CHEM

INTRODUCTION TO BIOCHEMISTRY​ ​ ​ ​ LECTURE - PRELIM

BIOCHEMISTRY

●​ “Biological Chemistry”
●​ Investigation of molecular basis of life
●​ Study of Chemistry in living organisms
●​ It deals with biomolecules and biochemical reactions
viewed in context of biological structures

ROOTS OF BIOCHEMISTRY
BIOMOLECULES
1.​ Carl Scheele (mid 1700) – Founder of biochemistry.
Studied the chemical composition of matter. ●​Present in plant and animal cells
2.​ Friedrich Wohler (1828) – prove the fallacy that ●​Composition of the cell:
biochemicals can only be produced by living organisms ➢​ 50-95% - H2O
by producing urea by heating ammonium cyanate. ➢​ 1% - Ions
3.​ Matthias Schleiden & Theodor Schwann (1840) – ➢​ others: organic molecules
formulated the cell theory. Organic molecules
4.​ Walther Flemming (1875) – discovered chromosomes ●​ Carbon based molecule that are covalently bonded to
5.​ Carl Neuberg – Coined the word “biochemistry” itself or other elements like H, O, N, S, P.
6.​ Eduard & Hans Buchner (1897) – found that extracts ●​ One important organic molecule is the Hydrocarbon.
from yeasts could bring about fermentation of sugar
into alcohol. Hydrocarbons
7.​ Embden & Meyerhof (1925) – describe the glycolytic ●​ Biomolecules are derived from HC
pathway ●​ Is non-polar, therefore, they are HYDROPHOBIC in H2O
8.​ Hans Krebs (1937) – Proposed the Krebs cycle of the
TCA tricarboxylic acid cycle. Hydrophobic
9.​ Avery, MacLeod & McCarty (1944) – identified DNA as ●​ Biomolecules with HC group – has hydrophobic
information molecules character (Cell membranes)
10.​ James Watson & Francis Crick (1953) – propose the
double helical structure of DNA.
11.​ Francis Crick (1958) – proposed the central dogma of SMALL BIOMOLECULES MACROMOLECULES
(Monomers) (Polymers)
biology
12.​ Paul Boyer & J. Walker (1997) – discovered the “rotary a.​Used to synthesize larger d.​Essential structures for the
engine” that generated ATP. molecules like polymers basis of life
13.​ Jens Christian Skou – Danish biochemist who studied (proteins, nucleic acids) e.​Control and regulate this
the “pump” that drives sodium and potassium across b.​Some have special processes
membranes. biological functions (ATP – f.​ Responsible for energy
14.​ Stanley Prusiner – discovered the organism that a nucleotide) exchanges, irritability,
c.​Involve in complex reaction metabolism, mobility and
caused “mad cow disease” - prions
pathways reproduction
15.​ Ruska, et.al. – discovered the electron microscope and
provided a whole new level of insight into cellular
structure. SMALL BIOMOLECULES (MONOMERS)

BIOCHEMICAL SUBSTANCE 1.​ AMINO ACIDS

●​ There are 20 common α-amino acids (usually
●​ a chemical substance found within a living organism in protein)
●​ Building blocks of long chain polymer called
protein/polypeptides
BIOINORGANIC BIOORGANIC (BIOMOLECULES)

●​ No carbon ●​ Contain carbon

●​ Includes water and ●​ include carbohydrates, lipids,
inorganic salts proteins, and nucleic acids
●​ Water - 2/3 of the mass ●​ ¼ of body mass
of the human body
●​ Inorganic salts - 4%–5%
of body mass

●​ Chemical properties is determined by the R

group
 C.​ Phospholipids
➢​ Short polypeptide – AA is less than 50 (and are called ●​ major component of cell membrane
peptide)
➢​ Longer polypeptides – are called Proteins

Peptide Bonds
●​ bond connecting the amino acids in the polypetide
●​ Amide bond
●​ R groups of the polypeptide determines its final 3-D
shape and therefore its biological functions
D.​ Other Examples of Lipids
2.​ SUGARS 1.​ Steroids
●​ Carbohydrates ➢​ Cholesterol - a sex hormone; an
●​ most abundant organic molecules in nature important part of animal cell
●​ Function as: membranes
➢​ Energy source 2.​ Fat-soluble Vitamins
➢​ Structural components ➢​ Vitamin E and Vitamin A
➢​ Intercellular communication 3.​ Carotenoids
➢​ a plant pigment molecule that plays a
MONOSACCHARIDES POLYSACCHARIDES role in photosynthesis

●​ Basic unit of sugar ●​ A polymer containing 4.​ NUCLEOTIDES

●​ Simple sugar large amount of ●​ primary component of Nucleic Acids
●​ ALDOSES - containing monosaccharides ●​ involves in biosynthetic and energy generating
aldehyde functional group Examples: reactions (Ex: Formation of Phosphate bonds
and are Polyhydroxyl 1. Glycogen – energy storage to form ATP)
Aldehyde molecule
●​ KETOSES - containing 2. Starch – energy storage
ketone functional group molecule
and are Polyhydroxyl 3. Cellulose – structural
Ketone material

Examples of Sugars:
g.​ Glucose
h.​ Fructose
i.​ Ribose 3 Components of Nucleotides
j.​ Deoxyribose 1.​ 5-C sugar
2.​ Phosphate group
3.​ LIPIDS 3.​ Nitrogenous Base
A.​ Fatty Acids
●​ Monocarboxylic acid 2 classes of the Bases:
●​ usually contains an even number of carbon 1.​ Purine – A and G
atoms 2.​ Pyrimidine – T, C
●​ FAs are components of Lipids and U

Name Description Example

1. Saturated FA Single Palmitic acid - hexadecenoic

Nucleic Acids
bonded acid
1.​ Deoxyribonucleic Acid (DNA) - Contains/Stores
genetic information
2.​ Ribonucleic Acid (RNA) - Involves in expressing the
information primarily in protein synthesis

2. Unsaturated One or more Oleic Acid (18:1)

FA double bond BIOCHEMICAL REACTIONS

●​ The sum of all the enzyme-catalyzed reactions in a

living organism is called “Metabolism”
B.​ Triacylglycerols (Fats and Oils)
●​ are ester containing glycerol and 3 FAs
4 Functions of Metabolism
●​ Glycerol- a three carbon-alcohol with 3
1.​ Acquisition and utilization of energy
hydroxyl group
2.​ Synthesis of molecules needed to cell structure and
function
3.​ Growth and development
4.​ Removal of waste products
➢​ A lipid molecule that resembles triacylglycerol
is Phosphoglycerides
 BIOCHEMICAL PROCESSES 3.​ ADDITIONAL REACTIONS
●​ Two molecules combine to form a single
product
1.​ NUCLEOPHILIC SUBSTITUTION ●​ From double bond to single bond

➢​ Electrophile - Electron-loving specie; usually

a cation, radical or lewis acid
➢​ Nucleophile - Nucleus-loving specie; usually
an anion or atom with a lone-pair
➢​ Leaving group - leaves with the bonding pair 4.​ ISOMERIZATION REACTIONS
of electrons, and is replaced by the ●​ Involves intra-molecular shift of atoms
nucleophile; can be negatively charged or
neutral Aldose-ketose pair

Reaction of glucose with ATP

5.​ REDOX
●​ Transfer of electron from a donor (RA) to an
electron acceptor (OA)

➢​ Oxidation – Gain of Oxygen, Loss of Hydrogen

➢​ Reduction – Loss of Oxygen, Gain of Hydrogen
Hydrolysis reaction
●​ cleavage of covalent bonds by WATER
●​ a kind of SN reaction and can be catalyzed by an acid,
base and enzymes
●​ Importance: digestion of food involves Hydrolysis

Hydrolysis of ATP - involves breaking of phosphate bonds METHODS OF DETERMINING BIOMOLECULAR

STRUCTURES

1.​ Elemental Analysis

2.​ UV, visible, infrared, and NMR spectroscopy
3.​ Mass Spectroscopy (MS)
4.​ X-ray Crystallography
5.​ Specific sequencing methods (e.g., for proteins and
nucleic acids)
6.​ Use of battery of enzymes of known specificity to
degrade biomolecule of study
2.​ ELIMINATION
7.​ Use of acid or alkaline hydrolysis to the degrade the
●​ A double (=) bond forms when atoms are
biomolecule of study
removed from the molecule

Dehydration of 2-phosphoglycerate
FUNCTIONAL GROUPS​ ​ ​ ​ ​ ​ LECTURE - PRELIM

3.​ OXYGEN-CONTAINING COMPOUNDS

ORGANIC VS INORGANIC COMPOUNDS ●​ Contain oxygen atoms bonded to carbon
atoms
●​ Have distinct functional groups that
Organic Chemistry: Study of hydrocarbons (only carbon and determine their chemical properties and
hydrogen atoms) and their various derivatives. reactivity

Inorganic Chemistry: Study of all substances other than

hydrocarbons and their derivatives

BONDING CHARACTERISTICS OF CARBON ATOM

●​ C - atom always makes total of 4 Bonds

●​ The sharing of four valence electrons requires the
formation of four covalent bonds which are represented
by four lines 4.​ CARBOXYLIC ACID DERIVATIVES
●​ Derived from carboxylic acids
FUNCTIONAL GROUPS ●​ Characterized by the presence of the carboxyl
group (-COOH) or a related functional group

●​ Groups of atoms in organic molecules that are

responsible for the characteristics, chemical reactions
of those molecules.
●​ Simple molecules that contain the same functional
group in their structure can be expected to react in
similar ways.
●​ More complicated chemical molecules may contain
more than one functional group within their structure.
5.​ NITROGEN-CONTAINING COMPOUNDS
1.​HYDROCARBONS
●​ Compounds contain nitrogen atoms bonded
●​ Composed of hydrogen (H) and carbon (C)
to carbon atoms in various ways
➢​ Aliphatic
●​ Often play essential roles in biological
1.​ alkanes (saturated with single bonds)
molecules (e.g., amino acids in proteins) and
2.​ alkenes (unsaturated with double bonds)
are important in medicinal chemistry
3.​ alkynes (unsaturated with triple bonds)
➢​ Aromatic contain one or more benzene rings and
exhibit special stability due to their ring structure.

2.​ HALOGEN-CONTAINING COMPOUNDS

●​ Contain one or more halogen atoms (fluorine,
chlorine, bromine, iodine) bonded to carbon
atoms.
●​ Halogen atoms in these compounds can
replace hydrogen atoms in hydrocarbons or
can be part of functional groups.
●​ Halogen compounds are often used as
intermediates in organic synthesis and as
reagents in various chemical reactions
BIOCHEMISTRY OF THE CELL​ ​ ​ ​ LECTURE - PRELIM

2.​ ARCHAEA
CELL ●​ Has the capacity to thrive in a challenging
habitat.
●​ Referred to as Extremophiles
●​ Biochemistry explores molecular mechanisms of ○​ Ex. 1. Halobacterium salinarum
normal cellular processes as well as diseases. 2. Thermoplasma acidophilum
●​ All higher living organisms including humans are made ●​ can be useful in bioremediation
up of cells.
3.​ EUKARYA
Two major classes: ●​ presence of nucleus in its cell
1. Prokaryotes ●​ Other significant distinctions:
2. Eukaryotes 1. Size - Larger than prokaryotic cell
2. Complexity - Has more number of
HISTORICAL NOTES subcellular structures
3. Multicellularity - All Eukaryotes are
multicellular Except, Protists
Robert Hooke - first person to use the term “cell”. He referred to
the small empty chambers in the structure of cork as cells.
Matthias Schleiden and Theodor Schwann - concluded that all EUKARYOTES PROKARYOTES
plant and animal tissues were composed of cells.
●​ DNA is found in the ●​ DNA is not enclosed
Rudolf Virchow proposed the theory of biogenesis where cells
nucleus of the cell within the membrane
only arise from pre-existing cells
●​ Membrane-bound ●​ Lack membrane-enclosed
organelles organelles
CELL THEORY
●​ Mitosis ●​ Binary Fission
●​ Basic structural and functional unit of living
organisms. So, when you define cell properties, you are
in fact defining the properties of life MOLECULAR COMPOSITION OF CELL
●​ The activity of an organism depends on the collective
activities of its cells.
●​ According to the principle of complementarity, the ●​ Water - 70-75% of the weight of the cell
activities of cells are dictated by their structure ●​ Organic compounds - 25-30% of the cell weight (nucleic
(anatomy), which determines function (physiology). acids, proteins, polysaccharides, lipids)
●​ Continuity of life has a cellular basis ●​ Inorganic compounds - rest of the cell weight

LIVING ORGANISMS EUKARYOTIC CELL

➢​ In terms of type of cells: PARTS/ STRUCTURE FUNCTIONS

1.​ Prokaryotic Cell - Ex. Bacteria, Archaea ORGANELLES
2.​ Eukaryotic Cell - Ex. Animalia, Plantae, Fungi,
single-celled Protists Plasma Phospholipid bilayer ●​ Physical barrier to
Membrane containing cholesterol enclose cell
and proteins and some contents
carbohydrates ●​ Regulates material
➢​forms a selectively movement into and
permeable out of the cell
boundary of the ●​ Functions in cell
cell communication.

Nucleus It is enclosed within a ●​ Contains the DNA

double membrane that serves as the
(nuclear envelope) genetic material
-Contains nucleolus for directing
protein synthesis
Nucleolus - Consists of
RNA and proteins.
1.​ BACTERIA Ribosome subunit
●​ Can cause diseases like cholera, tuberculosis, manufacture
tetanus, and syphilis. Nucleoplasm -
●​ Important in sustaining life on Earth Surrounds the
chromatin and the
○​ Ex. Rhizobium converts N2 to N3
nucleoli
(decomposition)
Interest of humans: Cytoplasm Seen between the ●​ Responsible for
1. Use in production of cheese, yogurt and sourdough plasma membrane and various cellular
bread (eg: yeasts) the nucleus where processes
2. Actinomycetes (decompose organic matter – soil) the other cellular
elements are
embedded
BIOCHEMISTRY OF THE CELL​ ​ ​ ​ LECTURE - PRELIM

Organelles - Lysosomes Spherical shaped ●​ Digest microbes or

membrane-bound membrane bound materials by the
structures which carry organelles formed from cell
out specific metabolic the golgi apparatus
activities of the cell. - Contain digestive
Cytosol - provides enzymes (hydrolases)
support for organelles The fluid inside
and serves as the lysosomes is much
viscous fluid medium more acidic, at about
pH 4.8, to activate
Mitochondria Double-membrane-bou ●​ Production of enzymes.
nd organelles energy in the form
containing a circular of ATP Cytoskeleton Organized network of ●​ Maintains integral
strand of DNA protein filaments structural support
and organization of
Outer membrane - cells
highly permeable to Microfilaments -
small molecules, due to muscle contraction
the presence of a Intermediate
pore-forming protein filaments - stable
called porin. cytoskeletal
Intermembrane - elements; resist
contains many proteins mechanical forces
that participate in Microtubules -
oxidative intracellular and
phosphorylation. cellular movements
Inner membrane - has
multiple folds
projecting inwards, PROKARYOTIC CELL
called cristae

Endoplasmic Rough Endoplasmic ●​ Modifies, ●​ Eubacteria and Archaebacteria

Reticulum Reticulum - Extensive transports, and ●​ Most abundant organisms on earth
interconnected stores proteins ●​ Does not contain a membrane-bound nucleus -
membrane network (glycoprotein)
primitive nucleus
that varies in shape produced by
●​ Surrounded by a plasma membrane
- Ribosomes attached attached
on the cytoplasmic ribosomes ●​ No subcellular organelles, only infoldings of the plasma
surfaces ●​ Synthesize membrane called mesosomes
- for outer through phospholipids ●​ Deoxyribonucleic acid (DNA) is condensed within the
secretory vesicle cytosol to form the nucleoid.
➢​Ribosomes - site ●​ Some prokaryotes have tail-like flagella.
of protein
synthesis;
composed or CELL PHYSIOLOGY
rRNA and protein ●​ Lipid metabolism
(fat, cholesterol),
Smooth Endoplasmic lipid and steroid ●​ All cells exhibit irritability (the ability to respond to
Reticulum - Extensive synthesis drug stimuli)
interconnected detoxification ➢​ Digest foods
membrane network ➢​ Excrete wastes
lacking ribosomes ➢​ Reproduce
➢​ Grow
Golgi Apparatus Series of several ●​ Modifies,packages,
➢​ Move
elongated, flattened and sorts protein,
saclike membranous
➢​ Metabolize
either incorporate
structures to plasma
membrane or MEMBRANE TRANSPORT
inclusion in
lysosome
A.​ PASSIVE PROCESSES
Vesicles - transport ●​ No ATP is required
cellular material.
Mature vesicles are
1.​ Diffusion - movement of a substance from an area of its
called secretory
vesicles
higher concentration to lower concentration. It occurs
because of kinetic energy of the molecules themselves.
Peroxisomes Smaller, spherical ●​ Detoxify toxic ➢​ Simple - lipid-soluble solutes through the
membrane bound substances (free plasma membrane (O2, CO2, steroid hormone,
organelles formed from radicals); catalase, drugs)
the endoplasmic breaks down ➢​ Facilitated - lipid-insoluble thru protein
reticulum hydrogen peroxide carrier
○​ Osmosis - diffusion of water point
across plasma membrane thru
BIOCHEMISTRY OF THE CELL​ ​ ​ ​ LECTURE - PRELIM

aquaporins; H2O moves from low to

high solute concentration

2.​ Filtration - movement of substances through a

membrane from an area of high hydrostatic pressure to CELL LIFE CYCLE
an area of lower fluid pressure. In the body, the driving
force of filtration is blood pressure.
Interphase
B.​ ACTIVE PROCESSES ●​ It is the longer phase of the cell cycle where the cell is
●​ ATP is required; energy is produced when 3rd active and preparing for cell division.
phosphate bond broke and become ADP, P is ●​ The DNA molecule is duplicated exactly in a process
attached to the pump called DNA replication which occurs toward the end of
the interphase.
1.​ Active Transport - substances are moved across the
membrane against an electrical or a concentration Cell Division
gradient by proteins called solute pumps. ●​ Cells arise from the division of other cells.
➢​ Solute Pumps - accounts for the transport of ➢​ Mitosis - four stages, two identical daughter nuclei
amino acids, some sugars, and most ions. (ex: 1.​ Prophase- each chromosome consists of two
Na-K activated ATPase) chromatids joined at the centromere.
2.​ Metaphase- chromosomes align at the center
of the cell.
3.​ Anaphase- chromatids separate at the
centromere and migrate to opposite poles.
4.​ Telophase- two new nuclei assume their
normal structure, and cell division is
completed, producing two new daughter cells

2.​ ATP-activated Vesicular Transport - transport of

macromolecules which can neither travel through the
membrane by diffusion nor by active transport
mechanisms.

2 TYPES:
➢​ Exocytosis - bulk movement of substance out
of the cell by fusion of secretory vesicles with
the plasma membrane.

➢​ Endocytosis - bulk movement of substance

into the cell by vesicles forming at the plasma
membrane.
PROTEINS​ ​ ​ ​ ​ ​ ​ LECTURE - PRELIM

2. Polar Acidic - contain carboxyl group

CHARACTERISTICS OF PROTEINS at part of the side chain
➢​ 2 amino acids

●​ naturally-occurring, unbranched polymer in

which the monomer units are amino acids
●​ Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen
(O), most also contain Sulfur (S).
●​ Average nitrogen content: 15.4% by mass
●​ Also present are Iron (Fe), phosphorus (P) and some
other metals in some specialized proteins.

AMINO ACIDS 3. Polar Basic - amino group as part of

the side chain
➢​ 3 amino acids
●​ Organic compound that contains both an amino (-NH2)
and carboxyl (-COOH) groups attached to same carbon
atom (ɑ carbon atom)
●​ R = side chain –vary in size, shape, charge, acidity,
functional groups present, hydrogen-bonding ability,
and chemical reactivity.
➢​ >700 known amino acids
➢​ Based on common “R” groups, there are 20
standard amino acids

9 Essential 11 Non-Essential

1. Histidine (basic) 1. Alanine (nonpolar) NOMENCLATURE

2. Isoleucine (nonpolar) 2. Arginine - required for growth
3. Leucine (nonpolar) in children but not for adults
4. Lysine (basic) (basic) ●​ Common names
5. Methionine (nonpolar) 3. Asparagine (neutral) ●​ Three letter abbreviations - widely used for naming:
6. Phenylalanine (nonpolar) 4. Aspartic acid (acidic) ➢​ 1st letter - compulsory and capitalized
7. Threonine (neutral) 5. Cysteine (neutral) ➢​ Next two letters not capitalized (except in the
8. Tryptophan (nonpolar) 6. Glutamic acid (acidic)
case of Asparagine (Asn), Glutamine (Gln) and
9. Valine (nonpolar) 7. Glutamine (neutral)
8. Glycine (nonpolar) tryptophan (Trp))
- Are not synthesized by 9. Proline (nonpolar) ●​ One-letter symbols - commonly used for comparing
the body but needed 10. Serine (neutral) amino acid sequences of proteins:
therefore must be 11.Tyrosine (neutral) ➢​ Usually the first letter of the name
obtained from dietary ➢​ When more than one amino acid has the same
sources in adequate
letter the most abundant amino acid gets the
amounts
1st letter

TYPES CHIRALITY AND AMINO ACIDS

NON-POLAR POLAR
●​ Should 4 different groups attached to carbon if have
●​ Hydrophobic ●​ Hydrophilic
similar means achiral
●​ Water fearing ●​ Water loving
●​ 19 of the 20 standard amino acids contain a chiral
●​ R-groups are polar
SUBTYPES: center (Achiral is Glycine because R group is hydrogen
-​ Alkyl SUBTYPES: atom)
-​ Aromatic 1. Polar Neutral - neutral side chain ●​ Chiral center - exhibit enantiomerism (left and right
➢​ 6 amino acids handed forms)
●​ Amino acids and proteins found in nature are L isomers
➢​ Bacteria do have some D-amino acids
➢​ With monosaccharides nature favors
D-isomers
●​ Rules for drawing Fischer projection formulas for amino
acid structures:
➢​ -COOH at top and R group at bottom to
position carbon chain vertically
➢​ -NH2 is in a horizontal position
➔​ L isomer - at the left
➔​ D isomer - at the right
 ISOMETRIC PEPTIDES
ACID-BASE PROPERTIES

●​ Peptides that contain the same amino acids but

●​ In pure form amino acids are white crystalline solids present in different order are different molecules
●​ Most amino acids decompose before they melt (constitutional isomers) with different properties.
●​ Not very soluble in water ●​ The number of isomeric peptides possible increases
●​ Exists as Zwitterion: An ion with + (positive) and – rapidly as the length of the peptide chain increases.
(Negative) charges on the same molecule with a net
zero charge BIOCHEMICALLY IMPORTANT SMALL PEPTIDES

●​ Small peptides are biochemically active:

SMALL PEPTIDES EXAMPLES

1. Hormone ●​ Best-known peptide hormones:

➢​ Carboxyl groups give-up a proton to get oxytocin (uterine contraction,
negative positive feedback) and
➢​ Amino groups accept a proton to become vasopressin (ADH, helps in
positive regulating water and blood
●​ Amino acids in solution exist in three different species pressure, it excretes water)
(zwitterions, positive ion, and negative ion) - ●​ Produced by the hypothalamus
Equilibrium shifts with change in pH stored in the posterior pituitary
●​ Isoelectric point (IP) – pH at which the concentration of gland
Zwitterion is maximum -- net charge is zero ●​ Nonapeptide (nine amino acid
○​ Different amino acids have different residues) with six of the residues
isoelectric points held in the form of a loop by a
○​ At isoelectric point - amino acids are not disulfide bond formed between two
attracted towards an applied electric field cysteine residues
because they net zero charge.

CYSTEINE: A CHEMICALLY UNIQUE AMINO ACID

●​ the only standard amino acid with a sulfhydryl group ( —

SH group).
2. Neurotransmitter ●​ Enkephalins - Pentapeptide
●​ The sulfhydryl group imparts cysteine, a chemical
neurotransmitters produced by the
property unique among the standard amino acids.
brain and bind receptor within the
●​ Cysteine in the presence of mild oxidizing agents
brain
dimerizes to form a cystine molecule.
●​ Help reduce pain
➢​ Cystine - two cysteine residues linked via a
covalent disulfide bond.
Best-known enkephalins:
➢​ Met-enkephalin:
PEPTIDES Tyr–Gly–Gly–Phe–Met
➢​ Leu-enkephalin:
●​ Linked amino acids Tyr–Gly–Gly–Phe–Leu
1.​ Dipeptide - bond between two amino acids
2.​ Oligopeptide - bond between 10-20 3. Antioxidants ●​ Glutathione (Glu–Cys–Gly) – a
3.​ Polypeptide - bond between large number of tripeptide – is present in high levels
amino acids in most cells
●​ Every peptide has an N-terminal end and a C-terminal ●​ Regulator of oxidation–reduction
end reactions.
+H3N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COO- ●​ Protects cellular contents from
oxidizing agents such as peroxides
NOMENCLATURE and superoxides.
RULE 1. The C-terminal amino acid residue keeps its full amino ➢​ Highly reactive forms of
acid name. oxygen often generated
RULE 2. All of the other amino acid residues have names that within the cell in response to
end in -yl. The -yl suffix replaces the -ine or -ic acid ending of the bacterial invasion
amino acid name, except for tryptophan, for which -yl is added to ●​ Unusual structural feature – Glu is
the name. bonded to Cys through the
RULE 3. The amino acid naming sequence begins at the N- side-chain carboxyl group.
terminal amino acid residue.

Example:
• Ala-leu-gly has the IUPAC name of alanylleucylglycine
GENERAL STRUCTURAL CHARACTERISTICS OF PROTEINS

●​ A protein is a peptide in which at least 40 amino acid

residues are present:
➢​ Several proteins: >10,000 amino acid residues
are known
➢​ Common proteins: 400–500 amino acid
2. Beta-pleated sheet (b-pleated sheet) -
residues
Completely extended amino acid chains
➢​ Small proteins: 40–100 amino acid residues
●​ H-bonding between two different
●​ Monomeric: one peptide chain
chains – inter and/or
●​ Multimeric: more than one peptide chain
intramolecular
●​ Side chains below or above the axis
PROTEIN CLASSIFICATION BASED ON CHEMICAL
COMPOSITION 3. Tertiary ●​ Overall three-dimensional shape of a
protein
●​ Results from the interactions between
SIMPLE ●​ A protein in which only amino acid amino acid side chains (R groups) that are
PROTEIN residues are present widely separated from each other.

CONJUGATED ●​ One or more non-amino acid entities Four Types of Interactions

PROTEIN (prosthetic groups) present in its 1. Disulfide bond: covalent, strong, between
structure: two cysteine groups
●​ One or more polypeptide chains may be 2. Electrostatic interactions: Salt Bridge
present between charged side chains of acidic and
●​ May be organic or inorganic - prosthetic basic amino acids
groups ➢​ -OH, -NH2, -COOH, -CONH2
➢​ Lipoproteins contain lipid 3. H-Bonding between polar, acidic and/or
prosthetic groups basic R groups
➢​ Glycoproteins contain ➢​ For H-bonding to occur, the H must
carbohydrate groups be attached on O, N or F
➢​ Metalloproteins contain a specific 4. Hydrophobic interactions: Between
metal as prosthetic group nonpolar side chains

4. Quaternary ●​ HIGHEST level of protein organization

FOUR TYPES OF STRUCTURES
●​ Most multimeric proteins contain an
even number of subunits (two subunits a
dimer, four subunits a tetramer, and so
STRUCTURES DESCRIPTION
on)
1. Primary ●​ Amino acids are linked together in a ●​ The subunits are held together mainly by
protein hydrophobic interactions between amino
●​ Every protein has its own unique amino acid R groups.
acid sequence
➢​ Frederick Sanger (1953) Hemoglobin - the oxygen carrying protein in
sequenced and determined the blood
primary structure for the first ●​ Tetramer - two identical a chains
protein - Insulin and two identical B chains.
●​ Each chain enfolds a heme group -
2. Secondary ●​ Arrangement of atoms of backbone in functional unit; the site where
space. oxygen binds to the protein.

Most common types:

1. alpha-helix (a-helix) - A single protein
chain adopts a shape that resembles a
coiled spring (helix):
●​ H-bonding between same amino
acid chains –intra molecular
●​ Coiled helical spring
●​ R-group outside of the helix -- not
enough room for them to stay
inside
 PROTEIN CLASSIFICATION cartilage
➢​ Keratin - gives mechanical
strength as well as protective
BASED ON SHAPE covering to hair, fingernails,
feathers, hooves, etc. prevents
FIBROUS PROTEIN GLOBULAR PROTEIN
the skin from desiccation
Collagen - Most abundant Myoglobin - Oxygen storage
7. Span a cell membrane and help control
proteins in humans (30% of molecule in muscles Transmembrane the movement of small molecules and
total body protein) ●​ Monomer - single peptide ions
●​ Major structural material
chain with one heme unit ➢​ Protein channels – help
in tendons, ligaments, molecules can enter and exit the
●​ Binds one O2 molecule
blood vessels, and skin cell.
●​ Has a higher affinity for
●​ Organic component of ➢​ Transport is very selective -
oxygen than hemoglobin.
bones and teeth allow passage of one type of
●​ Oxygen stored in myoglobin
●​ Predominant structure - molecule or ion
molecules serves as a
triple helix
reserve oxygen source for 8. Storage Bind (and store) small molecules
●​ Rich in proline (up to
working muscles ➢​ Ferritin - an iron-storage protein
20%) – important to - saves iron for use in the
maintain structure biosynthesis of new hemoglobin
Hemoglobin - oxygen carrier
molecules.
molecule in blood
➢​ Myoglobin - an oxygen-storage
●​ Transports oxygen from protein present in muscle
lungs to tissues
●​ Tetramer (four peptide 9. Regulatory Often found “embedded” in the exterior
chains) - each subunit has a surface of cell membranes - act as sites
heme group for receptor molecules
●​ Can transport up to 4 ➢​ Often the molecules that bind to
enzymes (catalytic proteins),
oxygen molecules at time
thereby turning them “on” and
●​ Iron atom in heme interacts “off,” and thus controlling
with oxygen enzymatic action

10. Nutrient Particularly important in the early stages

BASED ON FUNCTION
of life - from embryo to infant
●​ Ability to bind small molecules specifically and strongly ➢​ Casein (¾ in milk) and
●​ Ability to bind other proteins and form fiber-like ovalbumin (50% of egg white)
structures are nutrient proteins
●​ Ability integrated into cell membranes ➢​ Milk also provide immunological
protection for mammalian young
MAJOR DESCRIPTION
CATEGORIES
PROTEIN HYDROLYSIS
1. Catalytic Enzymes
●​ Almost every chemical reaction in the
●​ Results in the generation of an amine and a carboxylic
body is driven by an enzyme
acid functional groups.
●​ Digestion of ingested protein is enzyme-catalyzed
2. Defense Immunoglobulins or antibodies in body’s
immune system hydrolysis
●​ Free amino acids produced are absorbed into the
3. Transport Bind small biomolecules Ex. hemoglobin bloodstream and transported to the liver for the
➢​ Ex. oxygen and other ligands, synthesis of new proteins.
and transport them to other ●​ Hydrolysis of cellular proteins and their resynthesis is a
locations in the body and release
continuous process.
them on demand.

4. Messenger Transmit signals to coordinate PROTEIN DENATURATION

biochemical processes between different
cells, tissues, and organs.
➢​ Insulin and glucagon - regulate ●​ Partial or complete disorganization of protein’s tertiary
carbohydrate metabolism structure
➢​ Human growth hormone – ➢​ Cooking food denatures the protein but does
regulate body growth not change protein nutritional value. Makes
easy for enzymes in our body to
5. Contractile Necessary for all forms of movement.
➢​ Muscles contain filament-like hydrolyze/digest protein
contractile proteins (actin and ●​ Kills microorganisms
myosin). ➢​ Fever - > 104℉ - critical enzymes of the body
➢​ Human reproduction depends start getting denatured
on the movement of sperm –
possible because of contractile Coagulation: Precipitation (denaturation of proteins)
proteins.
●​ Egg white - a concentrated solution of protein albumin -
6. Structural Confer stiffness and rigidity when heated = jelly = albumin is denatured
➢​ Collagen - a component of
 GLYCOPROTEINS

●​ Conjugated proteins with carbohydrates linked to them:

➢​ Plasma membrane proteins
➢​ Blood group markers of the ABO system -
antigens
➢​ Collagen and immunoglobulins
1.​ Collagen
➢​ Most abundant protein in human body (30% of
total body protein)
➢​ Triple helix structure
➢​ Rich in 4-hydroxyproline (5%) and
5-hydroxylysine (1%) — derivatives
➢​ Some hydroxylysines are linked to glucose,
galactose, and their disaccharides – help in
aggregation of collagen fibrils.

Immunoglobulins
●​ Produced as a protective response to the invasion of
microorganisms or foreign molecules - antibodies
against antigens
●​ Bonding to an antigen via variable region of an
immunoglobulin occurs through hydrophobic
interactions, dipole – dipole interactions, and hydrogen
bonds

Purple - constant region

Red - variable region

LIPOPROTEINS

●​ a conjugated protein that contains lipids in addition to

amino acids
●​ help suspend lipids and transport them through the
bloodstream

Four major classes of plasma lipoproteins:

CLASSES FUNCTION

1. Chylomicrons Transport dietary exogenous

triacylglycerols from intestine - liver -
adipose tissue

2. Very- low- Transport endogenous triacylglycerols

density lipoproteins synthesized in the liver - adipose
(VLDL) tissue

3. Low-density Transport cholesterol synthesized in

lipoproteins (LDL) the liver to cells throughout the body
“Bad” “Lethal” cholesterol that form
plaques in arteries causing them to
harden and narrow

4. High-density Collect excess cholesterol from body

lipoproteins (HDL) tissues and transport it back to the
liver for degradation to bile acids
“Good” “Happy” cholesterol that help
arteries clear and free of plaques