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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 their o PHOSPHORUS P
interaction with cellular and physiological systems o MAGNESIUM Mg
o Seeks to describe the structure, organization and PROTEINS: CARBOHYDRATES
functions of living matter in molecular terms CELL MEMBRANE
o LIPIDS (PHOSPHOLIPIDS)
APPLICATION OF BIOCHEMISTRY: o BILAYER OF HYDROPHILIC &
o MEDICAL SCIENCE HYDROPHOBIC
o CLINICAL CHEMISTRY o PROTEINS
o PHARMACOLOGY o INTEGRAL PROTEINS – intraverses the
o TOXICOLOGY whole membrane; has contact; transfers
o AGRICULTURE substances in and out through 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 DNA RIBOSOMES for PROTEIN
replication SYNTHESIS
o Unicellular with no true nucleus  SMOOTH ER – for LIPID
SYNTHESIS
EUKARYOTES (plants, animals, fungi) o GOLGI APPARATUS – located just after
o SIZE: 10-50 um in (larger) the ROUGH ER and functions for further
o COMPARTMENT: several kinds of compartment modification/processing of substances from
o DNA CONTAINMENT: in nucleus, condensed with the ROUGH ER
proteins o LYSOSOMES – is membrane bound,
o PLOIDY: diploid serves as the intercellular digestive system
o REPLICATION: MITOSIS (somatic cells) and are formed in the GOLGI APPARATUS
MEIOSIS (sex cells)  SUICIDAL BAG – digestive cell &
o Multicellular with true nucleus bodies, bacteria
 PHAGOCYTOSIS – cell eating
KARYO – nucleus  PINOCYTOSIS – cell drinking
PLOIDY – contents of chromosomes o PEROXISOMES – OXIDASE ENZYME;
REPLICATION – simple diffusion capable of self replication found in the
PILI – serves as attachment site for prokaryotic cells SMOOTH ER and is responsible for
FLAGELLA – serves for locomotion of prokaryotic processing substances like ALCOHOL
cells o SECRETORY VESSICLE – found in the
SMOOTH ER
ORGANIZATION OF CELLS: o MITOCHONDRIA – POWERHOUSE OF
2 BASIC PARTS: THE CELL; has 2 lipid membranes( LIPID
o NUCLEUS BILAYER MEMBRANE)
o CYTOPLASM  ATP – energy currency of the cell

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o FILAMENTS & TUBULAR  ISOLEUCINE

STRUCTURES  METHIONINE
 FILAMENTS – ACTIN & o NON-POLAR AROMATIC AA
MYOSIN found in the muscles o Have BENZYL RING
 MICROTUBULES – CILIA & o Similar to uncharged aliphatic groups
FLAGELLA; acts as cytoskeleton; o HYDROPHOBIC
CENTRIOLES & MITOTIC o Clusters in the interior of protein
SPINDLE  PHENYLALANINE
o NUCLEUS  TRYPTOPHAN
 NUCLEAR MEMBRANE  TYROSINE
 NUCLEOLUS – genes (RNA) o POLAR UNCHARGED AA
 NUCLEUS – genes (DNA) o Has ZERO CHARGE at neutral pH
o With POLAR R-GROUPS which can from
LESSON 2: AMINO ACIDS H-bonds with other compounds
AMINO ACIDS  SERINE
o Building blocks of proteins  THREONINE
o Forms peptide bonds with each other resulting in  CYSTEINE
a POLYPEPTIDE CHAIN  PROLINE
o More than 300 different kinds of AA  ASPARGINE
o Only 20 are found in mammalian proteins  GLUTAMINE
o Only 10 are ESSENTIAL AMINO ACIDS o ACIDIC AA
o NEGATIVELY CHARGED at neutral pH
*ESSENTIAL AA – cannot be produced by own body o Proton donors
o Gives off H
STRUCTURE:  ASPARTATE
o ALPHA CARBON  GLUTAMATE
o CARBOXYLIC ACID GROUP o BASIC AA
o AMIDE GROUP o POSTITVELY CHARGED at neutral pH
o RESIDUE GROUP (R-GROUP) – responsible o Proton acceptors
for the unique properties of each AA (SIDE o Takes in H
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 hydrogen
2. The amide group is protonated bond; Acceptor of other groups of phosphate
PROTONATION - (+) H o SERINE
DEPROTONATION – (-) H (removal of H) o THREONINE
CLASSES OF AMINO ACIDS: o TYROSINE
o NON-POLAR ALIPHATIC AA
*SULFHYDRYL GROUP – can form active part with
o Do not bind or give off protons 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 aqueous *CYSTEINE DIMER – reaction of 2 cysteine residues
environment to form a covalent S-S
 GLYCINE *IMINO RING – forms rings with NH2
 ALANINE *TRYPTOPHAN – precursor of SEROTONIN
 VALINE *TYROSINE – precursor of MELANIN
 LEUCINE

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*BUFFERS – solution that neutralizes a solution and LYSINE K

resists change HISTIDINE H
*pH – defined as the negative logarithm of the hydrogen PHENYLALANINE F
ion concentration TRYPTOPHAN W
PROLINE P
ESSENTIAL AMINO ACIDS – must be acquired from
external sources LESSON 3: PROTEINS
10 ESSENTIAL AA: PROTEINS – amino acids linked together by peptide
o PROLINE bonds; polypeptide chains
o VALINE PEPTIDE BONDS – amide linkages between the alpha
o TRYPTOPHAN carboxyl group of the AA and the alpha amino group of
o THREONINE another AA
o ISOLEUCINE
o METHIONINE CHARACTERISTICS OF PEPTIDE BONDS:
o HISTIDINE o PARTIAL DOUBLE BOND
o ARGININE o Bond in character
o LEUCINE o Not so long but not so short
o LYSINE o RIGID AND PLANAR
DENTISTRY CORRELATION – most common AA in o 2 AA can’t move freely
the enamel of the teeth: o Present in trans configuration
o GLYCINE o TRANS CONFIGURATION
o GLUTAMIC ACID o UNCHARGED BUT POLAR
o SERINE o Can’t give off protons (charge from terminal
*Mature enamel has a reduced PROLINE content ends and side chains) H-bonds
STEREOCHEMISTRY CIS – side chains are on the same side
o All AA are optically active except GLYCINE TRANS – side chains are on the opposite sides (stable)
o Alpha carbon is CHIRAL UNCHARGE – cannot give off protons; participates in
o It can exist in DEXTRO (right) or LEVO (left) form hydrogen bonds
o Mirror images
o Almost all AA are L-type WAYS OF DESTROYING PEPTIDE BONDS:
CHIRAL CARBON – are optically active carbons with o ENZYMATIC – by the use of enzymes
4 different chains attached to it and it produces polarized o NON-ENZYMATIC – by the use of heat and strong
light acid
NOMENCLATURE:
ABBREVIATIONS OF AMINO ACIDS: * -ic, -ine, -an = -yl
AMINO ACID: ABBREVIATION * N terminal is written to the left while C terminal is
written on the right
GLYCINE G
* C terminal AA remains as is
ALANINE A
*DEHYDRATION – forms peptide bonds
VALINE V
LEUCINE L
DETERMINATION OF PROTEIN COMPONENTS:
ISOLEUCINE I o ACID HYDROLYSIS
METHIONINE M
o Determines polypeptide bonds
SERINE S
o Hydrolyzed by adding a strong acid at 110˚C
THREONINE T
for 24hours
TYROSINE Y
o Cleaves the peptide bonds and releases free
CYSTEINE C
amino acids
ASPARTIC ACID D
o CHROMATOGRAPHY
ASPARGINE N
o CATION EXCHANGE
GLUTAMIC ACID E
CHROMATOGRAPHY
GLUTAMINE Q
 Separates the individual AA\
ARGININE R
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 ELUTION – adding buffer o GENETIC CODE – normal production of proteins

 ELUENT – washed off solute o POST TRANSLATIONAL MODIFICATION –
 The negative charge will come off quality control of AA and proteins
first and the strongly positive charge
will come off last because the LEVEL OF ORGANIZATION OF PROTEINS BY
RESIN is negatively charged STRUCTURES:
o QUANTITATIVE ANALYSIS o PRIMARY STRUCTURE
o NINHYDRIN – reagent that forms a purple o Sequence of AA in a protein
compound with most AA, ammonia and o SECONDARY STRUCTURE
amines o Regular arrangements of AA that are located
o SPECTROPHOTOMETER – measures near to each other in the linear sequence
the absorbance of light of each substance o ALPHA HELIX
 Most common polypeptide helix in
SEQUENCING OF PEPTIDE FROM ITS N- nature
TERMINAL:  Spiral, right handed
o PHENYLTHIOHYDANTOIN  Intra-chain H-bonds
DERIVATIVE(PTH)  Side chains are outward
o Provides stability to the N-terminal peptide  KERATIN – fibrous proteins
o EDMAN’S REAGENT  HEMOGLOBIN – globular
o Weakens AA bond and labels the AA at the proteins
N-terminal end  Disrupted by PROLINE; charged or
o Can only be used in small polypeptide bulky side chains
chains (less than 100AA) o BETA PLEATED SHEET
 Secondary structure where all
CLEAVAGE OF POLYPEPTIDES INTO SMALLER peptide bonds are involved in
FRAGMENTS: hydrogen bonding
o ENZYMATIC CLEAVAGE  Usually anti-parallel
o TRYPSIN – cuts the peptide bond at the C-  Hydrogen bonds are perpendicular
terminal end of LYSINE & ARGININE to the polypeptide backbone
o CHEMICAL CLEAVAGE (interchain)
o CYANOGEN BROMIDE – cuts the  Found in AMYLOID PROTEIN;
peptide bind at the C-terminal end of HEMOGLOBIN
METHIONINE o TERTIARY STRUCTURE
o OVERLAPPING PEPTIDES o Overall 3 dimensional shape of a protein.
o Use of both enzymatic and chemical Domains basic unit of structure
cleavage o Interactions stabilizing tertiary structure:
o DENATURING AGENTS  DISULFIDE BONDS
o Form multimeric proteins  HYDROPHOBIC
 UREA INTERACTIONS – non-polar
 GUANIDINE amino acids
HYDROCHLORIDE  HYDROGEN BONDS – SERINE,
 PERFORMIC ACID THREONINE, TYROSINE
*MULTIMERIC PROTEINS – multiple polypeptide  IONIC INTERACTIONS –
chain charged amino acids
o QUATERNARY STRUCTURE
*MONOMERIC PROTEINS – one polypeptide chain o Arrangement of multimeric proteins
o MULTIMERIC PROTEINS – with several
DETERMINATION OF PROTEIN STRUCTURE polypeptide subunits
BY DNA SEQUENCING o Subunits are held together by non-covalent
o Knowledge of the DNA sequence will allow us to interaction (HYDROPHOBIC
identify the AA sequence of a protein

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INTERACTIONS, H-BONDS, IONIC o KERATIN – fibrous proteins found in tough

BONDS) structures like skin, hair, nails, etc.
FUNCTIONS OF PROTEINS: o COMPONENTS OF KERATIN:
DEFENSE  CYSTEINE – stabilized by
o IMMUNOGLOBULINS/ ANTIBODIES disulfide bonds
o IgA o ELASTIN – fibrous proteins with rubber-like
o IgD properties found in the lungs and blood vessels
o IgE o COMPONENTS OF ELASTIN:
o IgM  SMALL NON-POLAR –
STRUCTURE GLYCINE, ALANINE, VALINE
o COLLAGEN – most abundant protein in the body TRANSPORT
o TYPES OF COLLAGEN: o HEMEPROTEINS – specialized proteins that
TYPES EXAMPLES contain heme as a tightly bound prosthetic group
I SKIN & BONES with a special function dedicated by the environment
II CARTILAGE created by the three dimensional structure of protein
III BLOOD VESSELS o CYTOCHROMES – electron carriers
IV BASEMENT MEMBRANE o CATALASE – active site of the enzyme
o HEMOGLOBIN & MYOGLOBIN – oxygen
binders
o COMPOSITION OF COLLAGEN – o HEME (PROTOPORPHIRIN IX & Fe) – capable of
always GLYCINE in 3rd position with carrying 1 molecule of oxygen
HYDROXYPROLINE or o MYOGLOBIN – stores and transports oxygen
HYDROXYLYSINE located within the muscle and heart (with single
o SYNTHESIS OF COLLAGEN: polypeptide chain and single heme group)
o Formation of o HEMOGLOBIN – found only in RBC; has 4
PREPROALPHACHAIN (produced polypeptide chains and a quaternary or 4 heme
in the ribosome) molecules which means it can carry 4 oxygen
o Cleavage with signal peptidase at molecules
the ROUGH ER o HbA – most common and abundant in a
(PROALPHACHAIN) normal body of an adult with 2 alpha chains
o Hydroxylation of PROLINE & and 2 beta chains
LYSINE (needs ASCORBIC ACID) o HbA2 – minor hemoglobin with 2 alpha
o Glycosylation chains and 2 beta chains
(HYDROXYLYSINE) of o HbF – fetal hemoglobin with 2 alpha chains
GLUCOSE or GALACTOSE at the and 2 sigma chains
ROUGH ER o HbAic – with 2 alpha chains and 1 beta
o Assembly and secretion at the glycose
GOLGI BODY (connected by *P50 – 50% of myoglobin or hemoglobin is saturated
disulfide bonds) *secreted to the P50 = 1mmHg
extracellular compartment
o Cleavage of polypeptide (N- ALLOSTERIC EFFECTORS – regulate the binding of
terminal peptidase and C-terminal oxygen
peptidase) o PO2 (HEME-HEME INTERACTION)–
o Formation of collagen fibrils cooperative binding
o Cross linking of LYSYL OXIDASE o pH (BHOR EFFECT) – an increase in the pH will
by COPPER decrease the affinity of hemoglobin to oxygen
*SCURVY – results into bleeding of gums, mouth sores, o 2,3 BPG – one of the products of glucose
petechiae, and loose teeth metabolism
*EHLER’S-CHANLOS SYNDROME – gene for
collagen is abnormal LESSON 4: ENZYMES

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ENZYMES – are proteins that catalyze reactions Km (Michaelis Constant) – refers to the affinity of the
without being destroyed in the process enzyme to the substrate. Numerically, it is the amount of
o OXIDOREDUCTASE – catalyzes oxidation substrate required to reach ½ of the v-max
and reduction
o TRANSFERASE – catalyzes transfer groups *Km is INVERSELY PROPORTIONAL to AFFINITY
o HYDROXYLASE – catalyzes cleavage bonds
by adding water FIRST ORDER KINETICS – at low substrate
o LIGASE – catalyzes the formation of bonds concentration, the velocity increases at direct proportion
o LYASE – catalyzes he cleavage of bonds to the amount of substrate
o ISOMERASE – catalyzes the racemization of
isomer groups ZERO ORDER KINETICS – at high substrate
concentration, the velocity is independent and not
PROPERTIES OF ENZYMES: proportional to the amount of substrate
o ACTIVE SITES
INHIBITION
o CATALYTIC EFFICIENCY
o ACCORDING TO REVERSIBILITY
o SPECIFICITY
o REVERSIBLE – if the complex is diluted,
o COFACTORS
substrate will be dissociated by adding an
o REGULATED inhibitor to the enzyme
o LOCATION o IRREVERSIBLE – the enzyme cannot do
its action and will not dissociate
FREE ENERGY OF ACTIVATION – the amount of o ACCORDING TO BINDING SITE
energy required to transform a reactant to a 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 can
*Enzymes catalyze reactions by decreasing the FREE
be reversed
ENERGY OF ACTIVATION in all reactions
 Km will change the V-Max
o NON-COMPETITIVE – doesn’t bind to
FACTORS AFFECTING THE VELOCITY OF
REACTOINS: the active site but binds to other portions of
o SUBSTRATE CONCENTRATION the substrate binding site
 Cannot be reversed because it
 V-MAX – maximum velocity or speed that the
changes the configuration
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 increase and
the velocity increase but it will eventually INHIBITORS – substances that diminishes the activity
decrease 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 ACTIVITY:
 TRYPSIN – neutral o SUBSTRATE AVAILABILITY – adding more
substrate will increase the velocity of reaction
MICHAELIS-MENTEN EQUATION – explains the o PRODUCT INHIBITION – adding inhibitors will
relationship between substrate concentration and
increase the affinity
velocity of reaction
o ALLOSTERIC CONTROL – enhances 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 means 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