Cover To Cover Biochemistry

Lecture 1
•Biochemistry: Origin of Life

•Branches of Biochemistry
•Foundations of Biochemistry
•Applications and Significance of
Biochemistry in the Medical field
The application of
chemistry to the
study of biological
processes at the
cellular and
molecular level.
• Structural Biochemistry
- study of the chemical
architecture of biological
macromolecules (proteins and
nucleic acids)
• Bio-organic Chemistry
- study of the organic
compounds found in
living things
• Enzymology
- study of the behavior of
biological catalysts or enzymes
(proteins, catalytic RNA and
coenzymes or cofactors)
• Metabolic Biochemistry
- study of the cellular
biochemical reactions
(metabolic pathways) that
make life possible
• Xenobiotics
- study of the metabolic behavior of
the compounds whose chemical
structure is not proper in the regular
metabolism of a given organism
• Immunology
- study interested in the reaction
of the organism to other
organisms such as bacteria and
viruses
• Virology
- study of elementary biosystems:
viruses. Both classification and
recognition, and its operation and
molecular structure.
• Molecular Genetics and
Genetic Engineering
- studies the genes, their
heritage, and their expression
• All living things make use of the same types of biomolecules,
and all use energy
simple molecules
ORIGIN such as H2O,
CH4 , CO2, NH3,
N2, and H2
Levels of
Structural
Organization in
the Human Body
Features of Living Organisms
• High degree of complexity and
microscopic organization
• Systems for extracting, transforming

and using energy from the
environment
• Defined functions for each of an
organism’s components and
regulated interactions among
them
• Mechanisms for sensing and

responding to alterations in their
surroundings.
• A capacity for precise self-
replication and self-assembly
• A capacity to change over time by

gradual evolution
• Cellular Foundations
• Chemical Foundations
• Physical Foundations
• Genetic and Evolutionary Foundations
Structure
of a Cell
Cytosol – concentrated
aqueous solution (enzymes,
coenzymes, RNA, inorganic
ions, metabolites etc.
• Classification
of prokaryotes
depending of
the habitats:
Aerobic (needs
oxygen) and
anaerobic
(nitrates,
sulfate, CO2
and CH4)
Cells build
supramolecular
structures
• Cellular make >99% of cell
up of living mass
organisms are
mostly
organic
compounds
(biomolecules)
• Functional
Groups are
group of
atoms that
show
characteristic
of physical
and chemical
properties
Macromolecules
• Protein – enzyme, structural
function, transport, signal
transduction etc.
• Nucleic Acids (DNA & RNA) –
storage and transmission of genetic
information
• Polysaccharides – energy storage
• Lipids – constituent of membrane
and energy storage
• No equilibrium
• Dynamic steady state
• Exchange energy and matter
• Energy conservation
• Enzymes promotes sequences of chemical
reactions
• Mutation – provides opportunity for
evolution
• Chemical evolution – generation of organic
compounds under primitive atmospheric
conditions
• Biological Evolution – photosynthetic
bacteria and multicellular eukaryotes
• The development of new drugs involves
chemical analysis and synthesis of new
compounds
• Clinical laboratory testing uses a wide variety
of chemical techniques and instrumentation for
analysis.
• All nursing students must be good at
pharmacology in order to be able to
administer the right drugs to patients.
Lecture 2
Basic
Organic Chemistry
TOPIC OUTLINE
• Organic Chemistry
• Characteristics and Properties of Organic
Compounds
• Hydrocarbons
• Drawing and Naming Structures of Organic
Molecules
ORGANIC CHEMISTRY
• The branch of chemistry that deals with
carbon compounds
• over 16 million carbon-containing compounds
are known
• because the C-C single bond (348 kJ/mol)
and the C-H bond (412 kJ/mol) are strong,
carbon compounds are stable
• carbon can form chains and rings
Properties of Organic Compounds
Organic Compounds Inorganic Compounds
• Bonding is almost entirely covalent • Most have ionic bonds
• May be gases, liquids, or solids • Most are solids with high melting
with low melting points (less than points
360° C) • Many are soluble in water
• Most are insoluble to water • Almost all are insoluble in organic
• Most are soluble in organic solvents
solvents such as diethyl ether, • Aqueous solutions conduct
toluene, and dichloromethane electricity
• Aqueous solutions do not conduct • Very few compounds can easily
electricity burn
• Almost all are flammable • Reactions are very fast
• Reactions are usually slow
HYDROCARBONS
• Group of compounds where all organic
compounds are derived
• Made up of only hydrogen and carbon
• Types:
• Aliphatic: do not contain the benzene group, or the
benzene ring
• Aromatic: contain one or more benzene rings.
TYPES OF ALIPHATIC HYDROCARBONS
• Alkanes
• Alkyl halides
• Cycloalkanes
• Alkenes
• Alkynes
FUNCTIONAL GROUPS
• A group of atoms that is largely responsible for
the chemical behavior of the parent molecule
• Composed of alcohols, ethers, aldehydes and
ketones, carboxylic acids, and amines
ALKANES
• Have the general formula CnH2n+2 where n=1, 2…
• Only single covalent bonds are present
• Known as saturated hydrocarbons because they contain
the maximum number of hydrogen atoms that can bond
with the number of carbon atoms present
• Structural isomers: Isomers that differ in the order in
which atoms are connected
ALKANES
Source: Reusch, W. (n.d.) Naming Organic Compounds. Retrieved from

https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/nomen1.htm
• have similar chemical properties
• have physical properties that vary in a regular manner as the
number of carbon atoms increases
• Example: the alkanes
ISOMERS
Isomers of C6H14
- (structural) isomers: compounds with the same
molecular formula but different structure
(arrangement of atoms)
• different isomers are completely different compounds
• have different physical properties such as melting point
and boiling point
STRUCTURAL FORMULA
Ways of representing organic compounds:
• Extended structural formula
• Condensed structural formula
• Bond line structural formula
Example: C3H8 – Propane; C3H6 – Cyclopropane

Extended structural formula
• unambiguously shows how the atoms are bonded
together
• can use Condensed structural formulas

• bonds are omitted, repeated groups put together,
side chains put in brackets
• CH3CH2CH2CH2CH2CH3
• or even CH3(CH2)4CH3
• CH3CH(CH3)CH3
Skeletal formula (line structural formula)
• Shorthand representation of molecule’s bonding

• every “corner” or “point of intersection) represents a
carbon
• Hydrogen atoms are implied
ALKENES
• Unsaturated hydrocarbons(also called olefins)
contain at least one carbon-carbon double bond.
• Alkenes have the general formula CnH2n, where
n is the no. of carbon atom
• The simplest alkene is C2H4, ethylene
• Used in the synthesis of many plastics and
commercially important alcohols
ALKENES
• The numbers in the names of alkenes refer to
the lowest numbered carbon atom in the chain
that is part of the C=C bond of the alkene
ALKYNES
• Unsaturated hydrocarbon that contain at least
one carbon-carbon triple bond.
• Alkynes have the general formula CnH2n-2,
where n is the no. of carbon atom
• Ethyne (Acetylene gas) is commonly used in
welding torches
ALKYNES
• The numbers in the names of alkenes refer to
the lowest numbered carbon atom in the chain
that is part of the C=C bond of the alkene
ALKYL HALIDES
• Contain halogen substituents which are fluorine,
chlorine, bromine, and iodine
CYCLOALKANES
• Have one or more rings of carbon atoms.
• General formula is composed of n carbons is CnH2n or (CH2)n
• Although a cycloalkane has two fewer hydrogen atoms than
the equivalent alkane, each carbon is bonded to four other
atoms so such compounds are still considered to be saturated
with hydrogen.

NAMING BRANCHED HYDROCARBONS
1. Find and name the longest continuous carbon chain. (Parent Chain)
2. Identify and name the ALKYL groups attached to this chain.
3. Number the chain consecutively, starting at the end nearest a
substituent group.
4. Designate the location of each substituent group by an
appropriate number and name. (Alphabetically)
5. Assemble the name, listing groups in alphabetical order using the
full name (e.g. cyclopropyl before isobutyl). The prefixes di, tri, tetra
etc., used to designate several groups of the same kind, are not
considered when alphabetizing.
NAMING ALKANES
NAMING ALKANES
C3H8 – Propane
NAMING ALKANES
C3H6 – Cyclopropane
SAMPLE PROBLEMS
Give the extended, condensed, and line structures
of the following compounds:
1. Hexane
2. Cyclohexane
3. 4-methylheptane
4. 5-sec-butyl-2,7-dichlorononane
5. 2-ethyl-1,1,3,3-tetramethylcyclopentane
EXAMPLES
• Write the line structure, extended and condensed
structural formula of the following hydrocarbons
1. 3,5,5-trimethyl-3-octene
2. 1,4-dichloro-3-methyl-1,4-pentadiene
EXAMPLES
• Write the line structure, extended and condensed
structural formula of the following hydrocarbons
1. 1-iodo-2-hexyne
2. 5,5,5-trichloro-1,3-penta-di-yne
SEATWORK
• Write the ff. based on the given names of the
hydrocarbons: (a) class of hydrocarbon; (b) extended
structural formula; c) condensed structural formula; and
(d) line structure.
1. 4,4,5-trimethyl-2-nonyne
2. 1,2-dibromo-2-methylpropane
3. 1,2-dichloro-4-ethyl-6-fluoro-2,3-hepta-di-ene
4. 1-ethyl-4-iodo-4-methyl-2,2-dinitrocyclooctane
SAMPLE PROBLEMS
Give the name of the following compounds:
LECTURE 3
Functional
Groups
TOPIC OUTLINE
• Class of Functional Groups
• Properties and Characteristics of each
Functional Groups
• Drawing and Naming Structures of Functional
Groups
• Identify common examples and their uses
ALCOHOL
PROPERTIES:
• Colorless at room temperature.
• Alcohols containing 4-10 carbon atoms are oily
and have heavier fruity odor.
• Alcohols containing more than 12 carbon atoms
are solid at room temperature.
• As their molecular weight increase (increase of
carbon chain), they become less soluble in water,
and the boiling point increases
ALCOHOL
GENERAL STRUCTURE:
R-OH
Nomenclature:
• IUPAC Naming System: change the –e from the
hydrocarbon name and add the suffix –ol
• Common Name: use the alkyl name and add
the word alcohol
ALCOHOL
Examples:
• Methanol is used as solvent, raw material for the
manufacture of formaldehyde and special resins,
special fuels and cleaning materials.
• Ethanol is used in toiletries, pharmaceuticals, fuels
and to sterilize hospital instruments. It is found
more on alcoholic beverages.
• Isopropyl alcohol (2-Propanol) is commonly used
as rubbing alcohol antiseptic, also used in
aftershave lotions, hand lotions, and other
cosmetics.
ALCOHOL
CARBOXYLIC ACIDS
PROPERTIES:
• They are considered weak acids.
• The solubility of carboxylic acids in water is similar to that of
alcohols, aldehydes, and ketones. Acids with fewer than about five
carbons dissolve in water; those with a higher molecular weight are
insoluble owing to the larger hydrocarbon portion, which is
hydrophobic.
• They have much higher boiling points than hydrocarbons, alcohols,
ethers, aldehydes, or ketones of similar molecular weight.
• Unbranched-chain carboxylic acids (fatty acids) that are liquids at
room temperature, especially those from propanoic to decanoic acid,
have very foul, disagreeable odors. Most common are acetic acid
(vinegar) and butyric acid (human vomit). Conversely esters of
carboxylic acids tend to have pleasant odors and many are used in
perfume.
CARBOXYLIC ACIDS
GENERAL STRUCTURE:
R-COOH
Nomenclature:
• IUPAC Naming System: add the suffix –oic
plus the word ‘acid’
• Common Name: use the appropriate prefix of
the common names and add the suffix –ic plus
the word ‘acid’
CARBOXYLIC ACIDS
Examples:
• Formic Acid - (systematically called methanoic
acid) is the simplest carboxylic acid. It is an
important intermediate in chemical synthesis and
occurs naturally, most famously in the venom of bee
and ant stings.
• Acetic Acid – also called ethanoic acid, the most
important of the carboxylic acids. A dilute
(approximately 5 percent by volume) solution of
acetic acid produced by fermentation and
oxidation of natural carbohydrates is called
vinegar.
ETHERS
PROPERTIES:
• At room temperature, ethers are pleasant-
smelling colorless liquids. Relative to alcohols,
ethers are generally less dense, are less
soluble in water, and have lower boiling points.
• The solubility decreases with increase in the
number of carbon atoms. Ethers are
appreciably soluble in organic solvents like
alcohol, benzene, acetone etc.
ETHERS
GENERAL STRUCTURE:
R-O-R
Nomenclature:
• IUPAC Name: add the suffix –oxy to the shortest carbon
chain and name longest parent chain based on the
hydrocarbon prefixes
• Common Name: identify the alkyl group attached to the
oxygen atom and arranged them alphabetically and add the
word ether
ETHERS
EXAMPLES:
• Diethyl ether, which is extremely flammable
and was one of the first anesthetics used in
surgery. Due to its anesthetic effects, ether is
also used as an illicit drug to induce sedation
and euphoria.
• Dimethyl ether (DME) a low boiling solvent, a
refrigerant and an environmentally propellant
for spray cans
ESTERS
PROPERTIES:
• Boiling point is lower than alcohols and carboxylic
acid.
• Cannot form hydrogen bonds because they do not
have a hydrogen atom bonded to an oxygen
atom.
• Solubility: it rapidly decreases with increasing
carbon chain length.
• Most have pleasant odors (fruity scents) such as
raspberry, banana, pear, apple, and pineapple
ESTERS
GENERAL STRUCTURE:
R-COOR
Nomenclature:
• IUPAC Name: use the alkyl name of the alcohol chain
and change the suffix –oic of the carboxylic acid
chain to –oate
• Common Name: use the alkyl name of the alcohol
chain and use the common suffix for carboxylic acid
and add the suffix –oate or -ate
ESTERS
ALDEHYDE
PROPERTIES:
• The lower members (up to 4 carbons) of aldehydes and
ketones are soluble in water due to H-bonding. The
higher members do not dissolve in water because the
hydrocarbon part is larger and resists the formation of
hydrogen bonds with water molecules.
• The boiling point of aldehydes and ketones is higher than
that of non-polar compounds (hydrocarbons) but lower
than those of corresponding alcohols and carboxylic
acids as aldehydes and ketones do not form H-bonds with
themselves.
ALDEHYDE
GENERAL STRUCTURE:
R-CHO
Nomenclature:
• IUPAC Name: change –e from the hydrocarbon name
and add the suffix –al to the parent chain
• Common Name: use the prefix table for the common
name and add the suffix –aldehyde
ALDEHYDE
EXAMPLES:
• Vanillin from the vanilla bean and cinnamaldehyde,
which provides the smell and flavor of cinnamon.
• Aldehydes and ketones impart some very characteristics
fragrance in compounds. For instance, ketones help in the
formation a compound “acetophenone” which is
responsible for fragrances such as cherry, jasmine,
honeysuckle, almond, strawberry, etc.
• Formaldehyde – formalin
• Benzaldehyde – perfumes, cosmetic products and dyes
• Glue preparation and polymeric products, plastics,
coatings and adhesives
KETONE
PROPERTIES:
• Colorless liquid, pleasant smell, and highly reactive.
• Ketones are soluble in water. It is a hydrogen-bond
acceptor, but not a hydrogen-bond donator, and cannot
hydrogen-bond to itself. This makes ketones more volatile
than alcohols and carboxylic acids of similar molecular
weight.
• Boiling point is higher than hydrocarbons and ethers but
lower boiling point than those of alcohols of similar
molecular masses
KETONE
GENERAL STRUCTURE:
R-COR
Nomenclature:
• IUPAC Name: change –e from the hydrocarbon
name and add the suffix –one to the parent
carbon chain
• Common Name: use the prefix table for the
common name and add the suffix –one
KETONE
EXAMPLES:
• Acetone, also known as propanone used in
manufacture of plastics and other industrial
products limited extent in household products
and byproduct of metabolism.
• Cortisone a steroid prevents the release of
substances in the body that cause
inflammation.
•Acetophenone used as a chemical in a
perfume it has an aromatic odor
AMINES
PROPERTIES:
• Amines are compounds that contain a basic nitrogen atom
with a lone pair. Amines are formally derivatives of ammonia
(NH3), wherein one or more hydrogen atoms have been
replaced by a substituent such as an alkyl or aryl group.
• The lower aliphatic amines are gaseous in nature with a fishy
or rotting smell
• Primary amines with three or four carbon atoms are liquids
at room temperature whereas higher ones are solids.
• Lower aliphatic amines can form hydrogen bonds with water
molecules, hence they are soluble in water.
AMINES
PROPERTIES:
• Primary Amines - Only one of the hydrogen atoms in the
ammonia molecule has been replaced. That means that the
formula of the primary amine will be RNH2 where "R" is an
alkyl group.
• Secondary Amines - Two of the hydrogens in an ammonia
molecule have been replaced by hydrocarbon groups.
• Tertiary Amines - In a tertiary amine, all of the hydrogens
in an ammonia molecule have been replaced by
hydrocarbon groups.
AMINES
GENERAL STRUCTURE:
Nomenclature:
• IUPAC Name: add the suffix –amine to the parent
carbon chain
• Common Name: identify the alkyl group attached to
the nitrogen atom and arranged them alphabetically
and add the word amine
AMINES
EXAMPLES:
• Morphine, C17H19NO3 – Analgesics or pain-killers, help relieve
moderate to severe pain.
• Methamphetamine, also known as crystal meth or meth, is a highly
addictive drug. It is an artificial substance made from very toxic
materials, which can cause serious harm or death when handled or
inhaled
• Ephedrine, C10H15NO - medication and stimulant, often used to prevent
low blood pressure during spinal anesthesia
• Chlorpheniramine is an antihistamine that helps to relieve allergic
disorders due to cold, hay fever, itchy skin, insect bites and stings.
• Chlorpromazine is a tranquilizer that sedates without inducing sleep. It
is used to relieve anxiety, restlessness or even mental disorder
AMIDES
PROPERTIES:
• Melting point - although it is liquid, the other
higher carbon chain of amides are solid at room
temperature
• Solubility -low amides are soluble in water they
can have hydrogen bond with water molecules.
amides both act as hydrogen bond donor and
acceptor
• Basicity - amides show no measurable basicity
AMIDES
GENERAL STRUCTURE:
R-CONH2
Nomenclature:
• IUPAC Name: add the suffix –amide to the parent
carbon chain
• Common Name: identify the alkyl group attached to the
nitrogen atom and arranged them alphabetically and add
the word amide
AMIDES
EXAMPLES:
• Acetaminophen, common names: Tylenol, Paracetamol,
Panadol used as an aspirin substitute. It acts to reduce
fever and pain.
• Barbiturates are depressant drugs used to induce
sleep and release tension and use to treat seizure
disorder and severe trauma in the skull.
• Urea is used to treat dry or rough skin condition and
some nail problems (ingrown nails) and also used to
remove dead tissues and serves as a fertilizer
THIOLS
PROPERTIES:
•Lower melting and boiling points than alcohol
•Lower solubility in water and have nauseating
aromas
•It consists of a sulfhydryl group
•Cysteine is an amino acid that forms disulfide
bonds when oxidized.
THIOLS
GENERAL STRUCTURE:
R-SH
Nomenclature:
• IUPAC Name: retain the name of the alkane
and add the suffix -thiol
THIOLS
Examples: Draw the structures of the following thiols
•1,3-butanedithiols
•2-methyl-2pentanethiol
•2-chloro-2-propanethiol
•cyclopentanethiol
Lecture 4
TOPIC OUTLINE
• Chirality of Organic Molecules
• Functions and Classifications of Carbohydrates
• Enantiomers, Diastereomers and Epimers
• Draw structures using Fischer Projection and
Haworth Projections
• Reactions of monosaccharides
• Disaccharides, Oligosaccharides and
Polysaccharides
Chirality of Organic Molecules
• Stereochemistry -
the three-
dimensional structure
of molecules (spatial
orientation)
• Stereoisomers –
same molecular
formula, same
bonding patter, but
differ in spatial
orientation
• Chirality - essentially means 'mirror-image, non-
superimposable
HN molecules'
HN
O
O OO
CH33
NHCH
NH CH33NH
CH NH
Cl
Cl Cl
Cl
(S)-ketamine (R)-ketamine
anesthetic hallucinogen
• Chiral Molecule – must have one or more ‘chiral
centers’, ‘asymmetric carbon’ or ‘stereocenters’
• How many
H OH H H CH3 CH2CH3
chiral H H H
H C C C C H H3C
centers are
H H H H
found in
each
Br
structure? Br Br
Br H CH
3
• Chiral
Molecule – non
superimposable
mirror images
• Achiral
Molecule –
superimposable
mirror images
(identical)
Functions of Carbohydrates
• represented as CHO (often called sugars); general
formula Cn(H2O)n (for monosaccharides)
• Generally defined as polyhydroxy aldehydes or
ketones or substances that yield these compounds when
hydrolyzed
• Major sources of energy for the body
• Oligosaccharides play a key role in processes that take
place on the surface of the cells
• Polysaccharides are essential structural components of
bacterial cell walls and some classes of organisms
Classifications of Carbohydrates
1. MONOSACCHARIDE
• a carbohydrate that cannot be
hydrolyzed to a simpler
carbohydrate
• Building blocks of all
carbohydrates
• ALDOSE: a monosaccharide
containing an aldehyde group
• KETOSE: a monosaccharide
containing a ketone group
• The most common
monosaccharides in
nature are the
aldohexose D-glucose,
and the ketohexose D-
fructose.
• The aldopentoses D-
ribose and 2-deoxy-D-
ribose are components
of nucleotides and nucleic
acids.
Fischer Projections and the D, L Notation
Fischer projection: bonds are
written in a two dimensional
representation showing the
configuration of tetrahedral
stereocenters
• horizontal lines represent bonds
projecting forward
• vertical lines represent bonds
projecting to the rear
• the carbon atom at the
intersection of the horizontal
and vertical lines is not shown
According to the conventions
proposed by Fischer
• D-monosaccharide: a
monosaccharide that, when
written as a Fischer projection,
has the -OH on its penultimate
carbon on the right
• L-monosaccharide: a
monosaccharide that, when
written as a Fischer projection,
has the -OH on its penultimate
carbon on the left
Enantiomers:
• stereoisomers that are mirror
images
• example: D-erythrose and L-
erythrose are enantiomers
Diastereomers:
• stereoisomers that are not mirror
images
• example: D-erythrose and D-
threose
STRUCTURES OF D-ALDOSES
STRUCTURES OF D-KETOSES
Cyclic Sugars (Formation of a Cyclic Hemiacetal)
• Cyclization of sugars takes
place due to interaction
between functional groups
of aldehyde and alcohol
on distant carbons, C1 to
C5, to make a cyclic
hemiacetal
• Cyclization using C2 to C5
of ketones and alcohol
results in hemiketal
formation.
• In both cases, the carbonyl
carbon is new chiral center
and becomes an anomeric
carbon
Haworth Projections
• five- and six-membered
hemiacetals are represented as
planar pentagons or hexagons,
as the case may be, viewed
through the edge
• most commonly written with
the anomeric carbon on the
right and the hemiacetal oxygen
to the back right
• the designation - means that -
OH on the anomeric carbon is
cis to the terminal -CH2OH; -
means that it is trans
Haworth Projections
2 Hemiacetal Forms of D-glucose:
• Alpha-form (): -OH of C1 and CH2OH are on opposite sides
• Beta-form (): -OH of C1 and CH2OH are on same sides
6 6
CH2 OH Anomeric CH 2OH
O Carbon O OH
5 5
4 1
OH 4 OH
1
2 OH 2
OH OH
3 3 Anomeric
OH OH Carbon
a-D-Glucose b-D-Glucose
Comparison of Fischer and Haworth Projections
Converting Fischer Formula to Haworth Projections
1. Assign numbers for carbon atoms in the
Fischer stereochemistry
2. For C2-C4, consider the –OH group on right
side written downward and the -OH group
on the left side written upward in the
Haworth structure.
3. For C1(anomeric carbon), the –OH group is
either “up” or “down” depending on which
face of the carbonyl is attacked
For C1:
• the - anomer has –OH → down ( for D-sugars)
• the - anomer has –OH → up (for D-sugars)
1. Assign numbers for carbon atoms in the
Fischer stereochemistry
2. For C2-C4, consider the –OH group on right
side written downward and the -OH group
on the left side written upward in the
Haworth structure.
3. For C1(anomeric carbon), the –OH group is
either “up” or “down” depending on which
face of the carbonyl is attacked
For C1:
• the - anomer has –OH → down ( for D-sugars)
• the - anomer has –OH → up (for D-sugars)
4. For C5, if –OH is on the right side of
the Fischer, it’s a D-sugar. This will
place the C6 on the top of the
Haworth projection. If–OH is on the
left side, it’s an L-sugar so the C6 is
written at the bottom of the structure
Example:
• Convert D-mannose to a Haworth in the -
pyranose configuration
• Convert L-galactose to a Haworth in the  -
pyranose configuration
• Convert D-sorbose to a Haworth in the  -
furanose configuration
Converting Haworth Projections to Fischer Formula
Convert the ff. Haworth Projections to Fischer
Projections Formula
2. DISACCHARIDE
•a carbohydrate
composed of 2
monosaccharide
groups and can be
broken down into
simple sugars
Glycosidic Bond Formation
• Glycoside: a carbohydrate in which the -OH of
the anomeric carbon is replaced by -OR
• those derived from furanoses are furanosides; those
derived from pyranoses are pyranosides
• Glycosidic Bond: the bond from the anomeric carbon
to the -OR group
• This is the basis for the formation polysaccharides
and oligosaccharides
Condensation Polymerization – dehydration
H 2O
H H H H
HO C C
HO
+ HO C C
HO
H H Leaves an H H
monomer oxygen bridge monomer
H H H H
+
O HO
HO C C C C H 2O
H H H H
polymer
Glycosidic Bond Formation
Two Different Disaccharides of D-Glucose
• Glycosidic linkages can take various forms; the anomeric
carbon of one sugar to any of the -OH groups of another
sugar to forma an - or -glycosidic linkage
• Disaccharides can be broken into simple sugar units by
the hydrolysis reaction:
Disaccharide + water → 2 monosaccharides
Examples:
• Sucrose + water → glucose + fructose
• Lactose + water → galactose + glucose
• Maltose + water → glucose + glucose
• Trehalose + water → glucose + manose
Important Dissaccharides
SUCROSE
• A common table sugar extracted from sugarcane and sugar beets
• non reducing sugar (no free aldehyde or ketone in its structure)
• One unit of D-glucose and one unit of D-fructose joined by an a-1,2-
glycosidic bond
LACTOSE
• Milk sugar (breast milk -7% and cow’s milk –
4.7%)
• Made up of D-galactose and one unit of D-
glucose joined by a b-1,4-glycosidic bond
(reducing sugar)
MALTOSE
• Two units of D-glucose joined
by an a-1,4-glycosidic bond
• Formed from the hydrolysis of
starch
• Differs from cellobiose by the
conformation of the glycosidic
linkage
CELLOBIOSE
- hydrolyzed from cellulose
- white crystalline water-
soluble disaccharide. It is
made up of two molecules
of glucose joined by β-(1-
4)-glycosidic bond
- can be digested by
ruminants
3. OLIGOSACCHARIDES
• a carbohydrate composed
of 3 or more
monosaccharide groups
and can be broken down
into simple sugars
Ex. Raffinose: found in
sugar beet, cotton seed, and
many grains
Raffinose + water →
glucose + fructose +
galactose
REACTIONS OF MONOSACCHARIDES
OXIDATION: strong oxidizing agents can oxidize both ends of a
monosaccharide at the same time (the carbonyl group and the terminal primary
alcohol group) to produce a dicarboxylic acid
- such polyhydroxy dicarboxylic acids are known as aldaric acids.
- Ex. Oxidation using Tollen’s reagent (aldonic acid)
REDUCTION: The carbonyl group in a monosaccharide
(either an aldose or a ketose) is reduced to a hydroxyl group
using hydrogen as the reducing agent (alditols)
- Ex. Sorbitol - used as moisturizing agents in foods and
cosmetics and as a sweetening agent in chewing gum
H2 , Pt or Ni
PHOSPHATE ESTER FORMATION: The hydroxyl groups of a
monosaccharide can react with inorganic oxyacids to form inorganic
esters.
- Phosphate esters of various monosaccharides are stable in aqueous
solution and play important roles in the metabolism of carbohydrates.
4. POLYSACCHARIDE
• a carbohydrate composed of 7
or more units of
monosaccharide.
• Important in structural supports,
particularly in plants and serves
as storage depot for
monosaccharides
• Homopolysaccharides – 1 type of
monomer
• Heteropolysaccharides – 2 or more
types of monomer
Structure and Functions of Polysaccharides
CELLULOSE
• the major structural component
of plants, especially wood and
plant fibers
• a linear polymer of
approximately 2800 D-glucose
units per molecule joined by b-
1,4-glycosidic bonds
• fully extended conformation with
alternating 180° flips of glucose
units
• extensive intra- and
intermolecular hydrogen bonding
between chains
STARCH
• is used for energy storage in plants
• a polymers of -D-glucose units
• amylose: continuous, unbranched chains of up to 4000 -D-glucose
units joined by -1,4-glycosidic bonds
• amylopectin: a highly branched polymer consisting of 24-30 units of D-
glucose joined by -1,4-glycosidic bonds and branches created by -1,6-
glycosidic bonds
• amylases catalyze hydrolysis of -1,4-glycosidic bonds
• -amylase is an exoglycosidase and cleaves from the nonreducing end of the
polymer
• -amylase is an endoglycosidase and hydrolyzes glycosidic linkages anywhere
along the chain to produce glucose and maltose
• debranching enzymes catalyze the hydrolysis of -1,6-glycosidic bonds
STARCH IODINE-STARCH COMPLEX
• GLYCOGEN: Human and
animal storage polysaccharide
• Branched chain polymer
(contains only glucose units ) –
alpha (1→4) glycosidic bonds in
straight chains and alpha (1→6)
in branches
• Molecular Mass: 3,000,000 (up
to 1,000,000 glucose units)
• Three times more highly Glycogenesis
branched than amylopectin in Glucose Glycogen
Glycogenolysis
starch
• Excess glucose in blood stored in
the form of glycogen
• CHITIN: the major structural component of the exoskeletons of
invertebrates, such as insects and crustaceans; also occurs in cell walls of
algae, fungi, and yeasts
• composed of units of N-acetyl--D-glucosamine joined by -1,4-
glycosidic bonds
Acidic Polysaccharides
• Acidic Polysaccharides – these are heteropolysaccharides
contains repeating disaccharide unit containing an amino sugar
and a sugar with a negative charge due to a sulfate or a
carboxyl group.
• Structural polysaccharide present in connective tissue associated
with joints, cartilage, synovial fluids in animals and humans
• Primary function is lubrication necessary for joint movement
Structure and Functions of Acidic Polysaccharides
• Glycosaminoglycans: linear
acidic polysaccharides
classified according to structure
and families:
• Heparin: natural anticoagulant
• Hyaluronic acid: a component
of the vitreous humor of the eye
and the lubricating fluid of
joints
• Chondroitin sulfate and
keratan sulfate: components of
connective tissue
Structure and Functions of Acidic Polysaccharides
Glycoproteins: CELL RECOGNITION
Glycoproteins: contain
carbohydrate units covalently
bonded to a polypeptide chain
• antibodies are glycoproteins
• Oligosaccharide portion of
glycoproteins act as antigenic
determinants
• Among the first antigenic
determinants discovered were the
blood group substances
• In the ABO system, individuals are
classified according to four blood
types: A, B, AB, and O
Glycoproteins
Important Polysaccharides
Nutrition: Dietary Considerations
• Glycemic Food: A developing concern about intake of carbohydrates involves how
fast the given dietary carbohydrates are broken down to glucose within the human body
• Glycemic effect refers to: 1. how quickly carbohydrates are digested; 2. how high
blood glucose rises; and 3. how quickly blood glucose levels return to normal
Nutrition: Dietary Considerations
• The Dietary Guidelines for Americans (2015-2020) recommends
that carbohydrates make up 45 to 65 percent of your total daily
calories.
• So, if you get 2,000 calories a day, between 900 and 1,300
calories should be from carbohydrates. That translates to between
225 and 325 grams of carbohydrates a day.
• Philippines Dietary Reference Intake (2015): For Filipinos aged
19 years and above, the recommended intake of carbohydrates is
55% to 75% of the total energy intake. The recommended energy
intake of 1,930 kcal for females aged 19 to 29 years old should
therefore have 1,060 kcal to 1,450 kcal of carbohydrates, or
about 265 to 365 grams a day
BIOCHEMISTRY (MIDTERMS) Classification Based on Biochemical Function
For purposes of simplicity of study, lipids are divided into

LIPIDS five categories based on their biochemical function.
Topic Outline 1. Energy-storage lipids – triacylglycerols
 Structure and Classification of Lipids 2. Membrane lipids – phospholipids,
 Type of Fatty Acids sphingoglycolipids, and cholesterol
3. Emulsification lipids – bile acids
 Physical Properties of Fatty Acids
4. Chemical messenger lipids – steroid hormones
 The Chemical Natures of Lipid Types
and eicosanoids
 Biological Membranes
5. Protective-coating lipids – biological waxes
 Membrane Proteins
 The Function of Membranes Classification Based on Saponification
 The Lipid-Soluble Vitamins
Saponification reaction: Hydrolysis reaction that occurs
Lipids in a basic solution.
 An organic compound found in living organisms Based on saponification reaction, lipids are divided into
that is insoluble (or only sparingly soluble) in two categories:
water but soluble in non-polar organic
1. Saponifiable lipids – triacylglycerols,
solvents.
phospholipids, sphingoglycolipids, and biological
 Contains long chain of hydrocarbons (C-H) bonds
waxes
 Amphipathic in nature
2. Nonsaponifiable lipids – bile acids, steroid
 Classification of Lipids: hormones, and eicosanoids
o Biochemical Function
o Saponification (hydrolysis under basic Structure of Lipids
conditions)
 Lipids exhibit structural diversity
 Some are esters, some are amides, and some
are alcohols (acyclic and cyclic), and some are
polycyclic.
 Interaction of biochemical compounds with water

o When placed in water, amphipathic
molecules form structures such as
micelles, which attempt to address the Fatty Acids
conflict.
 An unbranched-chain carboxylic acid, most
commonly of 12-20 carbons, derived from
hydrolysis of animal fats, vegetable oils, or
phosphodiacylglycerols of biological membranes
 Even # of Carbon atoms: (a) Long chain fatty
acids: C12 - C26 (b) Medium chain fatty acids: C6
- C11 (c) Short-chain fatty acids: C4 - C5
 Two Types of Fatty Acids:
o Saturated – all C-C bonds are single
bonds
o Unsaturated
 Monounsaturated: one C=C
bond
 Polyunsaturated: 2 or more
C=C bonds present – up to 6
double bonds are present in fatty
acids.
Essential Fatty Acids
 Alpha Linolenic Acid (ALA)

o Found in plants (flaxseed, walnuts,
canola, and soybean)
 DHA and EPA
o Marine sources
o Produced by microalgae (anchovies,
mackerel, salmon, and sardines)
 Eicosapentaenoic Acid – an
omega-3 fatty acid found in the
flesh of cold-water fish like
mackerel, tuna, salmon, etc.
 Docosahexaenoic Acid – an
omega-3 fatty acid that is a
primary structural component of
the human brain, cerebral cortex,
skin, and retina. It can be
synthesized from ALA or
obtained directly from maternal
milk, fish oil, or algae oil.
 Linoleic Acid
o Found in safflower, corn, and soybean
oils
 Arachidonic Acid
o Fish, meat, and eggs
o Precursor of eicosanoids
Example of Common Fatty Acids
Properties of Fatty Acids
 The common fatty acids found in biological
systems are shown in Table 8.1  Water solubility: Short chain fatty acids are
sparingly soluble whereas long chain fatty acids
are insoluble
 Melting point: depends upon:
o Length of carbon chain
o Degree of unsaturation (number of
double bonds in a molecule)
 Omega Fatty Acids

o Nutritionally important Omega-3 and
Omega-6 fatty acids
 Linolenic acid – Omega-3
 Linoleic acid – Omega-6
 Linoleic Acid Deficiency
o Skin redness – becomes irritated
o Infections and dehydration
o Liver abnormalities
o Children need it the most
 Space-Filling Molecules: the numbers of bends  Hydrogenation – addition of hydrogen across
in a fatty acid chain increase as the number of double (=) bond and increases degree of
double bonds increase. saturation
o Less packing occurs
o Melting point is lower
o Tend to be liquids at room temperature
o Kink – the bent part
 Many food products are produced by partial

hydrogenation of oils and fats
o Peanut oil + H2 = Peanut Butter
o Vegetable oil + H2 = Margarine
 Partial Hydrogenation – produces trans fat
Triacylglycerols (Triglycerides)
 Simplest lipid constructed from fatty acids

 An ester of glycerol with three fatty acids
 Natural soaps are prepared by boiling
triglycerides (animal fats or vegetable oils) with
NaOH, in a reaction called Saponification (Latin,
sapo, soap)
 Triglycerides are energy storage form of fatty

acids in mammals.
 Often when blood tests are done, they measure
your triglyceride levels.
 High triglyceride levels in the blood are a risk
indicator for atherosclerosis (a disease of the
arteries characterized by the deposition of
plaques of fatty material on their inner walls)
 Soaps form water-insoluble salts when used in
water containing Ca(II), Mg(II), and Fe(III) ions
(hard water)
 Reactions with acids/bases as catalysts
 Salts formed by saponification
 Triglycerides made from unsaturated fatty acids

have lower melting points than those made from
saturated fatty acids.
 Triglycerides from animals tend to have a
higher proportion of saturated fatty acids.
o Most are solids at room temperature and
are called fats.
o Examples include: butter, lard, and
bacon grease.
 Triglycerides from plants tend to have a higher
proportion of unsaturated fatty acids.
o Most are liquids at room temperature and
are called oils.
o Examples include: corn oil, canola oil,
peanut oil, and olive oil.
Phosphoacylglycerols (Phospholipids)  There are two types of phospholipids:
o Glycerophospholipid
 When one alcohol group of glycerol is esterified  A lipid that contains two fatty
by a phosphoric acid rather than by a carboxylic acids and a phosphate group
acid, phosphatidic acid is produced. esterified to a glycerol molecule
 The second most abundant group of naturally and an alcohol esterified to the
occurring lipids, and they are found in plant and phosphate group.
animal membranes.  All attachments (bonds) between
groups in a Glycerophospholipid
are ester linkages.
 Up to 80% of the mass of a cell membrane can

be lipid materials – dominated by phospholipids.
 Phospholipid: contains one or more fatty acids,
a phosphate group, a platform molecule (glycerol o Sphingolipids
or sphingosine) to which the fatty acid(s) and the  Function similarly to the
phosphate group are attached, and an alcohol glycerophospholipids, but
that is attached to the phosphate group.
structurally different.
 The glycerol and one of the fatty
acids is replaced with a molecule
called sphingosine.
 Like the soaps, these molecules are highly

amphipathic, and when mixed with water
spontaneously form membranes that are
described as lipid bilayers.
 The classification of phosphatidyl ester

depends on the nature of the second alcohol
esterified to phosphoric acid.
 Phospholipids are used commercially as Biological Waxes
emulsifying agents.
o Lecithin – another name for the  A complex mixture of esters of long-chain
phospholipid phosphatidylcholine, is carboxylic acids and alcohols.
used as an emulsifying agent in  Found as protective coatings for plants and
mayonnaise and other prepared foods. animals.
o Cephalin – for blood coagulation (enter
the structure of thromboplastin)
 Glycolipid: a compound in which a carbohydrate

is bound to an –OH of the lipid.  Myricyl cerotate – a wax found in beeswax and
 In most cases, sugar is either glucose or carnauba wax
galactose.  Cetyl palmitate – ester of cetyl alcohol and
 Many glycolipids are derived from ceramides palmitic acid; a naturally occurring fatty acid
(composed of sphingosine and a fatty acid) found in plants and animals.
 Glycolipids with complex carbohydrate moiety
that contains more than 3 sugars are known as Steroid Hormones
gangliosides.
 A group of lipids that have fused-ring structure of
3 six-membered rings, and 1 five-membered ring.
 Derivatives of cholesterol
 Two major classes of steroid hormones:
o Sex hormones – control reproduction
and secondary sex characteristics
o Adrenocorticoid hormones – control
numerous biochemical processes in the
body
 Steroid Sex Hormones

o Androgen: male sex hormones
 Synthesized in the testes
 Responsible for the development
of male secondary sex
characteristics
 Testosterone
o Estrogens: female sex hormones
 Synthesized in the ovaries
 Responsible for the development
of female secondary sex
characteristics and control of the
menstrual cycle
 Prostaglandin
o Cyclopentane ring and oxygen-
 Testosterone – primary sex hormone and containing functional groups
anabolic steroid in males o Raising body temperature
 Progesterone – female hormone important for o Inhibiting the secretion of gastric juices
the regulation of ovulation and menstruation o Increasing the secretion of a protective
 Estradiol – a form of estrogen, a female sex mucus layer into the stomach
hormone that regulates many processes in the o Relaxing and contracting smooth muscle,
body and responsible for the development of directing water and electrolyte balance,
female secondary sexual characteristics such as intensifying pain, and enhancing
the breasts, widening of the hips, etc. inflammation responses.
Adrenocorticoid Hormones
 Produced by adrenal glands

 Glucocorticoid: control glucose metabolism and
counteract inflammation
 Mineralocorticoids: control the balance of Na
and K ions in cells.
 Thromboxane
o Cyclic ether ring and oxygen-containing
functional groups
o Promote platelet aggregation
 Aldosterone – a corticosteroid hormone which

stimulates absorption of sodium by the kidneys
and so regulates water and salt balance.
 Leukotriene
 Cortisol – “fight-or-flight” hormones; designed to
o Derivative containing three conjugated
let you know when you’re in danger.
double bonds and hydroxyl groups
Eicosanoids o Promote inflammatory and
hypersensitivity (allergy) responses
 Arachidonic acid (20:4) derivatives
 Have profound physiological effects at extremely
low concentrations
 Short-lived hormone-like molecules
 Physiological effects of eicosanoids
o Inflammatory response
o Production of pain and fever
o Regulation of blood pressure
o Induction of blood clotting
o Regulation of the sleep/wake cycle
Bile Acids  Cholesterol molecules are also components of
plasma membranes
 Polar derivatives of cholesterol made in the liver,  Cholesterol helps regulate membrane fluidity –
that act as detergent in the intestine, emulsifying
the fused ring system does not allow rotation of
dietary fats to make them more accessible to fatty acid tails in the vicinity
digestive enzymes.
 Fits between fatty acid chains of the lipid bilayer:
make it rigid
 Cholesterol thus acts a membrane plasticizer
 The higher the temperature, the wider the space
the cholesterol makes.
Saponifiable VS. Nonsaponifiable Lipids  The cell membranes also contain PROTEINS
 Responsible for moving substances such as
 Saponifiable Lipid: A lipid that undergoes nutrients and electrolytes across the membrane
hydrolysis in a basic solution to yield 2 or more  Receptors for hormones and
small molecules. neurotransmitters
 Saponification is possible in molecules that  Acts as markers: process by which different cells
contain the following linkages (bonds): recognize each other
 Ester, Amide, and Glycosidic  Every protein as its own neurotransmitter.
 Saponifiable Lipids:
o Triacylglycerols
o Glycerophospholipids
o Sphingophospholipids
o Sphingoglycolipids
o Biological waxes
 Nonsaponifiable Lipids:
o Cholesterol
o Bile acids
o Steroid hormones
o Eicosanoids
Biological Membranes Fluid Mosaic Model

 Cells are surrounded by plasma membranes  Fluid: there is lateral motion of components in the
 Separates aqueous interior of a cell from the membrane;
aqueous environment surrounding the cell  Proteins, for example, “float” in the membrane
 The presence of cholesterol is characteristic of and can move along its plane
animal rather than plant membranes  Mosaic: components in the membrane exist side-
 Bilayer: Nonpolar tails of phospholipids in the by-side as separate entities
middle and polar heads are on the surface.  The structure is that of a lipid bilayer with proteins,
 The membrane is a liquid like structure due to glycolipids, and steroids such as cholesterol
unsaturation in lipid tails. embedded in it.
Membrane Function: Membrane Transport  Vitamin A participates in the visual cycle in rod
cells
 Passive Transport  The active molecule is retinal (vitamin A
o Driven by a concentration gradient
aldehyde)
o Simple diffusion: a molecule or ion
 Retinal forms an imine with an -NH2 group of the
moves through an opening
protein opsin to form the visual pigment called
o Facilitated diffusion: a molecule or ion
rhodopsin
is carried across a membrane by a
 The primary chemical event of vision in rod cells
carrier/channel protein
is absorption of light by rhodopsin followed by
 Active Transport
isomerization of the 11-cis double bond to the 11-
o A substance is moved against a
trans double bond
concentration gradient
o Primary active transport: transport is
linked to the hydrolysis of ATP or other
high-energy molecule; for example, the
Na+/K+ ion pump
o Secondary active transport: driven by
H+ gradient
Lipid-Soluble Vitamins
 Vitamins – divided into two classes: lipid-soluble

and water-soluble
 A group of structurally related compounds that

are involved in the regulation of calcium and
phosphorus metabolism
o The most abundant form in the
circulatory system is vitamin D3.
 Vitamin A (Retinol) occurs only in animal
 Extensively unsaturated hydrocarbon ( -
carotene)
 Vitamin A is found in the plant world in the form of
a provitamin in a group of pigments called
carotenes
 Enzyme-catalyzed cleavage of  -carotene
followed by reduction gives two molecules of
vitamin A
 The most active of vitamin E is  -tocopherol

 Vitamin E is an antioxidant; traps HOO• and
ROO• radicals formed as a result of oxidation by
O2 of unsaturated hydrocarbon chains in
membrane phospholipids
 Vitamin K has an important role in the blood- Non-essential Amino Acids
clotting process
 Long unsaturated hydrocarbon side consists of  Amino acids that we can get from foods and we
repeating isoprene units can make ourselves
 There are five (5): alanine, asparagine, aspartic
acid, glutamic acid, and serine.
Conditionally Essential Amino Acids
 Healthy bodies can make them under normal

circumstances
 We can’t make them in cases like starvation or
certain inborn errors of metabolism.
 There are six (6): arginine, cysteine, glutamine,
glycine, proline, and tyrosine.
Essential Amino Acids
 Amino acids that we can only get from food

PROTEINS  There are nine (9): histidine, isoleucine,
Proteins leucine, lysine, methionine, phenylalanine,
threonine, tryptophan, and valine.
- Essential part of the human diet
- Found in a variety of foods like egg, dairy, Dietary Protein
seafood, legumes, nuts, and seeds.
 Provides the essential amino acids that are
- Regardless of the source, the protein that we eat
needed to make our own proteins, hormones, and
gets broken down and reformed into new proteins
other important molecules.
in our bodies.
 However, we need to break the dietary protein
- Do everything from fighting infections to helping
down first through a process called proteolysis.
cells divide
- A chain of amino acids bound to one another by Proteolysis
peptide bonds which gets twisted and folded into
a final protein shape  Begins when the food reaches the stomach
- When we eat protein, it gets broken down into its  First, hydrochloric acid denatures the protein,
individual amino acids. unfolding it and making the amino acid chain
more accessible to enzymatic action.
Amino Acids  Then, pepsin, which is a protein itself made by
- Most amino acids have a central carbon atom gastric chief cells enters the picture. Pepsin
bonded to one amino or nitrogen-containing cleaves any available protein into smaller
group and one carboxylic acid group. oligopeptide chains which moves into the
- The carbon also has one hydrogen atom and a duodenum where a second set of digestive
side chain or R group which is unique to each enzymes, made by the pancreas, further chops
amino acid with the exception of proline which is the oligopeptides into tripeptides, dipeptides,
a tiny little ring structure instead. and individual amino acids. These can all be
- Although there are hundreds of amino acids in taken up to the intestinal cells where di- and
nature, humans only use about 20 of them to tripeptides are then converted into amino acids.
make basically every type of protein.  Some amino acids remain in these cells and are
used to synthesize intestinal enzymes and new
cells but most entered the bloodstream and
transported to different parts of the body.
Animal-Based Protein
 Foods like eggs, dairy, seafood, and meat

provide all nine essential amino acids in adequate
amounts
Soy Foods  The conclusion of producing a long chain of
amino acids doesn’t necessarily equal a
 Unique in that they are plant-based and also functional protein. There are modifications to a
provide all nine essential amino acids in adequate protein that often need to happen in order for it to
amounts. be functional.
 Most other plant foods including whole grains,  Modifying means many things. It might be adding
legumes, nuts, and seeds have high amounts of certain chemical groups such as
some amino acids and low amounts of others phosphorylation but another important event to
 Not all plant foods are low in the same amino make a functional protein is folding.
acids so eating a variety of plant-based foods can
provide all nine of the essentials. Why shape is so important?
Daily Protein Requirements  Shape and function, in biology, frequently go

hand in hand.
 Based on studies that estimate the minimum  Protein receptors and the signal molecules that
amount of protein needed to avoid a progressive bind them can fit together so perfectly to start
nitrogen loss. some type of cellular response.
 The WHO guidelines and the U.S.  Enzymes, which are frequently proteins, have a
Recommended Dietary Allowance each estimate very specific shape for the substrates that they
that daily protein requirements for healthy adults build up or break down.
are about 0.80 g/Kg of body weight.
 Protein recommendation per day vary by age as Protein Structure
well. Children 1-3 years of age are
recommended to get 13 grams; for ages 4-8, 19  Primary Structure (1st level)
grams are recommended, and between ages 9 o The sequence of amino acids
and 13, 34 grams are recommended. (monomers; building blocks or protein)
that make up a protein
 Whether a person is male or female also impacts
o Held together by peptide bonds
protein needs. Females ages 14 and above are
o In protein synthesis, amino acids are
recommended to get 46 grams of protein per day.
added to form a polypeptide chain and
Males aged 14 to 18 needs slightly more about
proteins are made of 1 or more of these
52 grams per day and males 19 and older are
polypeptide chains.
recommended to get 56 grams per day.
o Genes, which are made of DNA,
 Some groups like pregnant and breastfeeding
determine the order and number of these
women as well as athletes have elevated needs
amino acids. That sequence is critical to
and older adults may also benefit from eating
the protein’s structure and function since
more protein.
one amino acid can be changed in sickle
 Getting the right amount of protein per day can be
cell disease. Even a single change of an
achieved in multiple ways.
amino acid has the potential to affect a
 It is still unclear what an optimal amount of protein
protein’s function.
is in different situations.
 Secondary Structure (2nd level)
 In clinical settings, there are certain individuals
o Folding starts to happen
who may be at risk for a protein deficiency
o The sequence of amino acids in primary
including patients with malnutrition, trauma, and
structure can fold in different ways. The
burn injuries as well as various conditions
most common ways are the alpha helix
impacting nutrient absorption like inflammatory
and beta – pleated sheet and which one
bowel disease. These individuals may have
of those foldings the protein does
increased protein needs compared to the general
depends on the amino acid arrangement
population.
it has.
 Except for certain circumstances like kidney o Both of these shapes are due largely in
disease, there usually isn’t a health risk part to hydrogen bonds that can occur
associated with eating a lot of protein because at specific areas of the protein’s amino
our bodies are able to process it. acids.
Protein Structure and Folding o These are hydrogen bonds involving
the backbone of the amino acid structure.
Folding – can actually have a lot to do with function  Tertiary Structure (3rd level)
o Looks at more folding that occurs in the
Protein synthesis – process of creating proteins
3D shape of a functional protein and a lot
of this is due to the R groups.
o R group can define the amino acid and is not ideal for them, the interactions taking place at the
can make amino acid behave in a certain different structural levels can be disrupted which can
way. For example, some R groups are denature the protein that disrupts its shape and prevents
hydrophilic while some are hydrophobic. it from functioning correctly. Sometimes, denaturing a
Since proteins contain many amino acids protein may be reversible, but in many other cases, it’s
which can contain different R groups, not.
different areas of the protein can
therefore be impacted based on those R Amino Acids and Peptides
groups.
Topic Outline
o When protein folding is going on, amino
acids with hydrophilic R groups may  Amino acids: Structure and Properties
hang out on the outside while  Ionization of Amino Acids
hydrophobic R groups may hang out in  Peptide Bonds
the inside part of the protein.  Peptides with Physiological Activity
o The 3D shape is due to other interactions
besides hydrophobic interactions. Ionic Amino Acids
bonds, Van der Waals interactions,
disulfide bonds, and hydrogen bonds  a compound that contains both an amino group
– all involving the R groups, also and a carboxyl group
influence the folding occurring in tertiary   -Amino acid has an amino group attached to the
structure. carbon adjacent to the carboxyl group
o Protein, a polypeptide chain that has   -carbon also bound to side chain group, R
been folded into a functional protein. (gives identity to amino acid)
 Quaternary Structure (4th level)  Two stereoisomers of amino acids are
o Protein can be made of 1 or more designated L - or D –
polypeptide chains.
o Each of these polypeptide chains can be
a subunit and interactions between them
such as hydrogen/disulfide bonds can
keep them together.
o The interactions mentioned like hydrogen
bonds and R groups interactions are
occurring depending on the protein’s own
amino acids. One reason why amino acid
sequences are very important for protein
function.
o Folding is far more complex and there
can be intermediate steps involved when
a protein is folding.
o Research has shown that proteins often
help in the folding process. For example,
chaperonins are almost barrel-shaped
proteins that can help with the folding
 Twenty amino acids are commonly found in
process. Proteins go into them, and the
proteins.
chaperonin tends to have an
 These amino acids contain a variety of different
environment that is ideal for the protein’s
functional groups:
folding. This can help the protein to be
o Alcohols (R-OH)
folded correctly so it’s functional.
o Phenols (Ph-OH)
There are many diseases that are related to protein o Carboxylic acids (R-COOH)
misfoldings. o Thiols (R-SH)
o Amines (R-NH2)
 Huntington’s Disease o Amide (R-CONH2)
 Parkinson’s Disease
20 Common Amino Acids
Note: Each protein has an ideal environment for
functioning which might include a certain temperature or Group A: Nonpolar side chains – Ala, Val, Leu, Ile, Pro,
pH range. If the protein is exposed to an environment that Phe, Trp, and Met.
 Ala, Val, Leu, Ile, Pro- contain aliphatic Amino Acids’ Important Structural Features
hydrocarbon group. Pro has cyclic structure.
 Phe - hydrocarbon aromatic ring. 1. All 20 are  -amino acids
 Trp - Indole ring side chain, aromatic. 2. For 19 of the 20, the  -amino group is primary;
for proline, it is secondary
 Met - Sulfur atom in side chain.
3. With the exception of glycine, the a-carbon of
each is a stereocenter
4. Isoleucine and threonine contain a second
stereocenter
20 Common Amino Acids
Group B: Neutral Polar side chains - Ser, Thr, Tyr, Cys,

Glu, Asn
 Ser, Thr- Side chain is polar hydroxyl group

 Tyr- hydroxyl group bonded to aromatic
hydrocarbon group
 Cys- Side chain contains thiol group (-SH)
 Gln, Asn- contain amide bonds in side chain
Ionization of Amino Acids
Group C: Acidic Side Chains: Glu, Asp  The process by which an atom or a molecule
acquires a negative or positive charge by
 Both have a carboxyl group in side chain gaining or losing electrons.
 Can lose a proton, forming a carboxylate ion  Amino acids are amphoteric molecules.
 These amino acids are negatively charged at  Amphoteric – can act as either an acid or a
neutral pH base
 Both groups have conjugate acid-base forms
depending on the pH of the solution
Group D: Basic Side Chains: His, Lys, Arg
 Side chains are positively charged at pH 7

 Arg- side chain is a guanidino group
 His- side chain is an imidazole group
 Lys- side chain NH3 group is attached to an
aliphatic hydrocarbon chain
 In amino acid, carboxyl group (-) and amino
group (+) are charged at neutral pH.
 In free amino acids  -carboxyl, and a-amino
groups have titratable protons. Some side
chains do as well.
Isoelectric Point (pI)
 the pH at which the majority of molecules of a

compound in solution have no net charge
 At pH 5.5, almost all molecules would be at 0 net

charge or in zwitterion form
Electrophoresis
 The process of separating compounds on the

basis of their electric charge
 Electrophoresis of amino acids can be carried
out using paper, starch, agar, certain plastics,
and cellulose acetate as solid supports
 pKa – apparent dissociation constant( refers as  In paper electrophoresis, a paper strip saturated
to how acidic or basic a given hydrogen atom in a with an aqueous buffer of predetermined pH
molecule is) serves as a bridge between two electrode vessels
 pH – power of Hydrogen (refers as to how acidic
or basic a solution is)
 At pH of 2, 50% of COOH are in conjugate acid
form and 50% are in its conjugate base form.
 At pH of solution <2, the COOH is uncharged;
pH>2, COOH has -1 charge
Examples:
 At low pH, proton concentration [H+] is high.

Therefore, both amines and carboxylic acids are
protonated. (-NH3+ & -COOH)
 At high pH, proton concentration is low.
Therefore, both amines and carboxylic acids are
deprotonated. (-NH2 & -COO-)
 At neutral pH, amines are protonated(-NH3+)
and carboxylates are deprotonated(-COO-)
(Zwitterion forms at neutral charge)
Geometry of Peptide Bonds
 the four atoms of a peptide bond and the two

alpha carbons joined to it lie in a plane with bond
angles of 120°about C and N
 to account for this geometry, a peptide bond is
most accurately represented as a hybrid of two
contributing structures (resonance structures)
 peptide: the name given to a short polymer of

amino acids joined by peptide bonds; they are
classified by the number of amino acids in the
chain
 dipeptide: a molecule containing two amino
acids joined by a peptide bond
 tripeptide: a molecule containing three amino
Peptide Bonds acids joined by peptide bonds
 polypeptide: a macromolecule containing many
 Individual amino acids can be linked by forming amino acids joined by peptide bonds
covalent bonds.  protein: a biological macromolecule of molecular
 Peptide bond: the special name given to the weight 5000 g/mol or greater, consisting of one or
amide bond between the  -carboxyl group of one more polypeptide chains
amino acid and the  -amino group of another
amino acid Peptides with Physiological Activity
 L-Carnosine
o comes from meat – useful in the
prevention of damage caused by too
much sugar
o Concentrated in muscles – used in the
treatment of complications of diabetes
such as nerve damage, eye disorders
and kidney problems
BIOCHEMISTRTY (FINALS) Enzyme structure
ENZYMES  Simple enzymes: composed only of

protein (amino acids)
Enzyme mechanisms and control  Conjugated enzymes: has non-protein

part.
- Apoenzyme: protein part
Enzyme catalysis -
- Holoenzyme: biochemically active
 Proteins that act as a catalyst for conjugated enzyme (substrate is
biochemical reactions already bonded with the enzyme)
 Enzymes can be used again after a (an active enzyme)
reaction- not consumed - Apoenzyme + co factors=
 Lowers the activation energy- holoenzyme (conjugated enzyme)
requirement needed for some reactions (vitamins, zinc, magnesium, mineral
to take place. (enzyme= faster rate of ions, organic or inorganic
reaction) compounds)
 Most enzymes are globular proteins - A cofactor: non-protein part
 Few enzymes are RNA- Riboenzymes
 Rate of reaction depends on its
activation energy
 Low activation energy, increase rate of

reaction
Models of enzyme action
Substrate, S: reactant
Active site: created because of the protein

folding process
- Crevice like portion (formed during

protein synthesis/folding)
- Hydrogen bonding
- Electrostatic attractions
- Van der waals
1. Absolute specificity (substrate
specificity)- restrictive, one specific
Enzyme+ substrate= enzyme-substrate complex
substrate only (not common)
- Lock and key model
- Catalase catalyze hydrogen
Binding models peroxide only.
- Lock-and-key model: 2. Stereochemical specificity- recognize

restrictive model- specific stereoisomerism of some molecules.
enzyme can only catalyze specific - L and D notations
substrate based on shape
3. Group specificity- can recognize certain
- Induced fit model: will adjust to the structures in some molecules as long as
shape of the substrate (diff it contains the same functional groups
molecules from the same family or - Pepsin
groups) - Chymotrypsin(pancreatic juice)
4. Linkage specificity- catalyze different

kinds of bonds. E.g. phospholipids
(cleave phosphate-ester bond)
- Peptidase (peptide bond)
- Amylase (a-1,4 glyosidic linkage)
Formation of products
Factors that affects enzyme activity
-Substrate change shape after reaction
-Enzymes remain the same and can be used Enzyme activity- measure of rate at which
over again (not consumed) enzyme converts substrate to products in a
biochemical reaction.
1. Temperature- if the temp is higher

than the optimum temp it will be
denatured (change shape)
- Once temp increase rate of reaction
Enzyme specificity will also increase until optimal
temp. beyond it will suddenly
- Ability of an enzyme to decrease (denatured)
choose/recognize an exact - Normal body temp (optimal temp)
substrate that it can catalyze. - Pag mataas ang lagnat – some of
the enzymes are deactivated (slows
down metabolic process)
4. Enzyme concentration- if enzyme
concentration increase, reaction rate
increase (no limit)
2. pH- if too basic or too acidic to optimal

ph reaction rate will decrease
- digestive enzymes (acidic
environment)
- our blood has pH level 7.4
- -most enzymes have optimal
activity in the ph of 7.0-7.5
-
Nomenclature of enzymes
- How enzymes are named
1. Usually end is –ase. (some ends in –

in)
2. Type of reaction catalyzed by an

3. Substrate concentration- reaction rate enzyme is often used as a prefix.
(velocity) (oxidase, amylase)
- Concentration of substrate reaction
rate increase until it reaches the 3. Identity of substrate is often used in
maximum rate (after that it will addition to the type of reaction
remain constant) (glucose oxidase- catalyze glucose
- Depends on the enzyme, when the through oxidation reaction)
active sites are full the enzyme can
no longer accommodate excess *Lactate (lactic acid)
substrate (negligible reaction) *isomerization- molecule has the
same molecules but different
bonding, change in the
arrangement (maleate isomerase)
Classification of enzymes
- 6 major classes
1.oxidoreductase enzyme- oxidation-reduction - Dehydratase: removal of the
reaction. Requires coenzyme components of water from a double
bond (remove water, formation of
- if the reaction involves removal or addition of
double bond)
hydrogen.
- Hydratase: addition of the
components of water to a double
bonds. (add water remove double
bond)
2. transferase- transfers functional group
-transaminases- transfers amino group
- kinases- phosphate group from ATP to 5.isomerases- rearrangement of atoms

substrate (ATP to ADP)
ASP aspartate transaminase
6.ligases- common cellular respiration (ATP

hydrolysis) (combine 2 molecules with the help
of ATP)
3.hydrolase- involves hydrolysis reaction
- breaks down larger molecules into 2 simple

units
Extremozymes
4. lyases- forms double bonds. Use water

 Enzymes that can thrive in harsh
molecules
conditions.
 Extremophiles- organisms that thrive in Enzymes inhibitions
extreme environment.
Enzyme inhibitor: slows down or stops

1.hydrothermophiles- thrive at 80-122 degrees enzymatic activities
and high pressure
2.acidophiles-optimal growth pH <3.0

- Competitive inhibitors: compete
with the substrate for the same
active site.
3.Alkaliphiles- optimal growth >9.0
- Same shape as the substrate
- Noncompetitive inhibitors: do not

4.Halophiles-live in highly saline conditions compete with the substrate for the
(>0.2 M NaCl)
same active site. Binds to the enzymes
other than active site.
5. Piezophiles- grow under high hydrostatic -allosteric site-site other than the
pressure (lives in sea beds) active site in the enzyme.
6.Cryophiles-grow at temps <15 degrees -inhibitor will bind to allosteric
Celsius. site and it will change the shape of the
-enzymes extracted from extremophiles are enzyme.
very useful for industrial application.
-genetic make-up are extracted from organisms

and made in the lab. Artificial enzymes
Extremozymes application
-biotechnology industry-production of enzymes

for industrial application
-replicate genetic make-up inside the lab

Inhibitor examples: pain killers, drugs
-Petroleum industry- oil well drilling operations that affect enzymatic activities,
-scavenging and removal of heavy metals. antibiotics (penicillin),
Noncompetitive: heavy metals (silver

-environmental cleanup using genetically
engineered extremophiles lead mercury), disinfectants.
- Laundry detergents used in cold wash cycle

Covalent modification of enzymes-
modification of non-metallic molecules
-a process in which enzyme activity is

altered by covalently modifying the
structure of the enzyme
- involves adding or removing a group

from an enzyme
- Example addition and removal of

phosphate group
Enzyme regulations
General mechanism involved in

regulation: if the body produces too
much enzymes, there is a problem in
that certain area
Proteolytic enzymes and zymogens-

involves protein degradation
- Mechanisms of regulation by
production of enzymes in an
inactive forms (zymogens). Feedback control regulation
- Zymogen-turned on when detects a

certain environmental condition. Allosteric site: gk allo+steric= other
(appropriate time and place) shape.
- Mostly digestive enzymes and Allosteric enzyme: an oligomer whose

blood-clotting enzymes biological activity is affected by other
substances binding to it
- Hydrolyze peptide bond in protein
-allosteric effector: allosteric inhibitor or
allosteric activator
Feedback mechanism: formation of -many common prescription drugs exert

product inhibits its continued their mode of action by inhibiting
production. enzymes.
Positive feedback loop and

negative feedback loop. Examples:
 Angiotensin converting
enzymes(ACE) inhibitor-
management of blood pressure
and other heart conditions
 Sulfa drugs- antibiotics
 Penicillin- antibiotics
ATCase feedback mechanism: Antibiotic: a substance that kills

Aspartate transcarbamoylase- bacteria or inhibits the growth (inhibits
catalyzes a first step in a biosynthetic enzyme produced by the bacteria so
pathway that produces pyrimidine that they won’t proliferate anymore)
nucleotides needed for nucleic acids,
energy storage, and enzyme cofactors.
ACE inhibitors: taken by people with
high blood pressure.
Enzyme Regulation
- Angiotensin I: allows blood vessels - Mode of antibiotic activity: many
to be dilated. (widen passage of the bacteria need PABA to produce
blood=lower blood pressure) coenzyme, folic acid
- Sulfanilamide is a competitive
inhibitor of enzymes responsible for
- Angiotensin II: constrict blood converting PABA to folic acid
vessel (makes blood vessel narrow= - Somehow similar structure to PABA
high blood pressure) - Bacteria needs folic acid for their
bacterial wall.
- When sulfanilamide attached to
- ACE angiotensin I to angiotensin II bacteria the bacteria will
in the blood. experience folic acid deficiency.
- ACE inhibitors block AE reaction and
thus reduce Blood pressure.
CIPRO: antibiotic
- The antibiotic ciproflaxin

hydrochloride
- Considered the best broad-

spectrum antibiotics- effective
against skin, bone, urinary,
gastrointestinal, and respiratory
infections.
- Drug choice in treatment of

traveler’s diarrhea
- Bacteria are slow to acquire

resistance to Cipro.
- Has historical value: drugs used

against anthrax- a biological
weapon
- Example: Lisinopril
Coenzymes/ co factors
SULFA Drugs: derivatives of sulfanilamide
Vitamin C – water soluble vitamins

- Antibiotic - Co-substrate in the formation of
- Derivatives of sulfanilamide structural protein collagen
- Involved in metabolism of certain
amino acids
- 100 mg/day saturates all body
tissues- excess vitamin is excreted
NUCLEIC ACIDS
through urine
- Can easily be oxidized when used - PCR most effective in detecting
on skin viruses
- Co factor of collagen- increase
collagen production - Stores genetic information and
- Sodium ascorbate-salt form express it.(specifically in the DNA)
- Ascorbic acid-acid form -Gives an organism a certain
identity
Vitamin B- prevents infection

- Protein synthesis- manufacturing of
- Promotes cell growth and rbc
proteins
growth
-dictates what kind of
- Niacin B3(niacinamide)- for
protein to be produced in the body
whitening of skin and prevention of
acne and acne marks
-allows genetic information to be
- Vitamin B complex- important in
passed down in next generations.
brain function, cell metabolism,
promotes cell growth and
production of red blood cells.
- Polymer in which repeating unit is
nucleotide:
- Folate-Folic acid
- Pentose sugar
- Vit C and niacinamide- bawal
- Phosphate group
pagsabayin in a same way (bawal
both topical or oral at the same
time)
- Heterocyclic base (nitrogenous
base)
Pentose sugar(monosaccharide)- in the form of - Derived from phosphoric acid
furanose - Creates ester linkage to another
nucleotide
RNA- Ribose (C2- OH)
- One component that creates DNA
DNA- 2-deoxyribose (C2-H) backbone
Nucleotide formation
- pentose sugar +nitrogenous base = nucleoside

Nitrogenous base (glyosidic bond)
Nitrogen-contains heterocyclic bases

-nucleoside+ phosphate group= nucleotide
Pyrimidine- 1 cyclic struc
Purine- 2 cyclic struc Nucleoside: a compound formed from a five-

carbon monosaccharide and a purine or
pyrimidine base derivative.
- The N9 of a purine or N1 of a
pyrimidine base is attached to C-1
position of sugar (beta-
confirmation)-N-glycosidic linkage.
- It is a condensation reaction (H2O

released)
Uracil in RNA
Thymine- DNA and some RNA
Nucleotide: addition of a phosphate group to a

Phosphate group – soluble to water nucleoside
- Attached to C5 position through a
phosphate ester bond
- Sugar-phosphate groups are
referred to as nucleic acid
- Condensation reaction (H2O
backbone- found in all nucleic acids
released)
- Named by appending 5’- - Due to changes in the bases

monophosphate to nucleoside
name
NOMENCLATURE
Ribonucleic acid - Phosphodiester bond between 3’

and 5’ position
Deoxyribonucleic acid
- Held together by hydrogen bonds

5’ and 3’ terminal end
Ribonucleic acid (send message to cells to

create replication of the genetic sequence that
it carries)- is a nucleotide polymer in which
each of the monomers contains ribose, a
phosphate group, and one of the heterocyclic
bases adenine, cytosine, guanine, or uracil
Deoxyribonucleic acid (storage of genetic

information)- is a nucleotide polymer in which
Primary structure: single strand (dna and rna) each of the monomers contains deoxyribose, a
phosphate group, and one of the heterocyclic
bases adenine, cytosine, guanine, or thymine.
The double helix
Base compound- gives identity to the nucleic

- Secondary and tertiary structure
acids
- Secondary structure involves two

polynucleotide chains coiled around
Phosphate group C5 of pentose sugar
each other in helical structure
3’- where phosphate group from other linkage - The two polynucleotides run anti-
will attach parallel to each other (5’to3’ and 3’
to 5’)
- Complimentary bases (A=T and
G=C)
-human dna : 30% A,30% T, 20% G, and 20% C
Comparison of the general primary structure of

nucleic acids and proteins
Backbone: phosphate-sugar- nucleic acid
Backbone: peptide bonds-proteins

- The DNA contains the necessary
genetic information for certain
organisms and are coded in the
RNA.
DNA sequence- the sequence of bases - The RNA will participate in the
on one polynucleotide is complimentary protein synthesis specifically in
to the other polynucleotide transcription and translation to
identify the arrangement of amino
acids that can be found in the
protein molecule.
- Complimentary bases are pairs of
bases in a nucleic acid structure
that can hydrogen-bond to each
other.
Base pairing- a pyrimidine is always paired with

purine
- Fits inside the dna double strand

- Hydrogen bonding is stronger with
A-T and G-C
DNA REPLICATION
- A-T and G-C are called
complimentary bases
Replication: process by which DNA molecules

produce exact duplicates of themselves.
- Happens in the nucleus where the

chromosomes are located.
- Double helix strand will be cut into

two single strands to create a
duplicate copy.
Central Dogma of Molecular Biology - an old strand acts as template for

the synthesis of new strands (semi-
conservative).
- Shows how DNA and RNA helps in

the protein synthesis.
- Semi-conservative structure- the
newly synthesized DNA have one
-Replication fork- when the
new strand and one old strand.
nitrogenous base is exposed.
- Occurs during synthesis phase of
the eukaryotic cell cycle.
- Important enzymes in the process - Primase: synthesizes short RNA
are the ff: DNA polymerase, sequences called primers.
helicase, primase, and ligase. -works together with the DNA
polymerase.
- DNA polymerase: checks the

correct base pairing and catalyzes
the formation of phosphodiester
linkages forming new strand of
DNA. (can only work on 5’ to 3’
direction)
- Ligase: catalyzes the joining of two

large molecules by forming a new
chemical bond.
-connects bonds and linkages
-acts as an adhesive or glue
-Lagging strand: top part from

3’ to 5’ (areas that are no connected- DNA
Replication Fork: fragments or okazaki fragments)
-Leading strand: bottom part

from 5’ to 3’ (where DNA polymerase works
- DNA polymerase: checks the
well without forming okazaki fragments)
correct base pairing and catalyzes
the formation of phosphodiester -ligase will act as a glue or
linkages. create a linkage in the okazaki fragments.
- Helicase: breaks the DNA strand

(remodeling or unwinding enzymes)
- breaks the hydrogen bonding

between the nitrogenous bases of
the complimentary strand.
-double strand to single strand

(the nitrogenous base will be exposed)
Protein synthesis - Ribosomal RNA (rRNA)- helps form
ribosome, the organelle where
- Divided into two phases
proteins are assembelled.
- RNA transcription: a process by - Transfer RNA (tRNA)- brings amino

which DNA directs the synthesis of acids to ribosomes, where they are
mRNA molecules. joined together to form proteins.
-gene: a segment of a DNA base

sequence responsible to produce a
-codons- are complimentary groups
specific hnRNA/mRNA molecule.
of bases in mRNA. Triplets are groups of three
-will travel outside the nucleus successive nucleotide bases in DNA.
to the cytoplasm going to the ribosome.
- RNA translation: a process in which

mRNA is deciphered to synthesize a
protein molecule.
Steps of transcription
- Initiation: the beginning of

transcription. It occurs when the
enzyme RNA polymerase binds to a
region of a gene called the
promoter.
RNA transcription -RNA polymerase- allows the
DNA to unwind
Types of RNA:
- Elongation: the addition of
nucleotides to the mRNA strand.
- Messenger RNA (mRNA)- copies RNA polymerase reads the
the genetic instructions from DNA unwound DNA strand and builds
in the nucleus and carries the the mRNA molecule, using
instruction to the cytoplasm. complimentary base pair.
- Termination: the ending of -translation: a process in which mRNA codons
transcription and occurs when RNA are deciphered to synthesize a protein
polymerase crosses a stop molecule.
(termination) sequence in the gen.
The mRNA strand is complete, and
it detaches from DNA.
-Ribosome: an rRNA-protei complex- serves as

the site of protein synthesis.
-Characteristics of the genetic code:
-the genetic code is universal (similar among all

Post-transcription processing: formation of organisms)
mRNA -The genetic code is unambiguous (a certain
code carried by the RNA can only translate a
certain amino acid)
- Involves conversion of hnRNA
(heterogeneous nuclear RNA) to - The genetic code is redundant (some codons
mRNA can translate two similar amino acids- one
amino acid could have many different codons)
- tRNA: delivers the needed amino acid base on

- Splicing: excision of introns and the codons.
joining of exons.
- Exon: a gene segment that codes

for genetic information.
- Intron: a DNA segment that

interrupt a genetic message.
-the splicing process (removal of

introns) is driven by snRNA (Small
Nuclear RNA).
RNA translation Genetic code

- Each tRNA molecule has an
anticodon for the amino acid it
An initiation codon exists:
carries. An anticodon is a sequence
of 3 bases, and is complimentary to
- The existence of “stop” codons

(UAG, UAA, and UGA) suggests the
existence of “start” codons.
- The codon- coding for amino acid

methionine (AUG) functions as
initiation codon.
the codon for an amino acid.
- for example, the amino acid lysine

has the codon AAG, so the
anticodon is UUC.
two important features of the tRNA structure
- The 3’ end of trNA is where an

amino acid is covalently bonded to
the tRNA.
- The loop opposite to the open end Mutations

of tRNA is the site for a sequence of
three bases called an anticodon - change in the sequence of bases in
DNA or RNA.
- Anticodon: a three-nucleotide - Errors in genetic information is

sequence on a tRNA molecule that passed on during transcription.
is complimentary to a codon on an
mRNA molecule.
- It is aprocess in which the genetic - Mutations are essential for
code in mRNA is read,one codon at evolution to occur.
a time, to make a protein.
- Caused by mutagens (substance or - Somatic mutation: occur in other
agent that causes a change in the cells of the body. These mutations
structure of a gene) may have little effect on the
organism because they are confined
-radiation and chemical agents to just one cell and its daughter
are two important types of cells
mutagens.
-Ultraviolet, X ray, radioactivity

and cosmic radiation are
mutagenic- cause cancer.
-chemical agents can also have

mutagenic effect.
Other types of mutations
- Chromosomal alterations: are

mutations that change
chromosome structure. They occur
when a section of a chromosome
breaks off and rejoins incorrectly or
does not rejoin at all.
-Very serious and may result to

death. -Example is down
syndrome.
Major types of mutation
- Germline mutation: occur in

gametes. It can be transmitted to
offspring and every cell in the
offspring will have the mutation.
- Point mutation: is a change in a
single nucleotide in DNA. This type
of mutation is usually less serious Viruses
than a chromosomal alteration. An
example of a point mutation the
changes the codon UUU to the - Viruses: attach to the host cell on
codon UCU. Point mutations can be the outside cell surface and
silent, missense or nonsense proteins of virus envelope catalyze
mutations. the breakdown of the cell
membrane and forma a hole.
- Viruses then inject their DNA or

RNA into the host cell.
- The viral genome is replicated,

protein coding for the viral
- Frameshift mutations: are deletion envelope are produced in hundreds
or insertion of one or more of copies.
nucleotides that changes the
reading frame of the base - Virus can replicate in a short period
sequence. Deletions remove of time
nucleotides, and insertions add
nucleotides. - Hundreds of new viruses are
produced using the host cell
-AUG-AAU-ACG-GCU= starr- asp- replicated genome and proteins in
thr-ala short time.
-insert nucleotide A after the start

codon
-AUG-AAA-AUC-GGC-U= start –lys-

tyr-gly
Replication of virus -disease resistance- increased crop yield
-drought resistance- consumption of less

water
-predator resistance- less insecticide
-frost resistance- resist changes in temps

below freezing
-deterioration resistance- long shelf-life
Recombinant DNA production using a bacterial

plasmid.
DNA recombinant and genetic engineering - Dissolution of cells

- Isolation of plasmid fraction
- DNA recombinant: DNA molecules
- Cleavage of plasmid DNA
that have been synthesized by
- Gene removal from another
splicing a sequence of segment DNA
organism
(usually a gene) from one organism
- Gene-plasmid splicing
to the DNA of another organism.
- Uptake of recombinant DNA.
- Genetic engineering
(biotechnology): a process in which
an organism is intentionally
changed at the molecular (DNA)
level so that it exhibits different
traits.
Polymerase chain reaction
-Benefits: many plants have now been - Polymerase chain reaction(PCR): a

genetically engineered and numerous beneficial method for rapidly producing
situations have been created. multiple copies of a DNA nucleotide
sequence (gene).
- This method allows to produce
billions of copies of a specific gene
in a few hours.
- PCR is very easy to carry out and

the requirements are:
-source of gene to be copied Gene therapy
-thermostable DNA polymerase (enzyme that -done to replace a mutated gene or structure in
can withstand higher temperature) an organism.
-Deoxynucleotide triphosphates (dATP, dGTP,

dCTP, and dTTP)
- Gene therapy: an experimental
-a set of two oligonucleotides with technique that uses genes to treat
complimentary sequence to the gene (primers) or prevent disease. In the future,
this technique may allow doctors to
-thermostable plastic container treat disorder by inserting a gene
- source of heat into a patient’s cells instead of using
drugs or surgery. Several
approaches to gene therapy
includes:
-replacing a mutated gene

that causes disease with a healthy copy of the
gene
-inactivating, or “knocking
out”, a mutated gene that is functioning
improperly.
- introducing a new gene into

the body to help fight a disease.
- Gene therapy is a promising

treatment option for several
diseases (inherited disorders, some
types of cancer, and certain viral
infections).

Cover To Cover Biochemistry

Uploaded by

Document Information

Original Description:

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Cover To Cover Biochemistry

Uploaded by

Copyright:

Available Formats

Lecture 1

•Biochemistry: Origin of Life

• Systems for extracting, transforming

• Mechanisms for sensing and

• A capacity to change over time by

Source: Reusch, W. (n.d.) Naming Organic Compounds. Retrieved from

Example: C3H8 – Propane; C3H6 – Cyclopropane

• can use Condensed structural formulas

• Shorthand representation of molecule’s bonding

Source: Reusch, W. (n.d.) Naming Organic Compounds. Retrieved from

For purposes of simplicity of study, lipids are divided into

 Interaction of biochemical compounds with water

 Alpha Linolenic Acid (ALA)

 Omega Fatty Acids

 Many food products are produced by partial

 Simplest lipid constructed from fatty acids

 Triglycerides are energy storage form of fatty

 Triglycerides made from unsaturated fatty acids

 Up to 80% of the mass of a cell membrane can

 Like the soaps, these molecules are highly

 The classification of phosphatidyl ester

 Glycolipid: a compound in which a carbohydrate

 Steroid Sex Hormones

 Produced by adrenal glands

 Aldosterone – a corticosteroid hormone which

Biological Membranes Fluid Mosaic Model

 Vitamins – divided into two classes: lipid-soluble

 A group of structurally related compounds that

 The most active of vitamin E is  -tocopherol

Conditionally Essential Amino Acids

 Healthy bodies can make them under normal

Essential Amino Acids

 Amino acids that we can only get from food

 Foods like eggs, dairy, seafood, and meat

Daily Protein Requirements  Shape and function, in biology, frequently go

20 Common Amino Acids

Group B: Neutral Polar side chains - Ser, Thr, Tyr, Cys,

 Ser, Thr- Side chain is polar hydroxyl group

Ionization of Amino Acids

Group D: Basic Side Chains: His, Lys, Arg

 Side chains are positively charged at pH 7

Isoelectric Point (pI)

 the pH at which the majority of molecules of a

 At pH 5.5, almost all molecules would be at 0 net

 The process of separating compounds on the

 At low pH, proton concentration [H+] is high.

 the four atoms of a peptide bond and the two

 peptide: the name given to a short polymer of

ENZYMES  Simple enzymes: composed only of

Enzyme mechanisms and control  Conjugated enzymes: has non-protein

 Low activation energy, increase rate of

Models of enzyme action

Active site: created because of the protein

- Crevice like portion (formed during

- Lock-and-key model: 2. Stereochemical specificity- recognize

4. Linkage specificity- catalyze different

-Substrate change shape after reaction

1. Temperature- if the temp is higher

2. pH- if too basic or too acidic to optimal

- How enzymes are named

1. Usually end is –ase. (some ends in –

2. Type of reaction catalyzed by an