Amino Acids, Proteins and Enzymes

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Amino Acids, Proteins and Enzymes

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Title: Amino Acids, Proteins and Enzymes

1
Amino Acids, Proteins and Enzymes

Amino acids are the building blocks of proteins,
20 amino acids are found in proteins
They are called a amino acids attached to the
alpha carbon is a H, NH2, COOH and R, four
different groups
The a carbon is a chiral carbon in all the amino
acids except glycine (Gly)
Amino acids that are not synthesized in the body
and must be obtained from the diet are called
essential amino acids (10)
All naturally occuring amino acids in the human
body are the L- enantiomers
The peptide bonds that link amino acids in a
protein are amide bonds.

2
Amino acids in proteins have L-configuration
3
Amino Acids

In body fluids the amino acids exist in the
dipolar form called a zwitterion which has a net
charge of zero.
The isoelectric point, pI, is the pH at which the
amino acid has a net charge of zero.
R-CH-COOH ? R-CH-COO-
NH2 NH3

4
Amino Acids as Acids Bases

In a solution more acidic than the pI, lower pH,
COO- acts as a base and accepts a H which gives
an overall positive charge to the amino acid.
In a solution more basic than the pI, higher pH,
NH3 acts as an acid and loses an H which gives
an overall negative charge to the amino acid.

5
Zwitterions

pH lt pI pH pI pH gt pI
At a pH lt the pI they have a positive charge.
At a pH gt the pI they have a negative charge.
Acidic amino acids have low pI values as the
extra -COO-
Group must be neutralized first.
Basic amino acids have high pI value as the extra
NH3
Group must be neutralized first.

6
Classification of Amino Acidsby the polarity of
the side chain

Hydrophobic (water fearing)
Nonpolar side chains
Gly, Ala, Val, Leu, Ile, Phe, Met, Pro, Trp
Hydrophilic (water loving)
Polar
Neutral Ser, Thr, Tyr, Cys, Gln, Asn
Acidic Glu, Asp
Basic Arg, Lys, His

7
Formation of a Peptidepeptide bonds amide bonds

Peptide bonds join amino acids to form peptides
by forming an amide bond between the carboxyl
group of one amino acid and the amino group of
the second amino acid.
In a peptide, the free amino acid written on the
left is called the N terminal and the free
carboxyl group of the last amino acid is called
the C terminal.
In a peptide each amino acid is named with a yl
ending followed by the full name of the amino
acid at the C terminal.
Histidylglycylglutamylalanine (HisGlyGluAla)

8
Small Peptides

With three AAs can get six possibilities, e.g. if
add serine
Glycylalanylserine (GAS) Serylalanylglycine
(SAG)
also AGS SGA GSA or ASG. With four AAs get 24
possibilities, e.g. add proline
PGAS GPAS GAPS GASP
PSAG SPAG SAPG SAGP
PAGS APGS AGPS AGSP
PSGA SPGA SGPA SGAP
PGSA GPSA GSPA GSAP
PASG APSG ASPG ASGP
The large number of possibilities is why proteins
can have so many different sequences.
The hormone angiotensin has the sequence
DRVYIHPF these eight amino acids can be arranged
in 40,320 ways.

9
Proteins

Proteins are long chains of more than 50 amino
acids
Proteins perform many functions in the body
Structural
Contractile
Transport
Storage
Hormone
Enzyme
protection

10
Levels of Protein Structure

Primary Structure
Provides the amino acid sequence held together by
peptide bonds
Human insulin has two polypeptide chains held
together by disulfide bonds formed by the side
chains of the cysteine amino acids in each of the
chains

11
Levels of Protein Structure

Secondary Structure
Alpha helix (myosin, actin, colicin Ia)
a-helix - a right-handed coil of AAs with 3.6 AAs
per turn, the side chains are on the outside
Beta pleated sheet (silk) folded, parallel chains
Triple helix (tropocollagen) three strands woven
together like a braid. Left-handed helix.
Is a result of hydrogen bonding between amino
acids within the protein.

12
Levels of Protein Structure

Tertiary Structure
Protein folds into a compact shape stabilized by
interactions between the R groups.
Interactions that stabilize the tertiary
structure
Hydrophobic attractions between nonpolar groups
in the interior of the molecule
Hydrophilic attractions between polar or
ionized groups and water on the exterior of the
molecule
Salt bridges ionic attractions between ionized
acidic and basic amino acids
Hydrogen bonds between H and O or N between the
same and/or different chains
Disulfide bonds strong covalent bonds between
sulfur atoms of two cysteine amino acids between
the same and/or different chains

13
Levels of Protein Structure

Tertiary Structure
Globular protein soluble in water, compact,
roughly spherical, used by cell proteins, 3-D
structure is tertiary.
Albumins, globulins
Myoglobin is a storage protein, stores oxygen in
skeletal muscle. It has one
heme.
Fibrous protein long, thin, fiber-like shapes
(filamentous), insoluble in water, used by cells
and connective tissues
a ß keratins hair, wool, skin, nails, silk,
collagen, myosin.

14
Levels of Protein Structure

Quaternary Structure
A combination of two or more protein subunits to
form a larger, biologically active protein. The
subunits are held together by the same
interactions found in tertiary structure.
Hemoglobin
Protein with a globular structure, it is an
oxygen transport protein
Has 4 protein chains two alpha and two beta
4 hemes
In a sickle-cell anemia the hemoglobin molecules
clump together into insoluble fibers

15
Protein Reactions

Hydrolysis
Acids or bases will hydrolyze the peptide
bonds to give AAs.
Denaturation
Process in which proteins can lose their
secondary, tertiary, quaternary structure,
destroying their function, without breaking the
peptide bonds.

16
Denaturation of Proteins

Disruption of any of the bonds that stabilize the
secondary, tertiary, quaternary structure. The
covalent amide bonds of the primary structure are
not affected.
Alters the shape of the protein and it becomes
biologically inactive.
Denaturing agents heat, acids, bases, organic
compounds, heavy metal ions, mechanical agitation.

17
Denaturation of Proteins

Acids and bases disrupt salt bridges and hydrogen
bonds
Heat,UV,microwave,agitation disrupt hydrophobic
bonds and hydrogen bonds
Heavy metals like Hg2, Ag, Pb2 disrupt the
disulfide bonds
Organic molecules disrupt hydrophobic interactions

18
Enzymes

Enzymes are protein catalysts, most are globular
proteins and are very specific. They increase the
rate of the reaction by lowering the activation
energy, and operate at mild temperature and pH.
Reactants are called substrates.
Classification
Named according to the type of reaction and the
substrate.
1. Oxidoreductases - biological oxidation and
reduction reactions, e.g. lactate dehydrogenase.
2. Transferases - switch functional groups
between molecules, e.g. transaminases.
3. Hydrolases - hydrolyze molecules, e.g.
sucrase.
4. Lyases - remove groups without using water,
break C-O, C-C, C-N bonds, e.g. pyruvate
decarboxylase.
5. Isomerases - change one molecule into one of
its isomers,(rearrange functional groups) e.g.
phosphoglucose isomerase.
6. Ligases - form new bonds between C and N, O,
S or another C, e.g. DNA polymerases.(join two
molecules)

19
Enzyme Constitution

Can be pure protein, e.g. trypsin.
Others are made up of a protein part called the
apoenzyme and a nonprotein part called a
cofactor, the combination is called a holoenzyme.
The cofactor(s) can be ions (Mg2,Mn2,Ni2,
Zn2,Fe2,Fe3,Cu2)or small organic molecules
called coenzymes, these are frequently built from
vitamins. (water soluble vitamins B C function
as coenzymes)
Some proteins are made in an inactive form called
a zymogen or proenzyme, these must be activated
by the active enzyme itself or some other enzyme,
Examples are pepsinogen the proenzyme for pepsin
and prochymotrypsin for chymotrypsin.

20
Mechanism 1

Active site, this is where the catalytic activity
takes place.
Functional groups in the active site interact
with substrate(s) in such a way as to facilitate
the making or breaking of bonds.
The active site of the enzyme may be fixed,
rigid, nonflexible shape, that fits the substrate
exactly, this is the lock-and-key model by Emil
Fisher 1890.
The active site of the enzyme may conform itself
to the substrate, the structure of the enzyme is
flexible, this is the induced-fit model proposed
by Daniel Koshland 1958.
Different enzymes vary between the two extremes.

21
Mechanism 2

In both cases a reversible reaction with the
substrate forms an enzyme-substrate complex, this
then changes to release the product.
E S ? E-S Then
E-S ? E P
Example
Sucrase Sucrose ?Sucrase-sucrose complex
Sucrase-sucrose complex?Sucrase Glucose
Fructose

22
Enzyme Specificity

Enzymes will only work on one substrate or a few
related molecules this is specificity.
Absolutely - only one substrate, not common.
Stereochemically - only work on one of two
stereoisomers, D- or L- form.
Group - work on different molecules containing
the same functional group.
Linkage - act on a particular kind of bond.

23
Factors Affecting Enzyme Activity

Substrate concentration
Each enzyme molecule has a limit to how fast it
works, the turnover number. As the amount
concentration) of substrate is increased(while
the enzyme concentration is kept constant) the
rate will increase until each molecule is working
at its maximal rate, then the activity is maximal
and adding more substrate will not increase the
rate any further.(when the enzyme gets saturated
with substrate the rate reaches its maximum so it
will level off, adding more substrate will not
affect the rate anymore.)

24
Factors Affecting Enzyme Activity

Enzyme concentration
With an unlimited amount of substrate, as more
enzyme is added the rate increases in direct
proportion this curve does not level off.
Temperature
As the temperature is raised initially the rate
increases. Later the increased vibration within
the molecule distort the active site and the rate
increase slows down, reaches a maximum - the
optimal temperature.
Beyond this point the rate gets slower and
finally stops when the enzyme is denatured.
For most tissues the optimum temperature will be
37oC, and it is the temperature at which an
enzyme operates at maximum efficiency.
(in the liver ca. 40oC).
At lower temperatures enzymes show little
activity and at higher than 50oC they lose their
activity, they become inactive.

25
Factors Affecting Enzyme Activity

pH
At the optimum pH an enzyme is most active
At one particular pH value, known as the optimal
pH7.4, the active site will be in the correct
configuration, above or below that value ionic
side groups may gain or lose charges. This will
affect the enzyme structure and/or alter the
active site, the shape, the solubility. This
will cause the activity to decrease, eventually
the enzyme will be denatured and activity will
cease. For most tissues the pH will be ca. 7.4,
stomach ca. 1-2 and small intestine ca. 8-9.

26
Enzyme Inhibition

Inhibitors---cause a loss of catalytic activity
(release materials that block the active site of
the enzyme toxins, drugs, metal complexes,
substrate analogs).
Irreversible---form covalent or very strong
noncovalent bonds
Reversible---form weak noncovalent bonds
Inhibitors
Competitive
Noncompetitive

27
Inhibitors

Competitive has a structure that resembles the
substrate and competes with the substrate for the
active site
Adding more substrate reverses the effect of the
inhibitor
Noncompetitive has a structure that does not
resemble the substrate and it binds at a location
other than the active site alters the 3-D
structure of the enzyme so that a substrate
cannot enter the active site
Adding more substrate will not reverse the effect
of the inhibitor
Examples heavy metal ions Pb2, Ag, Hg2 that
bond to COO- or OH
Antibiotics produced by bacteria, mold, or yeast
are inhibitors used to stop bacterial growth.

28
Enzymes in Medicine

Viral Hepatitis shown by presence in the blood
of glutamatepyruvate aminotransferase (GPT) and
glutamate oxalate aminotransferase (GOT).
Myocardial Infarction shown by presence in the
blood of creatine kinase (CK), GOT and lactate
dehydrogenase (LD). Also LD has 5 isoenzymes LD1
LD5. Normally the level of LD1 is lower than
that of LD2, with a heart attack the ratio flips.

29
Chemical reactions in the human body

Every second thousands of chemical reactions
occur in the cells of the human body.
The purpose of the many chemical reactions in our
bodies is to
Store chemical energy in the body for future use
Produce the essential amino acids
Produce the essential lipids
Release chemical energy for the production of
macromolecules

30
Nonpolar Amino Acids