASSIUM K & FLAGELLA; acts as
o PHOSPHORUS P cytoskeleton; CENTRIOLES
o MAGNESIUM Mg & MITOTIC SPINDLE
PROTEINS: CARBOHYDRATES o NUCLEUS
CELL MEMBRANE  NUCLEAR MEMBRANE
o LIPIDS (PHOSPHOLIPIDS)  NUCLEOLUS – genes
o BILAYER OF HYDROPHILIC & (RNA)
HYDROPHOBIC  NUCLEUS – genes (DNA)

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  THREONINE
LESSON 2: AMINO ACIDS
AMINO ACIDS  CYSTEINE
o Building blocks of proteins  PROLINE
o Forms peptide bonds with each other
resulting in a POLYPEPTIDE CHAIN  ASPARGINE
o More than 300 different kinds of AA  GLUTAMINE
o Only 20 are found in mammalian o ACIDIC AA
proteins o NEGATIVELY CHARGED at neutral
o Only 10 are ESSENTIAL AMINO ACIDS pH
o Proton donors
*ESSENTIAL AA – cannot be produced by own o Gives off H
body
 ASPARTATE
STRUCTURE:
o ALPHA CARBON
 GLUTAMATE
o BASIC AA
o CARBOXYLIC ACID GROUP
o POSTITVELY CHARGED at neutral
o AMIDE GROUP
pH
o RESIDUE GROUP (R-GROUP) – o Proton acceptors
responsible for the unique properties of o Takes in H
each AA (SIDE CHAINS)
o HYDROGEN GROUP  LYSINE
PHYSIOLOGIC Ph – 7.4  ARGININE
1. The carboxyl group is dissociated forming a
negatively charged carboxylate ion  HISTIDINE
2. The amide group is protonated
PROTONATION - (+) H *HYDROXYL GROUP - For formation of
DEPROTONATION – (-) H (removal of hydrogen bond; Acceptor of other groups of
H) phosphate
CLASSES OF AMINO ACIDS: o SERINE
o NON-POLAR ALIPHATIC AA
o Do not bind or give off protons
o THREONINE
o Do not participate in hydrogen or o TYROSINE
ionic bonds *SULFHYDRYL GROUP – can form active part
o R-groups are HYDROPHOBIC with enzymes
o Clusters in the interior of the o CYSTEINE
protein *IMINO GROUP – important in protein systems
o Similar to how oil coalesces in an because it forms kinks in the polypeptide chains
aqueous environment
o PROLINE
 GLYCINE *CYSTEINE DIMER – reaction of 2 cysteine
 ALANINE residues to form a covalent S-S
*IMINO RING – forms rings with NH2
 VALINE *TRYPTOPHAN – precursor of SEROTONIN
*TYROSINE – precursor of MELANIN
 LEUCINE
*BUFFERS – solution that neutralizes a solution
 ISOLEUCINE and resists change
*pH – defined as the negative logarithm of the
 METHIONINE hydrogen ion concentration
o NON-POLAR AROMATIC AA
o Have BENZYL RING ESSENTIAL AMINO ACIDS – must be acquired
o Similar to uncharged aliphatic from external sources
groups 10 ESSENTIAL AA:
o HYDROPHOBIC o PROLINE
o Clusters in the interior of protein
o VALINE
 PHENYLALANINE
o TRYPTOPHAN
 TRYPTOPHAN
o THREONINE

TYROSINE o ISOLEUCINE
o POLAR UNCHARGED AA
o Has ZERO CHARGE at neutral pH o METHIONINE
o With POLAR R-GROUPS which can o HISTIDINE
from H-bonds with other
compounds
o ARGININE

 SERINE
o LEUCINE
o LYSINE

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DENTISTRY CORRELATION – most common AA UNCHARGE – cannot give off protons;
in the enamel of the teeth: participates in hydrogen bonds
o GLYCINE
WAYS OF DESTROYING PEPTIDE BONDS:
o GLUTAMIC ACID
o ENZYMATIC – by the use of enzymes
o SERINE
o NON-ENZYMATIC – by the use of heat and
*Mature enamel has a reduced PROLINE content
strong acid
STEREOCHEMISTRY
NOMENCLATURE:
o All AA are optically active except GLYCINE
* -ic, -ine, -an = -yl
o Alpha carbon is CHIRAL
* N terminal is written to the left while C
o It can exist in DEXTRO (right) or LEVO (left) terminal is written on the right
form * C terminal AA remains as is
o Mirror images *DEHYDRATION – forms peptide bonds
o Almost all AA are L-type
CHIRAL CARBON – are optically active carbons DETERMINATION OF PROTEIN
with 4 different chains attached to it and it COMPONENTS:
produces polarized light o ACID HYDROLYSIS
oDetermines polypeptide bonds
ABBREVIATIONS OF AMINO ACIDS: oHydrolyzed by adding a strong acid
AMINO ACID: ABBREVIATIO at 110˚C for 24hours
N o Cleaves the peptide bonds and
GLYCINE G releases free amino acids
ALANINE A o CHROMATOGRAPHY
VALINE V o CATION EXCHANGE
LEUCINE L CHROMATOGRAPHY
ISOLEUCINE I  Separates the individual
METHIONINE M AA\
SERINE S
THREONINE T  ELUTION – adding buffer
TYROSINE Y 
ELUENT – washed off
CYSTEINE C solute
ASPARTIC ACID D  The negative charge will
ASPARGINE N come off first and the
GLUTAMIC E strongly positive charge
ACID will come off last because
GLUTAMINE Q the RESIN is negatively
ARGININE R charged
LYSINE K o QUANTITATIVE ANALYSIS
HISTIDINE H o NINHYDRIN – reagent that forms a
PHENYLALANIN F
purple compound with most AA,
E
ammonia and amines
TRYPTOPHAN W
PROLINE P o SPECTROPHOTOMETER –
measures the absorbance of light
of each substance
LESSON 3: PROTEINS
PROTEINS – amino acids linked together by
SEQUENCING OF PEPTIDE FROM ITS N-
peptide bonds; polypeptide chains
TERMINAL:
PEPTIDE BONDS – amide linkages between the
o PHENYLTHIOHYDANTOIN
alpha carboxyl group of the AA and the alpha
DERIVATIVE(PTH)
amino group of another AA
o Provides stability to the N-terminal
CHARACTERISTICS OF PEPTIDE BONDS: peptide
o PARTIAL DOUBLE BOND o EDMAN’S REAGENT
o Bond in character o Weakens AA bond and labels the
o Not so long but not so short AA at the N-terminal end
o Can only be used in small
o RIGID AND PLANAR
polypeptide chains (less than
o 2 AA can’t move freely 100AA)
o Present in trans configuration
o TRANS CONFIGURATION CLEAVAGE OF POLYPEPTIDES INTO
o UNCHARGED BUT POLAR SMALLER FRAGMENTS:
o Can’t give off protons (charge from o ENZYMATIC CLEAVAGE
terminal ends and side chains) H- o TRYPSIN – cuts the peptide bond
bonds at the C-terminal end of LYSINE &
CIS – side chains are on the same side ARGININE
TRANS – side chains are on the opposite sides o CHEMICAL CLEAVAGE
(stable)

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 o CYANOGEN BROMIDE – cuts the o Interactions stabilizing tertiary
peptide bind at the C-terminal end structure:
of METHIONINE  DISULFIDE BONDS
o OVERLAPPING PEPTIDES  HYDROPHOBIC
o Use of both enzymatic and INTERACTIONS – non-
chemical cleavage polar amino acids
o DENATURING AGENTS
o Form multimeric proteins  HYDROGEN BONDS –
SERINE, THREONINE,
 UREA
TYROSINE
 GUANIDINE
HYDROCHLORIDE  IONIC INTERACTIONS –
 PERFORMIC ACID charged amino acids
*MULTIMERIC PROTEINS – multiple o QUATERNARY STRUCTURE
polypeptide chain o Arrangement of multimeric
proteins
*MONOMERIC PROTEINS – one polypeptide o MULTIMERIC PROTEINS – with
chain
several polypeptide subunits
o Subunits are held together by non-
DETERMINATION OF PROTEIN STRUCTURE
BY DNA SEQUENCING covalent interaction
o Knowledge of the DNA sequence will allow (HYDROPHOBIC INTERACTIONS, H-
BONDS, IONIC BONDS)
us to identify the AA sequence of a protein
FUNCTIONS OF PROTEINS:
o GENETIC CODE – normal production of DEFENSE
proteins o IMMUNOGLOBULINS/ ANTIBODIES
o POST TRANSLATIONAL MODIFICATION – o IgA
quality control of AA and proteins o IgD
o IgE
LEVEL OF ORGANIZATION OF PROTEINS BY o IgM
STRUCTURES: STRUCTURE
o PRIMARY STRUCTURE o COLLAGEN – most abundant protein in the
o Sequence of AA in a protein body
o SECONDARY STRUCTURE o TYPES OF COLLAGEN:
o Regular arrangements of AA that TYPES EXAMPLES
are located near to each other in I SKIN & BONES
the linear sequence II CARTILAGE
o ALPHA HELIX III BLOOD VESSELS
 Most common polypeptide IV BASEMENT MEMBRANE
helix in nature
 Spiral, right handed
 Intra-chain H-bonds
 Side chains are outward
o COMPOSITION OF COLLAGEN –
always GLYCINE in 3rd position with
 KERATIN – fibrous HYDROXYPROLINE or
proteins HYDROXYLYSINE
o SYNTHESIS OF COLLAGEN:
 HEMOGLOBIN – globular
o Formation of
proteins
PREPROALPHACHAIN
 Disrupted by PROLINE; (produced in the
charged or bulky side ribosome)
chains o Cleavage with signal
o BETA PLEATED SHEET
peptidase at the ROUGH
 Secondary structure ER (PROALPHACHAIN)
where all peptide bonds
are involved in hydrogen o Hydroxylation of PROLINE
bonding & LYSINE (needs
 Usually anti-parallel ASCORBIC ACID)
 Hydrogen bonds are o Glycosylation
perpendicular to the (HYDROXYLYSINE) of
polypeptide backbone GLUCOSE or GALACTOSE
(interchain) at the ROUGH ER
 Found in AMYLOID o Assembly and secretion at
PROTEIN; HEMOGLOBIN the GOLGI BODY
o TERTIARY STRUCTURE (connected by disulfide
o Overall 3 dimensional shape of a bonds) *secreted to the
extracellular compartment
protein. Domains basic unit of
structure

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 o Cleavage of polypeptide
(N-terminal peptidase and
C-terminal peptidase)
o Formation of collagen
fibrils
o Cross linking of LYSYL
OXIDASE by COPPER
*SCURVY – results into bleeding of gums, mouth
sores, petechiae, and loose teeth
*EHLER’S-CHANLOS SYNDROME – gene for
collagen is abnormal
o KERATIN – fibrous proteins found in tough
structures like skin, hair, nails, etc.
o COMPONENTS OF KERATIN:
 CYSTEINE – stabilized by
disulfide bonds
o ELASTIN – fibrous proteins with rubber-like
properties found in the lungs and blood
vessels
o COMPONENTS OF ELASTIN:
 SMALL NON-POLAR –
GLYCINE, ALANINE,
VALINE
TRANSPORT
o HEMEPROTEINS – specialized proteins that
contain heme as a tightly bound prosthetic
group with a special function dedicated by
the environment created by the three
dimensional structure of protein
o CYTOCHROMES – electron carriers
o CATALASE – active site of the enzyme
o HEMOGLOBIN & MYOGLOBIN – oxygen
binders
o HEME (PROTOPORPHIRIN IX & Fe) – capable
of carrying 1 molecule of oxygen
o MYOGLOBIN – stores and transports
oxygen located within the muscle and heart
(with single polypeptide chain and single
heme group)
o HEMOGLOBIN – found only in RBC; has 4
polypeptide chains and a quaternary or 4
heme molecules which means it can carry 4
oxygen molecules
o HbA – most common and abundant
in a normal body of an adult with 2
alpha chains and 2 beta chains
o HbA2 – minor hemoglobin with 2
alpha chains and 2 beta chains
o HbF – fetal hemoglobin with 2
alpha chains and 2 sigma chains
o HbAic – with 2 alpha chains and 1
beta glycose
*P50 – 50% of myoglobin or hemoglobin is
saturated
P50 = 1mmHg
ALLOSTERIC EFFECTORS – regulate the
binding of oxygen
o PO2 (HEME-HEME INTERACTION)–
cooperative binding
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o pH (BHOR EFFECT) – an increase in the pH
will decrease the affinity of hemoglobin to
oxygen
o 2,3 BPG – one of the products of glucose
metabolism
LESSON 4: ENZYMES
ENZYMES – are proteins that catalyze reactions
without being destroyed in the process
o OXIDOREDUCTASE – catalyzes
oxidation and reduction
o TRANSFERASE – catalyzes transfer
groups
o HYDROXYLASE – catalyzes cleavage
bonds by adding water
o LIGASE – catalyzes the formation of
bonds
o LYASE – catalyzes he cleavage of
bonds
o ISOMERASE – catalyzes the
racemization of isomer groups
PROPERTIES OF ENZYMES:
o ACTIVE SITES
o CATALYTIC EFFICIENCY
o SPECIFICITY
o COFACTORS
o REGULATED
o LOCATION
FREE ENERGY OF ACTIVATION – the amount
of energy required to transform a reactant to a
product
TRANSITION ZONE – the point that has to be
overcome for a reaction to take place
*Enzymes catalyze reactions by decreasing the
FREE ENERGY OF ACTIVATION in all reactions
FACTORS AFFECTING THE VELOCITY OF
REACTOINS:
o SUBSTRATE CONCENTRATION
 V-MAX – maximum velocity or speed
that the reaction maintains
 HYPERBOLIC graph
o TEMPERATURE
 BELL SHAPED graph
 At a certain point, the temperature
increase and the velocity increase but it
will eventually decrease
 High temperature denatures the action
of enzymes
o pH
 PEPSIN – acidic
 ALKALINE PHOSPHADASE – basic
 TRYPSIN – neutral
MICHAELIS-MENTEN EQUATION – explains
the relationship between substrate
concentration and velocity of reaction
Km (Michaelis Constant) – refers to the
affinity of the enzyme to the substrate.
Numerically, it is the amount of substrate  Some enzymes are activated upon the
required to reach ½ of the v-max addition of phosphate groups while
some are inhibited
*Km is INVERSELY PROPORTIONAL to AFFINITY o SYNTHESIS & DEGREDATION –
increase enzyme activity by synthesizing
FIRST ORDER KINETICS – at low substrate
more of the enzyme and decrease enzyme
concentration, the velocity increases at direct
activity by degrading the enzyme
proportion to the amount of substrate
*Enzymes are useful in clinical diagnosis
ZERO ORDER KINETICS – at high substrate
because they identify diseases by the absence
concentration, the velocity is independent and
or presence of enzymes in the body
not proportional to the amount of substrate
* Elevated levels of CREATINE KINASE means
INHIBITION
the patient had myocardial infarction
o ACCORDING TO REVERSIBILITY
oREVERSIBLE – if the complex is MYOGLOBIN
diluted, substrate will be o Hyperbolic curve
dissociated by adding an inhibitor o Decrease P50, increase affinity
to the enzyme HEMOGLOBIN
o IRREVERSIBLE – the enzyme o Sigmoidal curve
cannot do its action and will not o Increase P50, decrease affinity
dissociate
o ACCORDING TO BINDING SITE *SHIFT TO THE LEFT – high hydrogen ion
*SHIFT TO THE RIGHT – increase affinity
o COMPETITIVE – the inhibitor binds
to the active site. -Rosette Go 073108 
 Can be reversed by
adding more substrate
 No change in V-Max
because it can be
reversed
 Km will change the V-Max
o NON-COMPETITIVE – doesn’t bind
to the active site but binds to other
portions of the substrate binding
site
 Cannot be reversed
because it changes the
configuration
 V-Max decreases because
it is irreversible
 Has no change in both Km
and affinity

INHIBITORS – substances that diminishes the

activity of the enzymes
MITOCHONDRIA – fat oxidation
NUCLEUS – DNA synthesis
CYTOSOL – glucose

WAYS OF REGULATING ENZYME ACTIVITY:

o SUBSTRATE AVAILABILITY – adding more
substrate will increase the velocity of
reaction
o PRODUCT INHIBITION – adding inhibitors
will increase the affinity
o ALLOSTERIC CONTROL – enhances
activity of enzymes by binding to other sites
o COVALENT MODIFICATION – activation
and inhibition of enzymes with phosphate
 PHOSPHORYLATION – PROTEIN
KINASE
 DEPHOSPHORYLATION – PROTEIN
PHOSPHATASE