1-3 Biomolecules-Aa & Protein_1

8/11/2019 1-3 Biomolecules-Aa & Protein_1

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BIOMOLECULES


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Outline

Amino acids and proteins

Structure, classes, properties, reactions of AA,peptides, proteins

Lipids and membrane Fatty acids, lipids, chemical & physical properties

of membranes

Sugars and polysaccharides Nucleotides and nucleic acid

Nucleotides, nucleic acids, genetic information


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AMINO ACIDS, PEPTIDES ANDPROTEINS
http://en.wikipedia.org/wiki/File:AminoAcidball.svg


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Simplest compounds, contain of amino group (NH2) and carboxylic acid

group (COOH)

Major elements of an amino acid are carbon, hydrogen, oxygen and

nitrogen

Exist in either dextro (D)or levo (L)form, also known as stereoisomer

All other amino acids (except glycine) can be described as chiral

Major part of them, which are found in nature are L-type

D-type can be found in bacterial cell walls and a number of peptide

antibiotics.

More than three hundred kinds of amino acids have been discovered innature.

20 of them are usually found as compounds of human peptides and

proteins.

AMINO ACIDS

Notes: An object or a system is chiral if it is not identical to

its mirror image
http://en.wikipedia.org/wiki/File:AminoAcidball.svg


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Common type of amino acid: alanine

Glycine is the only amino acid found in protein that is notchiral (Achiral)

AMINO ACIDS

The two optical isomers of alanine, D-Alanine and L-Alanine


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2-10 amino acids are called peptides

10-100 are often called polypeptides

Longer chains are known as proteins

AMINO ACIDS


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One amino acid molecule can

react with another and become

joined through an amide linkage.

This polymerization of aminoacids is what creates proteins.

PEPTIDE BOND
http://en.wikipedia.org/wiki/File:Peptidformationball.svg


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Amino Acid Structure

Amino acids may becharacterized as , b, or g

amino acids depending on

the location of the amino

group in the carbon chain.are on

bare on the

gon the

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AMINO ACID CLASSES

Nonpolar and neutral-contain mostly

hydrocarbon R group (glycine, alanine,

valine)

Polar and neutral-have functional group

capable of H bonding (serine, threonine,

tyrosine, asparagine, glutamine)


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Acidic-COOH group>NH2group (aspartic &

glutamic acid)

Basic NH2group > COOH group (lysine,

arginine, histidine)


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5P1-11

Amino Acid Titration Amino acids are amphoteric. They are

capable of behaving as both an acid and a

base, since they have both a proton donorgroup and a proton acceptor group.

In neutral aqueous solutions the protontypically migrates from the carboxyl group tothe amino group, leaving an ion with both a(+) and a (-)charge.

At physiological pH, the carboxyl group of the AAis negatively charged and the amino group ispositively charged.


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This dipolar ion form is known as a Zwitterion.


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Amino Acid Titration

At low pH, a nonacidic/nonbasic aminoacid is protonated and has the

structure below.

H3N+CHRCOOH

The charge behavior of acidic and basic

AAs is more complex.


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5P1-14

Titration of Alanine

1

mole base added1 2

pH

5

10

1

A A=B

pK1=2.3

B, pI=pH=6.0

B=C

pK2=9.73

C


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Isoelectric point

The isoelectric point (pI) for an AA occurs when there

is no net charge.

For a neutral AA, the pI is calculated using the

equation (pK1+ pK2)/2 (Also known as half equivalentpoint)

Eg.: alanine: (2.34 + 9.7) / 2 = 6.0

For acidic or basic AAs, the pI is the average of the

two pKavalues bracketing the isoelectric structure.


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Isoelectric point

In general the pI is

the average of thetwo pKas

bracketing the

isoelectric

structure.

Eg.: glutamic acid,pI = 3.2

pK1=2.2

pK2=4.3

pK3=9.9


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PROTEINS


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INTRODUCTION

Biochemical compounds consisting of one or

more polypeptidestypically fold into globular

or fibrous form.

A polypeptide is a

__________________________________

together by peptide bond between the

____________________________of adjacentamino acid residues.


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Proteins are Linear Polymers of Amino Acids


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FIBROUS

Fibrous proteins exist as long stranded molecules: Eg.

Silk, collagen, wool. A collagen segment in space-filling

mode illustrates this point.

Red spheres represent oxygen,

grey carbon, and blue nitrogen

Gl b l


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Globular

Globular proteins

have somewhatspherical shapes.

Most enzymes are

globular. Eg.

myoglobin,

hemoglobin.

Myoglobin in space-

filling mode is thechosen example.


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Protein

One or more polypeptide chains

One polypeptide chain - a monomeric protein

More than one - multimeric protein Homomultimer - one kind of chain

Heteromultimer - two or more different chains

Hemoglobin, for example, is a heterotetramer It has two alpha chains and two beta chains


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THE SEQUENCE OF AMINO ACIDS IN

A PROTEIN

is a unique characteristic of every protein

is encoded by the nucleotide sequence ofDNA

is thus a form of genetic information

is read from the amino terminus to thecarboxyl terminus


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PEPTIDES

A peptide is written with the N-terminal end to the leftand the C-terminal end to the right.

H2N-Tyr-Ala-Cys-Gly-COOHName = Tyrosylalanylcysteinylglycine


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The sequence of ribonuclease A


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PEPTIDES Peptide: a polymer of about 2-100 AAs linked by the

peptide(amide) bond. As the amino group and the

carboxyl group link, water is lost.

C CR1

H

NH3

+

O

O

Peptide bonds

C CR1

H

NH3

+

O

O

C CR1

H

NH3

+

O

O

C C

R1

H

NH3

+ OC C

R1

H

NH

OC C

R1

H

NH

OO

-H2O -H2O


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PEPTIDE BOND

When two amino acids combine, there is a

formation of an amide and a loss of a watermolecule

+ H2O


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PROTEINS- LEVELS OF STRUCTURE

Amino acids can undergo condensation reactions in

any order, thus making it possible to form large

numbers of proteins.

Structurally, proteins can be described in four ways. Primary

Secondary

Tertiary Quaternary structure.

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WHAT FORCES DETERMINE THE

STRUCTURE?

Primary structure

Secondary, Tertiary, Quaternary structures

Weak forces


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PRIMARY STRUCTURE

The primary structure of a protein is defined by thesequence of amino acids, which form the protein. Thissequence is determined by the base pair sequence in theDNA used to create it. The sequence for bovine insulin isshown below


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SECONDARY STRUCTURE

The secondary structure describes the way that the

chain of amino acids folds itself due to intramolecularhydrogen bonding

Two common secondary

structures are

the a-Helix

and the b-sheet


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CLASSES OF SECONDARY STRUCTURE

All these are local structures that are stabilized

by hydrogen bonds

Alpha helix

Other helices

Beta sheet (composed of "beta strands")

Tight turns (beta turns or beta bends)

Beta bulge


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TERTIARY STRUCTURE

The tertiary structure

maintains the three

dimensional shape of the

protein.

Three-dimensional structure,as defined by the atomic

coordinates

The amino acid chain (in the

helical, pleated or random

coil form) links itself in placesto form the unique twisted or

folded shape of the protein.


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TERTIARY STRUCTURE There are four ways in which parts of the amino acid chains

interact to stabilize its tertiary shape.They include:

I.-- Covalent bonding,

II.-- Hydrogen bonding

III.-- Salt bridges

IV.-- Hydrophobic interactions.

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TERTIARY STRUCTURE

Several important principles:

Secondary structures form wherever

possible (due to formation of large

numbers of H-bonds)

Helices and sheets often pack close

together


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Tertiary Structure

Several important principles:

The backbone links between elements of

secondary structure are usually short anddirect

Proteins fold to make the most stable

structures (make H-bonds and minimizesolvent contact)


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Quaternary Structure

Many proteins are not single strands

the arrangement of multiple folded protein or coiling protein

molecules in a multi-subunit complex.

The diagram below shows the quaternary structure of an

enzyme having four interwoven amino acid strands

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BIOLOGICAL FUNCTIONS OF

PROTEINS

Proteins are the agents of biological function

Enzymes - Ribonuclease

Regulatory proteins - Insulin Transport proteins - Hemoglobin

Structural proteins - Collagen

Contractile proteins - Actin, Myosin

Exotic proteins - Antifreeze proteins in fish


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OTHER CHEMICAL GROUPS IN PROTEINS

Proteins may be "conjugated" with other chemical

groups

If the non-amino acid part of the protein is

important to its function, it is called a prostheticgroup.

Be familiar with the terms: glycoprotein,

lipoprotein, nucleoprotein, phosphoprotein,metalloprotein, hemoprotein, flavoprotein.

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1-3 Biomolecules-Aa & Protein_1