BIOCHEMISTRY PRELIM REVIEWER: PROTOPLASM – collective term for the

substances inside the cell

LESSON 1: INTRODUCTION *composed of 70% water
BIOCHEMISTRY IONS:
o Deals with the structures, properties and o POTASSIUM K
metabolism of biomolecular compounds and o PHOSPHORUS P
their interaction with cellular and physiological o MAGNESIUM Mg
systems PROTEINS: CARBOHYDRATES
o Seeks to describe the structure, organization and CELL MEMBRANE
functions of living matter in molecular terms o LIPIDS (PHOSPHOLIPIDS)
o BILAYER OF HYDROPHILIC &
APPLICATION OF BIOCHEMISTRY: HYDROPHOBIC
o MEDICAL SCIENCE o PROTEINS
o CLINICAL CHEMISTRY o INTEGRAL PROTEINS – intraverses
o PHARMACOLOGY the whole membrane; has contact;
o TOXICOLOGY transfers substances in and out through
o AGRICULTURE channels
o NUTRITION o PERIPHERAL PROTEINS – surface
of the cells; can act as enzymes
THE CELL o CARBOHYDRATES
PROKARYOTES (bacteria) o CHOLESTEROL
o SIZE: 0.2-5 um in CYTOPLASM
o COMPARTMENT: has no compartments o CYTOSOL
o DNA CONTAINMENT: DNA is free in the o ORGANELLES
cytoplasm as NUCLEOID o ENDOPLASMIC RETICULUM
o PLOIDY: usually haploid  ROUGH ER – studded with
o REPLICATION: simple division following RIBOSOMES for PROTEIN
DNA replication SYNTHESIS
o Unicellular with no true nucleus  SMOOTH ER – for LIPID
SYNTHESIS
EUKARYOTES (plants, animals, fungi) o GOLGI APPARATUS – located just
o SIZE: 10-50 um in (larger) after the ROUGH ER and functions for
o COMPARTMENT: several kinds of further modification/processing of
compartment substances from the ROUGH ER
o DNA CONTAINMENT: in nucleus, condensed o LYSOSOMES – is membrane bound,
with proteins serves as the intercellular digestive
o PLOIDY: diploid system and are formed in the GOLGI
o REPLICATION: MITOSIS (somatic cells) APPARATUS
MEIOSIS (sex cells)  SUICIDAL BAG – digestive
o Multicellular with true nucleus cell & bodies, bacteria
 PHAGOCYTOSIS – cell
KARYO – nucleus eating
PLOIDY – contents of chromosomes  PINOCYTOSIS – cell drinking
REPLICATION – simple diffusion o PEROXISOMES – OXIDASE
PILI – serves as attachment site for prokaryotic ENZYME; capable of self replication
cells found in the SMOOTH ER and is
FLAGELLA – serves for locomotion of prokaryotic responsible for processing substances
cells like ALCOHOL
o SECRETORY VESSICLE – found in
ORGANIZATION OF CELLS: the SMOOTH ER
2 BASIC PARTS: o MITOCHONDRIA – POWERHOUSE
o NUCLEUS OF THE CELL; has 2 lipid membranes
o CYTOPLASM (LIPID BILAYER MEMBRANE)

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

ESSENTIAL AMINO ACIDS – must be acquired LESSON 3: PROTEINS

from external sources PROTEINS – amino acids linked together by
10 ESSENTIAL AA: peptide bonds; polypeptide chains
o PROLINE PEPTIDE BONDS – amide linkages between the
o VALINE alpha carboxyl group of the AA and the alpha amino
o TRYPTOPHAN group of another AA
o THREONINE
o ISOLEUCINE CHARACTERISTICS OF PEPTIDE BONDS:
o METHIONINE o PARTIAL DOUBLE BOND
o HISTIDINE o Bond in character
o ARGININE o Not so long but not so short
o LEUCINE o RIGID AND PLANAR
o LYSINE o 2 AA can’t move freely
DENTISTRY CORRELATION – most common o Present in trans configuration
AA in the enamel of the teeth: o TRANS CONFIGURATION
o GLYCINE o UNCHARGED BUT POLAR
o GLUTAMIC ACID o Can’t give off protons (charge from
o SERINE terminal ends and side chains) H-bonds
*Mature enamel has a reduced PROLINE content CIS – side chains are on the same side
STEREOCHEMISTRY TRANS – side chains are on the opposite sides
o All AA are optically active except GLYCINE (stable)
o Alpha carbon is CHIRAL UNCHARGE – cannot give off protons;
o It can exist in DEXTRO (right) or LEVO (left) participates in hydrogen bonds
form
o Mirror images WAYS OF DESTROYING PEPTIDE BONDS:
o Almost all AA are L-type o ENZYMATIC – by the use of enzymes
CHIRAL CARBON – are optically active carbons o NON-ENZYMATIC – by the use of heat and
with 4 different chains attached to it and it produces strong acid
polarized light NOMENCLATURE:
* -ic, -ine, -an = -yl
ABBREVIATIONS OF AMINO ACIDS: * N terminal is written to the left while C terminal is
AMINO ACID: ABBREVIATION written on the right
* C terminal AA remains as is
GLYCINE G
*DEHYDRATION – forms peptide bonds
ALANINE A
VALINE V
DETERMINATION OF PROTEIN
LEUCINE L COMPONENTS:
ISOLEUCINE I o ACID HYDROLYSIS
METHIONINE M o Determines polypeptide bonds
SERINE S o Hydrolyzed by adding a strong acid at
THREONINE T
110˚C for 24hours
TYROSINE Y o Cleaves the peptide bonds and releases
CYSTEINE C
free amino acids
ASPARTIC ACID D o CHROMATOGRAPHY
ASPARGINE N
o CATION EXCHANGE
GLUTAMIC ACID E
CHROMATOGRAPHY
GLUTAMINE Q
 Separates the individual AA\
ARGININE R  ELUTION – adding buffer
LYSINE K  ELUENT – washed off solute
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 The negative charge will come o GENETIC CODE – normal production of
off first and the strongly proteins
positive charge will come off o POST TRANSLATIONAL
last because the RESIN is MODIFICATION – quality control of AA and
negatively charged proteins
o QUANTITATIVE ANALYSIS
o NINHYDRIN – reagent that forms a LEVEL OF ORGANIZATION OF PROTEINS
purple compound with most AA, BY STRUCTURES:
ammonia and amines o PRIMARY STRUCTURE
o SPECTROPHOTOMETER – o Sequence of AA in a protein
measures the absorbance of light of each o SECONDARY STRUCTURE
substance o Regular arrangements of AA that are
located near to each other in the linear
SEQUENCING OF PEPTIDE FROM ITS N- sequence
TERMINAL: o ALPHA HELIX
o PHENYLTHIOHYDANTOIN  Most common polypeptide helix
DERIVATIVE(PTH) in nature
o Provides stability to the N-terminal  Spiral, right handed
peptide  Intra-chain H-bonds
o EDMAN’S REAGENT  Side chains are outward
o Weakens AA bond and labels the AA at  KERATIN – fibrous proteins
the N-terminal end  HEMOGLOBIN – globular
o Can only be used in small polypeptide proteins
chains (less than 100AA)  Disrupted by PROLINE;
charged or bulky side chains
CLEAVAGE OF POLYPEPTIDES INTO o BETA PLEATED SHEET
SMALLER FRAGMENTS:  Secondary structure where all
o ENZYMATIC CLEAVAGE peptide bonds are involved in
o TRYPSIN – cuts the peptide bond at hydrogen bonding
the C-terminal end of LYSINE &  Usually anti-parallel
ARGININE  Hydrogen bonds are
o CHEMICAL CLEAVAGE perpendicular to the polypeptide
o CYANOGEN BROMIDE – cuts the backbone (interchain)
peptide bind at the C-terminal end of  Found in AMYLOID
METHIONINE PROTEIN; HEMOGLOBIN
o OVERLAPPING PEPTIDES o TERTIARY STRUCTURE
o Use of both enzymatic and chemical o Overall 3 dimensional shape of a
cleavage protein. Domains basic unit of structure
o DENATURING AGENTS o Interactions stabilizing tertiary structure:
o Form multimeric proteins  DISULFIDE BONDS
 UREA  HYDROPHOBIC
 GUANIDINE INTERACTIONS – non-polar
HYDROCHLORIDE amino acids
 PERFORMIC ACID  HYDROGEN BONDS –
*MULTIMERIC PROTEINS – multiple SERINE, THREONINE,
polypeptide chain TYROSINE
 IONIC INTERACTIONS –
*MONOMERIC PROTEINS – one polypeptide charged amino acids
chain o QUATERNARY STRUCTURE
o Arrangement of multimeric proteins
DETERMINATION OF PROTEIN o MULTIMERIC PROTEINS – with
STRUCTURE BY DNA SEQUENCING several polypeptide subunits
o Knowledge of the DNA sequence will allow us o Subunits are held together by non-
to identify the AA sequence of a protein covalent interaction (HYDROPHOBIC

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 INTERACTIONS, H-BONDS, IONIC o COMPONENTS OF KERATIN:
BONDS)  CYSTEINE – stabilized by
FUNCTIONS OF PROTEINS: disulfide bonds
DEFENSE o ELASTIN – fibrous proteins with rubber-like
o IMMUNOGLOBULINS/ ANTIBODIES properties found in the lungs and blood vessels
o IgA o COMPONENTS OF ELASTIN:
o IgD  SMALL NON-POLAR –
o IgE GLYCINE, ALANINE,
o IgM VALINE
STRUCTURE TRANSPORT
o COLLAGEN – most abundant protein in the o HEMEPROTEINS – specialized proteins that
body contain heme as a tightly bound prosthetic group
o TYPES OF COLLAGENS: with a special function dedicated by the
TYPES EXAMPLES environment created by the three-dimensional
I SKIN & BONES structure of protein
II CARTILAGE o CYTOCHROMES – electron carriers
III BLOOD VESSELS o CATALASE – active site of the enzyme
IV BASEMENT MEMBRANE o HEMOGLOBIN & MYOGLOBIN – oxygen
binders
o HEME (PROTOPORPHIRIN IX & Fe) –
o COMPOSITION OF COLLAGEN – capable of carrying 1 molecule of oxygen
always GLYCINE in 3rd position with o MYOGLOBIN – stores and transports oxygen
HYDROXYPROLINE or located within the muscle and heart (with single
HYDROXYLYSINE polypeptide chain and single heme group)
o SYNTHESIS OF COLLAGEN: o HEMOGLOBIN – found only in RBC; has 4
o Formation of polypeptide chains and a quaternary or 4 heme
PREPROALPHACHAIN molecules which means it can carry 4 oxygen
(produced in the ribosome) molecules
o Cleavage with signal peptidase o HbA – most common and abundant in a
at the ROUGH ER normal body of an adult with 2 alpha
(PROALPHACHAIN) chains and 2 beta chains
o Hydroxylation of PROLINE & o HbA2 – minor hemoglobin with 2 alpha
LYSINE (needs ASCORBIC chains and 2 beta chains
ACID) o HbF – fetal hemoglobin with 2 alpha
o Glycosylation chains and 2 sigma chains
(HYDROXYLYSINE) of o HbAic – with 2 alpha chains and 1 beta
GLUCOSE or GALACTOSE at glycose
the ROUGH ER *P50 – 50% of myoglobin or hemoglobin is
o Assembly and secretion at the saturated
GOLGI BODY (connected by P50 = 1mmHg
disulfide bonds) *secreted to the
extracellular compartment ALLOSTERIC EFFECTORS – regulate the
o Cleavage of polypeptide (N- binding of oxygen
terminal peptidase and C- o PO2 (HEME-HEME INTERACTION)–
terminal peptidase) cooperative binding
o Formation of collagen fibrils o pH (BHOR EFFECT) – an increase in the pH
o Cross linking of LYSYL will decrease the affinity of hemoglobin to
OXIDASE by COPPER oxygen
*SCURVY – results into bleeding of gums, mouth o 2,3 BPG – one of the products of glucose
sores, petechiae, and loose teeth metabolism
*EHLER’S-CHANLOS SYNDROME – gene for
collagen is abnormal LESSON 4: ENZYMES
o KERATIN – fibrous proteins found in tough ENZYMES – are proteins that catalyze reactions
structures like skin, hair, nails, etc. without being destroyed in the process
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 o OXIDOREDUCTASE – catalyzes amount of substrate required to reach ½ of the v-
oxidation and reduction max
o TRANSFERASE – catalyzes transfer
groups *Km is INVERSELY PROPORTIONAL to
o HYDROXYLASE – catalyzes cleavage AFFINITY
bonds by adding water
o LIGASE – catalyzes the formation of bonds FIRST ORDER KINETICS – at low substrate
o LYASE – catalyzes he cleavage of bonds concentration, the velocity increases at direct
o ISOMERASE – catalyzes the racemization proportion to the amount of substrate
of isomer groups
ZERO ORDER KINETICS – at high substrate
PROPERTIES OF ENZYMES: concentration, the velocity is independent and not
o ACTIVE SITES proportional to the amount of substrate
o CATALYTIC EFFICIENCY
INHIBITION
o SPECIFICITY o ACCORDING TO REVERSIBILITY
o COFACTORS o REVERSIBLE – if the complex is
o REGULATED diluted, substrate will be dissociated by
o LOCATION adding an inhibitor to the enzyme
o IRREVERSIBLE – the enzyme cannot
FREE ENERGY OF ACTIVATION – the amount do its action and will not dissociate
of energy required to transform a reactant to a o ACCORDING TO BINDING SITE
product o COMPETITIVE – the inhibitor binds
to the active site.
TRANSITION ZONE – the point that has to be
 Can be reversed by adding more
overcome for a reaction to take place
substrate
 No change in V-Max because it
*Enzymes catalyze reactions by decreasing the
can be reversed
FREE ENERGY OF ACTIVATION in all reactions
 Km will change the V-Max
o NON-COMPETITIVE – doesn’t bind
FACTORS AFFECTING THE VELOCITY OF
REACTOINS: to the active site but binds to other
o SUBSTRATE CONCENTRATION portions of the substrate binding site
 Cannot be reversed because it
 V-MAX – maximum velocity or speed that
changes the configuration
the reaction maintains
 V-Max decreases because it is
 HYPERBOLIC graph
irreversible
o TEMPERATURE
 Has no change in both Km and
 BELL SHAPED graph affinity
 At a certain point, the temperature increases
and the velocity increase but it will INHIBITORS – substances that diminishes the
eventually decrease activity of the enzymes
 High temperature denatures the action of MITOCHONDRIA – fat oxidation
enzymes NUCLEUS – DNA synthesis
o pH CYTOSOL – glucose
 PEPSIN – acidic
 ALKALINE PHOSPHADASE – basic WAYS OF REGULATING ENZYME
 TRYPSIN – neutral ACTIVITY:
o SUBSTRATE AVAILABILITY – adding
MICHAELIS-MENTEN EQUATION – explains more substrate will increase the velocity of
the relationship between substrate concentration and reaction
velocity of reaction o PRODUCT INHIBITION – adding inhibitors
will increase the affinity
Km (Michaelis Constant) – refers to the affinity of
o ALLOSTERIC CONTROL – enhances
the enzyme to the substrate. Numerically, it is the
activity of enzymes by binding to other sites

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o COVALENT MODIFICATION – activation
and inhibition of enzymes with phosphate
 PHOSPHORYLATION – PROTEIN
KINASE
 DEPHOSPHORYLATION – PROTEIN
PHOSPHATASE
 Some enzymes are activated upon the
addition of phosphate groups while some are
inhibited
o SYNTHESIS & DEGREDATION – increase
enzyme activity by synthesizing more of the
enzyme and decrease enzyme activity by
degrading the enzyme

*Enzymes are useful in clinical diagnosis because

they identify diseases by the absence or presence of
enzymes in the body

* Elevated levels of CREATINE KINASE mean

the patient had myocardial infarction

MYOGLOBIN
o Hyperbolic curve
o Decrease P50, increase affinity
HEMOGLOBIN
o Sigmoidal curve
o Increase P50, decrease affinity

*SHIFT TO THE LEFT – high hydrogen ion

*SHIFT TO THE RIGHT – increase affinity