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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 o pH (BHOR EFFECT) – an increase in the pH
(N-terminal peptidase and will decrease the affinity of hemoglobin to
C-terminal peptidase) oxygen
o Formation of collagen
fibrils o 2,3 BPG – one of the products of glucose
o Cross linking of LYSYL metabolism
OXIDASE by COPPER
*SCURVY – results into bleeding of gums, mouth LESSON 4: ENZYMES
sores, petechiae, and loose teeth ENZYMES – are proteins that catalyze reactions
*EHLER’S-CHANLOS SYNDROME – gene for without being destroyed in the process
collagen is abnormal o OXIDOREDUCTASE – catalyzes
o KERATIN – fibrous proteins found in tough oxidation and reduction
structures like skin, hair, nails, etc. o TRANSFERASE – catalyzes transfer
o COMPONENTS OF KERATIN: groups
 CYSTEINE – stabilized by o HYDROXYLASE – catalyzes cleavage
disulfide bonds bonds by adding water
o ELASTIN – fibrous proteins with rubber-like o LIGASE – catalyzes the formation of
properties found in the lungs and blood bonds
vessels o LYASE – catalyzes he cleavage of
o COMPONENTS OF ELASTIN: bonds
 SMALL NON-POLAR – o ISOMERASE – catalyzes the
GLYCINE, ALANINE, racemization of isomer groups
VALINE
TRANSPORT PROPERTIES OF ENZYMES:
o ACTIVE SITES
o HEMEPROTEINS – specialized proteins that o CATALYTIC EFFICIENCY
contain heme as a tightly bound prosthetic o SPECIFICITY
group with a special function dedicated by
o COFACTORS
the environment created by the three
o REGULATED
dimensional structure of protein
o LOCATION
o CYTOCHROMES – electron carriers
o CATALASE – active site of the enzyme FREE ENERGY OF ACTIVATION – the amount
of energy required to transform a reactant to a
o HEMOGLOBIN & MYOGLOBIN – oxygen
product
binders
o HEME (PROTOPORPHIRIN IX & Fe) – capable TRANSITION ZONE – the point that has to be
of carrying 1 molecule of oxygen overcome for a reaction to take place
o MYOGLOBIN – stores and transports *Enzymes catalyze reactions by decreasing the
oxygen located within the muscle and heart FREE ENERGY OF ACTIVATION in all reactions
(with single polypeptide chain and single
heme group) FACTORS AFFECTING THE VELOCITY OF
o HEMOGLOBIN – found only in RBC; has 4 REACTOINS:
polypeptide chains and a quaternary or 4 o SUBSTRATE CONCENTRATION
heme molecules which means it can carry 4
oxygen molecules
 V-MAX – maximum velocity or speed
that the reaction maintains
o HbA – most common and abundant  HYPERBOLIC graph
in a normal body of an adult with 2 o TEMPERATURE
alpha chains and 2 beta chains  BELL SHAPED graph
o HbA2 – minor hemoglobin with 2  At a certain point, the temperature
alpha chains and 2 beta chains increase and the velocity increase but it
o HbF – fetal hemoglobin with 2 will eventually decrease
 High temperature denatures the action
alpha chains and 2 sigma chains
of enzymes
o HbAic – with 2 alpha chains and 1 o pH
beta glycose  PEPSIN – acidic
*P50 – 50% of myoglobin or hemoglobin is  ALKALINE PHOSPHADASE – basic
saturated  TRYPSIN – neutral
P50 = 1mmHg
MICHAELIS-MENTEN EQUATION – explains
ALLOSTERIC EFFECTORS – regulate the the relationship between substrate
binding of oxygen concentration and velocity of reaction
o PO2 (HEME-HEME INTERACTION)–
cooperative binding Km (Michaelis Constant) – refers to the
affinity of the enzyme to the substrate.

5
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