Proteins

Chemical Constituents of Organisms: Part II Peptides and Proteins

Peptides and Proteins Proteins are polyamides When formed by amino acids, each amide group is called a peptide bond Peptides are formed by condensation of the COOH group of one amino acid and the NH group of another amino acid The acid forming the peptide bond is named first. Example: if a dipeptide is formed from alanine and glycine so that the COOH group of glycine reacts with the NH group of alanine, then the dipeptide is called glycylalanine

In the Biuret test the solution with protein turns purple potassium hydroxide shake

copper sulphate

purple = protein chopped up food

TEST

NEGATIVE

POSITIVE

Iodine solution Starch

Orangey-brown Blue-black

Benedict’s test Glucose

Blue

Orangey-red

Protein

Blue

Purple

Fats

Clear

Cloudy white

Biuret test Ethanol test

For each food, decide on the chemicals found in them.

Food sample

Protein

Test

Result

Iodine solution

orangey-brown

Benedict’s test

blue

Biuret test

purple

Ethanol test

cloudy white

Fats

Starch

Glucose

For each food, decide on the chemicals found in them.

Food sample

Protein

Test

Result

Iodine solution

blue-black

Benedict’s test

blue

Biuret test

blue

Ethanol test

clear

Fats

Starch

Glucose

For each food, decide on the chemicals found in them.

Food sample

Protein

Test

Result

Iodine solution

orangey-brown

Benedict’s test

orangey-red

Biuret test

blue

Ethanol test

clear

Fats

Starch

Glucose

For each food, decide on the chemicals found in them.

Food sample

Protein

Test

Result

Iodine solution

orangey-brown

Benedict’s test

orangey-red

Biuret test

blue

Ethanol test

clear

Fats

Starch

Glucose

Glycylalanine is abbreviated gly-ala or GA Polypeptides are formed with a large number of amino acids

Glycylalanine Gly-Ala Alanyltyrosylaspartylgylcine GA AlanylTyrosylAspartylGlycine Ala-Tyr-Asp-Gly AYDG

Protein Structure and Function A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines its function

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Groove

(a) A ribbon model of lysozyme

Groove

(b) A space-filling model of lysozyme

Protein categories Globular proteins Fibrous proteins

Globular proteins Usually water soluble, compact, roughly spherical Hydrophobic interior, hydrophilic surface Globular proteins include enzymes, carrier and regulatory proteins

Fibrous proteins

Provide mechanical support

Often assembled into large cables or threads -Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones and teeth

Protein Structure 1o : The linear sequence of amino acids and disulfide bonds, e.g. ARDV:Ala.Arg.Asp.Val 2o : Local structures which include, folds, turns, -helices and -sheets held in place by hydrogen bonds 3o : 3-D arrangement of all atoms in a single polypeptide chain 4o : Arrangement of polypeptide chains into a functional protein, e.g. hemoglobin Animation: Protein Structure Introduction

Primary Protein Structure Primary structure is the sequence of the amino acids in the protein Primary structure is determined by inherited genetic information A change in one amino acid can alter the biochemical behavior of the protein

Animation: Primary Protein Structure

Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein’s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

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10 µm

Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen.

10 µm

Fibers of abnormal hemoglobin deform red blood cell into sickle shape.

Secondary Protein Structure Two types exist!! -helix -pleated sheets

The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an α helix and a folded structure called a β pleated sheet

Animation: Secondary Protein Structure

-helix Amino acids interact with each other The H on the NH group is attracted to the O on the CO group The H is slightly positive and the O is slightly negative H bond forms between these two atoms

……..individually weak!

Hydrogen bonds are numerous…….

The H bonds that keep Alpha helices together are vulnerable to fluctuations in pH & temperature

Secondary Structure pleated sheet

Examples of amino acid subunits

helix

-pleated sheets

Hydrogen bonds hold adjacent primary chains together

-Sheets (a) parallel, (b) antiparallel

Common motifs

Common domain folds

To go above secondary structure Tertiary Protein Structure Proteins need more bond types Disulphide bonds: Adjacent cysteine AA S-S bond is a weak bond, broken by reducing agents Hydrophobic Interactions: Between non polar R-groups Ionic bonds: Forms between ionised amine & carboxylic groups, broken by extreme pH

Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds namely disulfide bridges may reinforce the protein’s structure

Animation: Tertiary Protein Structure

Tertiary Structure

Quaternary Structure

Quaternary Structure Refers to the organization of subunits in a protein with multiple subunits (an “oligomer”) Subunits (may be identical or different) have a defined stoichiometry and arrangement Subunits are held together by many weak, noncovalent interactions (hydrophobic, electrostatic) Homodimer vs. heterotrimer and etc.

Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains

Animation: Quaternary Protein Structure

Quaternary structure of multidomain proteins

HAEMOGLOBIN Made of 4 polypeptide chains 2 alpha chains and 2 beta chains Hydrophobic R groups point into the molecule Hydrophilic R groups point out of the molecule This makes haemoglobin highly soluble

Each of the 4 chains has a haem group The haem group is not made of AA, but is an integral part of the protein – prosthetic group Each haem group contains an ion of iron (Fe2+) Each haem binds with one molecule of O2 Haemoglobin can carry O8

What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native structure is called denaturation A denatured protein is biologically inactive

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Denaturation Denaturation- disruption of the normal 3D shape Denaturation agents: alcohol weak acid or base heat detergents reducing agents

Protein Folding in the Cell It is hard to predict a protein’s structure from its primary structure Most proteins probably go through several states on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins

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Scientists use X-ray crystallography to determine a protein’s structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics uses computer programs to predict protein structure from amino acid sequences

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Animation: Structural Proteins Animation: Storage Proteins Animation: Transport Proteins Animation: Receptor Proteins Animation: Contractile Proteins Animation: Defensive Proteins Animation: Hormonal Proteins Animation: Sensory Proteins Animation: Gene Regulatory Proteins

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Nucleic acids store and transmit hereditary information amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid

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The Roles of Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

DNA

1 Synthesis of mRNA in the nucleus

mRNA

NUCLEUS CYTOPLASM

DNA

1 Synthesis of mRNA in the nucleus

mRNA

NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore

DNA

1 Synthesis of mRNA in the nucleus

mRNA

NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore

Ribosome

3 Synthesis of protein

Polypeptide

Amino acids

Amino acids

Polypeptide

Tr

p

Ribosome

tRNA with amino acid attached

Phe

Gly

tRNA Anticodon

Codons

5′′ mRNA

3′′

Next lesson: DNA