Biomolecules

- Chemical substances found within a living organism

Biochemical substance
Bio- inorganic substances Bio- organic substances
Do not contain carbon Contain carbon

Water Proteins
Inorganic salts Lipids
Carbohydrates
Nucleic acids
Carbohydrates
- Most abundant organic compounds in nature with a variety of functions in the plant world
- Should be majority of energy source (45- 65%)
- 4kcal/gram
- (CH2O) n
- Hydrates of carbon
- Saccharide because of sweet tasting sugars
- “Saccharum”- sugar
- Polyhydroxyaldehyde or polyhydroxyketone
Functions
1. Carbohydrate’s oxidation provides energy
2. Storage, in the form of glycogen, provides a short- term energy reserve
3. Supply carbon atoms for the synthesis of other biochemical substances (proteins, lipids, and
nucleic acid)
4. Essential components of nucleic acid (RNA- D-ribose; DNA- D- Deoxyribose)
5. Linked to lipids are structural components of cell membranes
6. Linked to proteins function in a variety of cell- cell and cell- molecule recognition process.
7. Supportive structure in plants
8. Structural components of bacterial cell wall and exoskeleton of insects
Physical Properties
Colorless
Crystalline solids
Very soluble in water
Insoluble in non- polar solvents
Classification
According to molecular size
1. Monosaccharide
- Contains a single polyhydroxyaldehyde or polyhydroxyketone unit (Simple sugars)

2. Oligosaccharide
- Contains 2 to 20 monosaccharide units covalently bonded to each other
- Disaccharide- contains 2 monosaccharide units covalently bonded to each other.; crystalline
water- soluble substances

3. Polysaccharide
- Contains many monosaccharide units covalently bonded to each other.

Number of Carbons
Triose 3 carbon monosaccharide
Tetrose 4 carbon monosaccharide
Pentose 5 carbon monosaccharide
Hexose 6 carbon monosaccharide
 Lipids
- Soluble in organic solvents, but are not soluble in water.
- Collection of organic molecules of varying chemical composition
- Grouped on the basis of their solubility in non- polar solvents
- Non- polar (polar O-H bonds; more non- polar C- H bonds)
- Fatty acids consist of hydrocarbon chain with a carboxylic acid at 1 end
- Most membrane are amphipathic
Classes of lipids
1. Fatty Acids - terminal carboxylic acid moiety and
long saturated or unsaturated carbon
atoms
2. Phosphologlycerides or - from fatty acids & glycerol-3-phosphate,
glycerophospholipids and triglycerides
3. Sphingolipids - from fatty acids and sphingosine
4. Sterols - four fused rings (the steroid nucleus)
5. Terpenes - isoprene units (2-methyl-1,3-butadiene)
Roles Functions and properties
1. Form phospholipids and glycolipids 1. Source of energy (9kcal/g)
2. As hormones and messengers inside 2. Energy reserve/storage
cells, for communication and regulation 3. Provide insulation to the body from
3. As fuel molecules and as a way for cells cold
to store energy 4. Supply essential fatty acids
4. As “molecular recognition” features 5. Helps in the formation of cell
membranes
6. Mechanical insulation
Fatty Acids and Glycerides
- Long chain monocarboxylic acids
- CH3 (CH2) n COOH
- Length of the chain ranges from 12 to 24, always with an even number of carbon atoms
Saturated Unsaturated
- No double bonds - One or more double bonds (reduces
-Fatty acid with a carbon chain in which all C-C melting point)
bonds are single bonds - A monounsaturated fatty acid is a fatty acid with
-Numbering starts at the end of -COOH grp a carbon chain in which one carbon–carbon
-Structural notation: it indicates number of C double bond is present.
atoms -Different ways of depicting the structure
-e.g.Lauricacid has 12 C atoms and no double
bondsso it is (12:0)

- Closely packed - Nonlinear chains do not allow molecules

- Strong attractions between chains to pack closely
- High melting points - Few Interactions between chains
- Solid at RT - Low melting points
- Liquids at RT
2 types
1. Omega- 3 fatty -An unsaturated fatty
acids acid with its endmost
 double bond three
carbon atoms away
from its methyl end.
- 2. Omega- 6 fatty -An unsaturated fatty
acid acid with its endmost
double bond six carbon
atoms away from its
methyl end.
Things in common
1. Fatty acids are practically all unbranched carboxylic acids
2. Range in size from 10- 20 carbons
3. Contain an even number of carbon atoms
4. Apart from the – COOH group, they have no functional groups, except that some do have
double bonds
5. In most fatty acids that have double bonds, the cis isomers predominate.
Triglycerides - Animal fats and plant oils
- Triesters of glycerol and long chain
carboxylic acids called fatty acids
- Alcohol is glycerol
- Acid components may be any number of
fatty acids
Monoglycerides - only one or two –OH groups of the
glycerol are esterified by fatty acids.
Properties of Triglycerides
1. Physical State - Fats from animals are generally solids
at rt
- Solid animal fats contain mainly saturated
fatty acids
- Oils are liquid fats from plants or fish
- Vegetable oils contain high amounts of
unsaturated fatty acids
2. Hydrogenation - Convert unsaturated liquid oils to solid
- Manufacturers must be careful not to
hydrogenate all of the double bonds,
because a fat with no double bonds would
be too solid
- Partial hydrogenation- results in a product
with just the right consistency of cooking
- E. g. Margarine- contains more
unsaturation than fully hydrogenated
shortenings- the source of trans fatty acids
3. Saponification - Hydrolysis with a strong base
- Triglycerides split into glycerol and the
salts of fatty acids
- The salts of fatty acids are “soaps”
- NaOH gives hard soaps
- KOH gives softer soaps
Physical properties of fatty acids
1. Melting point Depends upon length of chain and degree of
unsaturation
- Greater than that of an unsaturated fatty
acid of the same chain length
2. Space- Filling Molecules The number of bends in a fatty acid chain
increase as the number of double bonds
increase
- Less packing occurs
- Melting point is lower
- Tend to be liquids at room temp
3. Selected Unsaturated Fatty Acids of Numbering starts from the other end of -COOH
Biological Importance - Structural notation: It indicates number of
C atoms
- e.g.18:2 –18 carbons, 2 double bonds

Types of Lipids
Homo Lipids
1. Fats and - Fats consist of a wide group of compounds that are generally soluble in
Oils organic solvents and largely insoluble in water
- Lipids used to refer to both liquid and solid fats
- Oild used for any substance that does not mix with water and has a
greasy feel, such as petroleum and heating oil
2. Waxes - fatty acids and an alcohol
- more hydrophobic than fats
- the natural coatings for apples and pears
Compound Lipids
1. Phospholip - have two regions named as head and tail
ids - heads are hydrophilic while tails are hydrophobic

Primary Functions:
1. As membrane component
- predominant constituent of most membranes

2. In surfactant action
- Dipalmitoyl Lecithin in the lung serves to reduce surface tension in
alveoli and allow expansion and contraction of lung tissue

3. Phosphatidycholine
- acts as phatidlins, a detergent and solubilizing agent in bile, to dissolve
and transport cholesterol

4. For communication-
- Phosphatidylinositol 4,5- biphosphate plays a central role in one of the
major signal transduction pathways
2. Glycolipids - Compounds of fatty acids with carbohydrates and contain nitrogen but
no phosphoric acid
Categories of Lipids based on function
1. Energy - Triglycerols
 storage - Connected in adipocytes
- Large quantities of them can be packed into a very small volume
- Triesters
- Alcohol- glycerol
- Formed by esterification of 3 fatty acids to a glycerol molecule
Fats- naturally occurring complex mixtures of triacylglycerol molecules in
which many different kinds of triacylglycerol molecules are present

Oils- naturally occurring complex mixtures of triacylglycerol molecules in

which there are many different kind of triacyglycerol molecules present
2. Membrane Phospholipids Lipid that contains one or more fatty acids;
phosphate group, platform to which phosphate
group and fatty acid are attached, alcohol that is
attached to phosphate group
- 3- carbon alcohol glycerol or a more complex
C18 aminodialcohol called sphingosine
- Most abundant type of membrane lipid

Glycerophospholipids - Glycerol- based

- Contains 2 fatty
acids and a
phosphate group
esterified to a
glycerol molecule
and an alcohol
esterified to the
phosphate group
- Because of ester
linkages, they
undergo
hydrolysis and
saponification
reactions similar
to glycoproteins
- H3PO4 parent
source for the
minus one
charged phosphate
group used I the
formation of
glycerophopholipi
ds
Phosphatidylcholine - Also known as
lecithins
- Waxy solids that
form colloidal
suspensions in
water
- E. g. egg yolks
and soybeans
Lecithinase - Enzyme in the
intestine that
hydrolyzes most
of the
phosphatidylchol
ine
- Used as
emulsifiers to
promote the
mixing of
otherwise
immiscible
materials
(mayonnaise, ice
cream and
custards)
Phosphatidylethanolami - Found in heart
nes and and liver tissue
phosphatidylserines and in high
concentration in
the brain
- Important in
blood clotting
- A.k.a cephalins
Inositides - Phospholipids in
which inositol is
the attached
alcohol
- Important role in
biological signal
transduction and
in anchoring
glycoproteins to
the plasma
membrane of the
cell
Phosphatidate - Phospholipids
with no alcohol
attached
Lysophosphatidate - If only one fatty
acid is attached
to glycerol
backbone
- Is a
monoacylglycerol
phosphate
Lysolecithin - Lyso comes from
the detergent
action, which
readily solubilizes
 biomembranes
and causes cell
lysis
Cardiolipin - Complex
phosphoglyceride
which may help
to stiffen certain
biological
membranes
Sphingophospholipi - Based on the 18- carbon monounsaturated
ds aminodialcohol sphingosine
- Contains: 1 fatty acid; 1 phosphate group
attached to a sphingosine molecule and an
alcohol attached to the phosphate group.
Roles:
1. Certain sphingolipids act intracellularly as
second messengers in signal transduction
pathways, helping to regulate cell division,
differentiation, migration, and apoptosis
(programmed cell death)

2.As membrane components, they tend to rigidify or

stiffen the lipid bilayer and to reduce diffusibility of
integral membrane components.

14. With CHO modifications, sphingolipids in cell

membranes act as points for biological
recognition, as in the human group types.

Sphingomyelins - Sphingopholipid
s in which the
alcohol
esterified to the
phosphate group
is choline

- Found in all cell

membranes and
are important
structural
components of
the myelin
sheath, the
protective and
insulating
coating that
surrounds
nerves
Ceramide - The N-acetyl
derivative of
 sphingosine;
fatty acid is
behenic acid
- Its reaction
leads to
sphingomyelin
and cerebrosides
galactosylceram
ide and
glucosylceramid
e
Cerebrosides - The simplest
sphingoglycolip
ids
- Contain a single
monosaccharide
unit- either
glucose or
galactose
- Occur primarily
in the brain
- Present in the
myelin sheath of
nerves
Gangliosides - More complex
sphingoglycolip
ids, contain a
branched chain
of up to seven
monosaccharide
residues
- Occur in the
gray matter of
the brain as well
as in the myelin
sheath
Cholesterol - C27 steroid molecule that is a component of cell
membranes and a precursor for the other
steroid- based lipids
- Most abundant steroid in the human body
- Found in cell membranes: 25% by mass in
nerve tissue; 10% in brain tissue
- In all fluids

Roles:
1. Precursor to digestive and solubilizing agents
2. Precursor to steroid hormones such as the
gonadal hormones estradiol and testosterone
and cortisol
3. Serves as membrane constituents that helps to
 stiffen neighboring acyl groups and reduce their
flexibility
20. Emulsificat
ion
21. Messenger
22. Protective-
coating
 Proteins
Characteristics of proteins Amino Acids
1. A naturally-occurring, unbranched - An organic compound that contains both an
polymer in which the monomer units amino (-NH2) and a carboxyl (-COOH)
are amino acids group attached to same carbon atom

2. Most abundant molecules in the cells
after water –account for about 15% of
a cell’s overall mass
3. Elemental composition -Contain
Carbon (C), Hydrogen (H), Nitrogen
(N), Oxygen (O), and Sulfur (S)
- position of carbon atom is Alpha (a)
- NH2group is attached at alpha (a) carbon
atom
- COOH group is attached at alpha (a) carbon
atom

4. The average nitrogen content of
proteins is 15.4% by mass
5. Present are Iron (Fe), phosphorus (P)
and some other metals in some
specialized proteins
- R = side chain –vary in size, shape, charge,
acidity, functional groups present, hydrogen-
bonding ability, and chemical reactivity
- >700 amino acids are known
- Based on common “R”groups, there are 20
standard amino acids

- differ from one another by their R-groups

- There are 20 common (standard) amino acids

- Standard amino acids are divided into four

groups based on the properties of R-groups

- Non-polar amino acids: R-groups are non-

polar

- Such amino acids are hydrophobic-water

fearing (insoluble in water)

- 8 of the 20 standard amino acids are non-

polar

- When present in proteins, they are located in

the interior of protein where there is no
polarity

Polar amino acids (R- Three types: Polar

groups are polar) neutral; Polar acidic; and
Polar basic
Polar-neutral contains polar but
neutral side chains
- Seven amino
 acids belong to
this category
Polar acidic Contain carboxy group
as part of the side
chain.
- Two amino
acids belong to
this category
Polar basic Contain amino group as
part of the side chain
- Two amino
acids belong to
this category
Roles of Amino Acids Nomenclature
1. Polymerized to form peptides •Common names assigned to the amino acids are
currently used.
2. Serve as precursors for other small •Three letter abbreviations -widely used for naming:
biomolecules (e. g. purines, - First letter of amino acid name is compulsory
pyrimidines, porphyrins) and capitalized followed by next two letters
not capitalized except in the case of
3. Oxidized to serve as an energy Asparagine (Asn), Glutamine (Gln) and
source (fuel) for the cell tryptophan (Trp).
•One-letter symbols -commonly used for comparing
amino acid sequences of proteins:
- Usually, the first letter of the name
- When more than one amino acid has the
same letter the most abundant amino acid
gets the 1st letter.
•Both types of abbreviations are given in the
following slides
Essential Amino Acids Classification by properties
•Essential Amino acid: A standard amino Class Members Properties
acid needed for protein synthesis that must 1 Gly Simple
be obtained from dietary sources –adequate hydrogenatom
amounts cannot be synthesized in human body. side chain; Non-
polar The H
•Nine of the 20 standard amino acids are atom presents
considered essential the least steric
hindrance to
1. Arganine rotation or
2. Histidine packing of
3. Isoleucine neighboring
4. Leucine groups in a
5. Lysine protein, so Gly
6. Methionine residues can
7. Phenylalanine contribute
8. Threonine strongly to
9. Trytophan protein
10. Valine flexibility.
2 Ala, Val, Aliphatic side
 Leu, Ile chains, bulky
and non- polar

The nonpolar
character of the
side chains of
these amino
acids makes their
surface
hydrophobic and
the packing of
these side chains
also contributes
to forming
specific shapes
for binding sites
on the surface of
proteins.
3 Pro Side-chain loop
connecting α-
carbon and α-
amino group;
non-polar and
rigid

The rigidity of
Pro residues is
an important
factor in
determining how
a polypeptide
chain will fold
into its native
protein structure.
4 Phe, Tyr, Trp Aromatic
sidechains;
bulky, nonpolar

The aromatic
side chains are
hydrophobic and
bulky; they
affect protein
packaging.
These side
chains may also
be used for
molecular
recognition in
binding sites on
 protein surfaces.
5 Cys, Met Sulfur-
containing non-
polar side
chains; reactive
thiol on Cys

Two Cys
residues can
form a disulfide
bridge (a Cystine
residue) and they
can cross-link a
peptide chain
with itself or
with another
chain; this is
important in
stabilizing
tertiary or
quaternary
protein
conformations.
The sulfur atom
in Met is
relatively
polarizable and
can contribute to
molecular
recognition in
binding sites.
6 Ser, Thr Alcohols;
hydrophilic and
reactive
hydroxyl
groups

The hydroxyl
group on the side
chain is only
very weakly
acidic, but it is
an important site
for protein
modification that
can affect the
overall
functioning of
the protein.
7 Glu, Asp Carboxylic
acids; anionic
 The carboxyl
groups of their
side chains are
ionized to anions
under
physiological
conditions; this
contributes to the
overall charge on
a protein,
important for its
solubility and for
recognition of
binding partners.
8 Gln, Asn Amides of
carboxylic
acids; polar,
bulky

These amides are

not titrable, but
they are highly
polar, and they
participate in
hydrogen
bonding quite
readily.
9 His, Lys, Arg Basic side
chains; cationic
Lys and Arg,
but titrable
imidazole ring
on His

The imidazole-
ring nitrogens
can also help
bind metal ions.
Lys has its
amino group at
the end of a
relatively long
chain, allowing
flexibility in
positioning the
terminus in
active sites, or
forming amide
links to carboxyl
groups of
 cofactors such as
biotin.
Chirality and Amino Acids Acid–Base Properties of Amino Acids
•Four different groups are attached to the a- •In pure form amino acids are white crystalline solids
carbon atom in all of the standard amino acids •Most amino acids decompose before they melt
except glycine •Not very soluble in water
- In glycine R-group is hydrogen •Under physiological conditions exists as
•Therefore 19 of the 20 standard amino acids Zwitterions: An ion with + (positive) and –
contain a chiral center (Negative) charges on the same molecule with a net
•Molecules with chiral centers exhibit zero charge
enantiomerism (left-and right-handed forms) - Carboxyl groups give-up a proton to get
negative charge
•The amino acids found in nature as well as in - Amino groups accept a proton to become
proteins are L isomers. positive
- Bacteria do have some D-amino acids
- With monosaccharides nature favors Isoelectric Point (pI)
D-isomers •Amino acids in solution exist in three different
•The rules for drawing Fischer projection species (zwitterions, positive ion, and negative ion)
formulas for amino acid structures -Equilibrium shifts with change in pH
- The —COOH group is put at the top,
- The R group is place at the bottom •Isoelectric point (pI) –pH at which the concentration
position of the carbon chain vertically of Zwitterion is maximum --net charge is zero
- The —NH2group is placed in a - Different amino acids have different
horizontal position. isoelectric points
- Positioning —NH2on the left -L - At isoelectric point -amino acids are not
isomer attracted towards an applied electric field
- Positioning —NH2on the right -D because they carry net zero charge.
isomer.
Cysteine: A Chemically Unique Amino Acid
the only standard amino acid with a sulfhydrylgroup ( —SH group).
•The sulfhydryl group imparts cysteine a chemical property unique among the standard amino acids.
•Cysteine in the presence of mild oxidizing agents dimerizesto form a cystine molecule.
- Cystine-two cysteine residues linked via a covalent disulfide bond.
Peptides
Nature of Peptide bond Biochemically Important Small Peptides
•Under proper conditions, amino acids can •Many relatively small peptides are biochemically
bond together to produce an unbranched chain active:–Hormones–Neurotransmitters–Antioxidants
of amino acids.
- The reactions are between amino •Small Peptide Hormones:–Best-known peptide
group of one amino acid and carboxyl hormones: oxytocin and vasopressin –Produced by
group of another amino acid. the pituitary gland–Nonapeptide (nine amino acid
•The length of the amino acid chain can residues) with six of the residues held in the form of
vary from a few amino acids to hundreds a loop by a disulfide bond formed between two
of amino acids. cysteine residues
•Such a chain of covalently-linked amino
acids are called a peptide.
•The covalent bonds between amino acids
in a peptide are called peptide
bonds(amide).
Dipeptide bond between two Small Peptide •Enkephalins are
 amino acids Neurotransmitters pentapeptide
neurotransmitters
produced by the brain
and bind receptors
within the brain
•Help reduce pain

•Best-known
enkephalins:–Met-
enkephalin: Tyr–Gly–
Gly–Phe–Met–Leu-
enkephalin: Tyr–Gly–
Gly–Phe–Leu

Oligopeptide bond between ~ 10 -20 Small Peptide •Glutathione (Glu–Cys–

amino acids Antioxidants Gly) –a tripeptide –is
present is in high levels
in most cells

•Regulator of oxidation–
reduction reactions.

•Glutathioneis an
antioxidant and protects
cellular contents from
oxidizing agents such as
peroxides and
superoxides
- Highly reactive
forms of oxygen
often generated
within the cell
in response to
bacterial
invasion
•Unusual structural
feature –Glu is bonded
to Cys through the side-
chain carboxyl group.
Polypeptide bond between large
number of amino acids
Peptide Nomenclature
•The C-terminal amino acid residue keeps its
full amino acid name.
•All ofthe other amino acid residues have
names that end in -yl. The -yl suffix replaces
the -ine or -ic acid ending of the amino acid
name, except for tryptophan, for which -yl is
added to the name.
•The amino acid naming sequence begins at
the N-terminal amino acid residue.

•Example:–Ala-leu-gly has the IUPAC name

of alanylleucylglycine

Isomeric Peptides •Peptides that contain

the same amino acids
but present in different
order are different
molecules
(constitutional isomers)
with different
properties–For
example, two different
dipeptides can be
formed between alanine
and glycine

•The number of
isomeric peptides
possible increases
rapidly as the length of
the peptide chain
increases
General Structural Characteristics of Proteins
•General definition: A protein is a naturally-occurring, unbranched polymer in which the monomer
units are amino acids.

•Specific definition: A protein is a peptide in which at least 40 amino acid residues are present:
- The terms polypeptide and protein are often used interchangeably to describe a protein
- Several proteins with >10,000 amino acid residues are known
- Common proteins contain 400–500 amino acid residues
- Small proteins contain 40–100 amino acid residues

•More than one polypeptide chain may be present in a protein:

- Monomeric: Contains one polypeptide chain
- Multimeric: Contains 2 or polypeptide chains

- Peptide chains are called protein subunits

- Protein subunits may all be identical to each other or may have different kinds of subunits

•Insulin-a small protein which functions as a hormone in the human body-a multimericprotein

-contains 2 protein subunits:

- one subunit contains 21 AA residues

- another subunit contains 30 AA residues

Protein Classification Based on Chemical Composition

Simple proteins A protein in which only amino acid residues are
 present:
–More than one protein subunit may be present but
all subunits contain only amino acids

Conjugated (complex) proteins
A protein that has one or more non-amino acid
entities (prosthetic groups) present in its structure:
- One or more polypeptide chains may be
present
- Non-amino acid components -may be
organic or inorganic -prosthetic groups
- Lipoproteins contain lipid prosthetic groups
- Glycoproteins contain carbohydrate groups,
- Metalloproteins contain a specific metal as
prosthetic group

Four types of structure

Primary Primary structure of protein refers to the order in
which amino acids are linked together in a protein

•Every protein has its own unique amino acid

sequence
- Frederick Sanger (1953) sequenced and
determined the primary structure for the first
protein –Insulin, completed the sequencing
of the 51 AA in 1953 after 8 years of work.
•Proteins of the same organism always same
sequence.

•Same protein from different sources: e.g., Insulin

from pigs, cows, sheep, humans, are similar but not
identical.

•Due to the differences, insulin may show some

difference in response over time
•Now human insulin produced from genetically
engineered bacteria

Secondary •Arrangement of atoms of backbone in space.

•The two most common types: alpha-helix (a-helix)
and the beta-pleated sheet (b-pleated sheet).
•The peptide linkages are essentially planar thus
allows only two possible arrangements for the
peptide backbone for the following reasons:
- For two amino acids linked through a peptide
bond six atoms lie in the same plane
- The planar peptide linkage structure has
considerable rigidity, therefore rotation of
groups about the C–N bond is hindered
- Cis–transisomerism is possible about C–N
bond.
 - The transisomer is the preferred orientation

Alpha-helix (a- •A single protein chain

helix) adopts a shape that resembles
a coiled spring (helix):
- H-bonding between
amino acids with inthe
same chain –
intramolecular H-
bonding
- Coiled helical spring
- R-groups stay outside
of the helix --not
enough room for them
to stay inside

Beta-Pleated •Completely extended amino

Sheets acid chains
•H-bonding between two
different chains –inter and/or
intramolecular
•Side chains below or above
the axis
Tertiary •The overall three-dimensional shape of a protein
•Results from the interactions between amino acid
side chains (R groups) that are widely separated
from each other.
•In general4 types of interactions are observed.

Four Types of Interactions

•Disulfide bond: covalent, strong, between two
cysteine groups

•Electrostatic interactions: Salt Bridge between

charged side chains of acidic and basic amino
acids–-OH, -NH2, -COOH, -CONH2

•H-Bonding: between polar, acidic and/or basic R

groups –For H-bonding to occur, the H must be
attached to O, N or F

•Hydrophobic interactions: Between non-polar

side chains

Quarternary •Quaternary structure of protein refers to the

organization among the various polypeptide
chains in a multimeric protein:

•Highest level of protein organization

•Present only in proteins that have 2 or more
 polypeptide chains (subunits)

•Subunits are generally independent of each other

-not covalently bonded

•Proteins with quaternary structure are often referred

to as oligomeric proteins
•Contain even number of subunits (2 subunits –
dimer, 4 subunits –tetramer, and so on)

Protein Hydrolysis
•Hydrolysis of proteins-reverse of peptide bond formation:
- Results in the generation of an amine and a carboxylic acid functional group.
- Digestion of ingested protein is enzyme-catalyzed hydrolysis
- Free amino acids produced are absorbed into the bloodstream and transported to the liver for
the synthesis of new proteins.
- Hydrolysis of cellular proteins and their resynthesis is a continuous process.

Protein Denaturation
•Partial or complete disorganization of protein’s tertiary structure

•Cooking food denatures the protein but does not change protein nutritional value
•Coagulation: Precipitation (denaturation of proteins)
- Egg white -a concentrated solution of protein albumin -forms a jelly when heated because the
albumin is denatured
•Cooking:
- Denatures proteins –Makes it easy for enzymes in our body to hydrolyze/digest protein
- Kills microorganisms by denaturation of proteins
- Fever: >104ºF –the critical enzymes of the body start getting denatured

Alcohol Disrupts Hydrogen Bonding:

- Hydrogen bonding occurs between amide groups in the secondary protein structure.
- Hydrogen bonding between "side chains" occurs in tertiary protein structure in a variety of
amino acid combinations.
- All of these are disrupted by the addition of another alcohol.
- A 70% alcohol solution is used as a disinfectant on the skin.
- This concentration of alcohol is able to penetrate the bacterial cell wall and denature the
proteins and enzymes inside of the cell.
- mA 95% alcohol solution merely coagulates the protein on the outside of the cell wall and
prevents any alcohol from entering the cell.
- Alcohol denatures proteins by disrupting the side chain intramolecular hydrogen bonding.
-New hydrogen bonds are formed instead between the new alcohol molecule and the protein
side chains.

Salt bridges- result from the neutralization of an acid and amine on side chains.
- The final interaction is ionic between the positive ammonium group and the negative acid
group.
- Any combination of the various acidic or amine amino acid side chains will have this effect.
Heavy Metal Salts: Heavy metal salts act to denature proteins in much the same manner as acids and
bases.
- contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 and other metals with high atomic weights.
Disrupt Disulfide Bonds: Heavy metals may also disrupt disulfide bonds because of their high affinity
and attraction for sulfur and will also lead to the denaturation of proteins.

Protein Classification Based on Shape

Fibrous proteins protein molecules with elongated shape:
- Generally insoluble in water–Single type of secondary
structure
- Tend to have simple, regular, linear structures
- Tend to aggregate together to form macromolecular
structures, e.g., hair, nails, etc

Alpha-Keratin
•Provide protective coating for organs
•Major protein constituent of hair, feather, nails, horns and turtle
shells
•Mainly made of hydrophobic amino acid residues
•Hardness of keratin depends upon -S-S-bonds
- More –S-S–bonds make nail and bones hard and hair
brittle

Collagen
•Most abundant proteins in humans (30% of total body protein)
•Major structural material in tendons, ligaments, blood vessels,
and skin
•Organic component of bones and teeth
•Predominant structure -triple helix
•Rich in proline (up to 20%) –important to maintain structure

Globular proteins protein molecules with peptide chains folded into spherical or
globular shapes:
- Generally, water soluble –hydrophobic amino acid
residues are in the protein core
- Function as enzymes and intracellular signaling
molecules
Myoglobin
- An oxygen storage molecule in muscles.
- Monomer -single peptide chain with one heme unit
- Binds one O2molecule
- Has a higher affinity for oxygen than hemoglobin
- Oxygen stored in myoglobin molecules serves as a
reserve oxygen source for working muscles

Hemoglobin
•An oxygen carrier molecule in blood
•Transports oxygen from lungs to tissues
•Tetramer (four polypeptide chains) -each subunit has a heme
group
 •Can transport up to 4 oxygen molecules at time
•Iron atom in heme interacts with oxygen

Membrane proteins associated with cell membranes

- Insoluble in water –hydrophobic amino acid residues on
the surface
- Help in transport of molecules across the membrane

Protein Classification Based on Function

•Proteins play crucial roles in most biochemical processes.
•The diversity of functions exhibited by proteins far exceeds the role of other biochemical molecules
•The functional versatility of proteins stems from:
- Ability to bind small molecules specifically and strongly
- Ability to bind other proteins and form fiber-like structures
- Ability integrated into cell membranes

Major Categories of Proteins Based on Function

Contractile proteins
Necessary for all forms of movement.
- Muscles contain filament-like contractile proteins (actin
and myosin).
- Human reproduction depends on the movement of sperm
–possible because of contractile proteins.

Structural proteins Confer stiffness and rigidity

- Collagen is a component of cartilage
- Keratin gives mechanical strength as well as protective
covering to hair, fingernails, feathers, hooves, etc.

Transmembrane proteins
Span a cell membrane and help control the movement of small
molecules and ions.
- Have channels –help molecules to enter and exit the cell.
- Transport is very selective -allow passage of one type of
molecule or ion.

Storage proteins Bind (and store) small molecules.

- Ferritin -an iron-storage protein -saves iron for use in the
biosynthesis of new hemoglobin molecules.
- Myoglobin -an oxygen-storage protein present in muscle

Regulatory proteins
Often found “embedded”in the exterior surface of cell membranes
-act as sites for receptor molecules
- Often the molecules that bind to enzymes (catalytic
proteins), thereby turning them “on”and “off,”and thus
controlling enzymatic action.

Nutrient proteins Particularly important in the early stages of life -from

embryo to infant.
- Casein (milk) and ovalalbumin (egg white) are nutrient
proteins
 - Milk also provides immunological protection for
mammalian young.

Enzymes
- Biological catalyst that speeds up rate of the biochemical reaction
- Most are three dimensional globular proteins (tertiary and quaternary structures)
- Ribozyme- special RNA species act as enzyme

Structure Active site

- The active site of an enzyme is the region Binding site It chooses the substrate
that binds substrates, cofactors, and and binds it to active
prosthetic groups and contains residue site
that helps to hold the substrate
- Active sites generally occupy less than
5% of the total surface area of enzyme
- Has specific shape due to tertiary Catalytic site It performs the catalytic
structure of protein action of enzyme
- Change in the shape of protein affects the
shape of active site and function of the
enzyme

Co- factors Substrate

Non protein molecule which carries out chemical - Reactant in biochemical reaction
reactions that can not be performed by standard - When a substrate binds to an enzyme it
20 amino acids forms an enzyme substrate complex

Apoenzyme- co-factor removed

Holoenzyme of holoprotein- complete complex
of a protein with al necessary small organic
molecules, metal ions and other components
Organic Organic molecules
required for the proper
activity of enzymes

Prosthetic- tightly
bound organic co-factor
(Flavins, heme groups
and biotin)

Coenzyme- loosely
bound (NAD+)
Inorganic Inorganic molecules
required for the proper
activity of enzymes
Sites of enzyme synthesis
- Enzymes are synthesized by ribosomes which are attached to the rough endoplasmic reticulum
- Information for the synthesis of enzyme is carried by DNA
- Amino acids are bonded together to form specific enzyme according to the DNA’s codes
Intracellular Enzymes are synthesized and retained in the cell
for the use of cell itself
Found in the cytoplasm, nucleus, mitochondria
and chloroplast
Extracellular Synthesized in the cell but secreted from the cell
to work externally

Characteristics
1. Enzymes speed up the reaction by lowering the activation energy of the reaction
2. Their presence does not affect the nature and properties of end product
3. Highly specific in their action that is each enzyme can catalyze one kind of substrate
4. Small number of enzymes can accelerate chemical reactions
5. Enzymes are sensitive to change in pH, temperature and substrate concentration
6. Turnover number- as the number of substrate molecules transformed per mnute by one enzyme
molecule

Nomenclature
- Named according to the name of the substrate it catalyzes
- Adding suffix -ase
Classes
- Based on the type of rections catalyzed by enzymes
Oxidoreductases Reduction- oxidation Lactate Dehydrogenase
(redox)
Transferases Move chemical group Hexokinase
Hydrolases Hydrolysis; bond Lysozyme
cleavage with transfer
of functional group of
water
Lysases Non- hydrolytic bond Fumarase
cleavage
Isomerases Intramolecular group Triose phosphate
transfer (isomerization) isomerase
Ligases RNA polymerase
Mechanism of enzyme action

Inhibition
- Prevention of an enzyme process as a result of interaction of inhibitors with the enzyme

Inhibitors- any substance that can diminish the velocity of an enzyme catalyzed reaction
Reversible An inhibition activity in which the inhibiting
molecular entity can associate and dissociate from
the protein’s binding site
Types
Competitive The inhibitors compete with the substrate for the
active site. Formation of E.S complex is reduced
while a new E.I complex is formed
e.g. Statin

Uncompetitive Does not compete with the substrate for the active
site of enzyme instead it binds to another site
 known as allosteric site

e.g. drugs to treat methanol poisoning or ethylene

glycol; tetramethylene sulfoxide and 3
butylthiolene 1- oxide

Mixed inhibition Both E.I and E.S.I complexes are formed; both are
catalytically inactive
Non- competitive Special case of inhibition
Inhibitor has the same affinity for either enzyme E
or the E.S complex

Irreversible Involves the covalent attachment of the inhibitor

to the enzyme
Catalytic activity of enzyme is completely lost
Can only be restored only by synthesizing
molecules
Suicide inhibition- an unusual type of irreversible
inhibition where the enzyme converts the inhibitor
into a reactive form in its active site

E.g. Aspirin

Activation
- The conversion of an inactive form of an enzyme to active form which processes the metabolic
activity
Activation by co- factors e.g. DNA polymerase is a holoenzyme that
catalyzes the polymerization of
deoxyribonucleotide into a DNA strand. It uses
Mg-ion for catalytic activity
Conversion of an enzyme precursor Specific proteolysis is a common method of
activating enzymes and other proteins in
biological system

e.g. The generation of trypsin from trypsinogen

leads to the activation of other zymogens