Packet #9

Over 300 have been described in nature

Only 20 common as constituents of mammalian proteins

Carboxyl group At a pH of 7.4, group is

dissociated forming a negatively charged carboxylate ion

Amino group At a pH of 7.4, group is

protonated forming a positively charged ion

Distinctive side chain “R-group” Linked to the α-carbon

atom Nature of the side chain

determines the role an amino acid plays in a protein

Non-polar Uncharged Acidic Basic

More details to come in Cell Biology & Biochemistry @ the University level

Does not bind, or give off protons

Does not participate in hydrogen or ionic bonds

Oily and lipid like Promotes

hydrophobic interactions

Fill up the interior of proteins

Zero net charge at neutral pH

Cluster at the surface of membrane proteins

Proton donors At neutral pH, the

side chains are fully ionized containing a negatively charged carbozylate group

Accept protons At physiologic pH, the side chains are

fully ionized and positively charged

The 20 common amino acids found in proteins are linked together by peptide bonds.

The sequence contains information necessary to generate a protein molecule with a unique 3D shape

Four organizational levels Primary Secondary Tertiary Quaternary

The sequence of amino acids in a protein is called the primary structure of the protein

Understanding the primary sequence is important because many genetic diseases result in proteins with abnormal amino acid sequences. If the normal sequence is known, information

may be used to diagnose or study the disease when the mutated sequence arises

Primary Structure Long chain of amino acids

Secondary Structure Polypeptide chain folded into or helixes.

Tertiary Structure Occurs when the helix folds on into itself

Quaternary Structure Combination of a number of polypeptide chains

along with associated non protein groups

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Proteins are amphoteric Have both positive and negative charges

on them Attraction of these charges form weak

hydrogen bonds causing the chain to forma complex 3D structure

Globular proteins

Ionic bonds, disulfide bridges and hydrophobic interactions all contribute to the final shape of a given protein molecule

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Two amino acids are linked together by a condensation reaction Forms a dipeptide

Many amino acids, joined via condensation reactions, are called polypeptides

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How are amino acids joined together? Covalently by

peptide bonds Α-carboxyl group of

one amino acid binds to the α-amino group of another

Acid Hydrolysis Hydrolyzed by strong acid at 110˚C for 24 hours

Chromatography Individual amino acids are separated by cation-exchange

chromatography Amino acids is applied to a column that contains resin to which a negatively

charged group is tightly attached Each amino acid is sequentially released from the chromatography column by

eluting with solutions of increasing ionic strength and pH As the pH increases, the amino acids lose hydrogen ions

Carboxyl groups Side chains Amino groups

First becoming neutral, then negatively charged and are released from the resin Each amino acid emerges from the column at a specific pH and ionic strength

Quantitative Analysis Determination of the amount of amino acids

Heated with ninhydrin Amount determined by spectrophotometrically measuring the amount of light

absorbed by the ninhydrin derivative

Determined by using Edman’s reagent Cleavage into smaller fragments DNA sequencing

Occurs when the polypeptide backbone does not assume a random 3D structure

Generally forms regular arrangements of amino acids that are located near to each other in the linear sequence. Α-Helix Β-Sheet

α-Helix Very diverse

Keratins Fibrous proteins Major component of hair and skin

Rigidity determined by the number of disulfide bonds between constituent polypeptide chains

Stabilized by hydrogen bonds between peptide bond carbonyl oxygens and amide hydrogens that are part of the polypeptide backbone

β-Sheet All peptide bond components are involved in hydrogen

bonding Surfaces appear “pleated” How do they relate to Alzheimer’s disease?

Globular proteins Primary structure determines its tertiary

structure Hydrophobic side chains buried in interior Hydrophilic groups found on the surface of

molecule Stabilized by

Disulfide bonds Hydrophobic interactions Hydrogen bonds Ionic interactions

Consist of two or more polypeptide chains that may be structurally identical or totally unrelated Two subunits

Dimeric Three subunits

Trimeric Several subunits

Multimeric

Globular Proteins All enzymes, and some hormones, are

globular proteins Depends on the precise shape of the protein

molecule Hemeproteins

Hemoglobin Also known as a conjugated protein Occurs in combination with a non-protein substance

(prosthetic group) Myoglobin

Fibrous Proteins Proteins that consist of long parallel chains with cross links Insoluble Structural functions

Collagen in cartilage Keratin in hooves, feathers and hair Actin and myosin in muscle

Collagen Most abundant protein in human body More to come later

Elastin Tough High tensile strength Connective tissue protein with rubber like properties Found in lungs, walls of large blood vessels and elastic ligaments

α-Keratins Proteins that form tough fibers

Hair, nail, outer epidermal layer of mammals, intermediate filaments of cytoskeleton in certain cells

If a globular protein is heated or treated with a strong acid or alkali (base), the hydrogen bonds are broken and it reverts back to its fibrous nature

Results in the unfolding and disorganization of the protein’s structure

Agents of denaturation Heat Organic solvents Mechanical mixing Strong acids or bases Detergents Ions of heavy metals

Lead Mercury

Nutrition Respiration & transport Growth Excretion Support & movement Sensitivity & coordination Reproduction

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Digestive Enzymes Trypsin

Catalyses the hydrolysis of proteins to polypeptides

Amylase Catalyses the hydrolysis of starch to maltose

Lipase Catalyses the hydrolysis of fats to fatty acids

and glycerol

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Fibrous proteins in granallamellae Help to arrange chlorophyll molecules in a

position to receive maximum amount of light for photosynthesis

Ovalbumin Storage protein in egg white

Casein Storage protein in milk

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Hemoglobin Transport of oxygen

Myoglobin Stores oxygen in muscle

Prothrombin/Fibrinogen Required for the clotting of blood

Mucin Keeps respiratory surface moist

Antibodies Essential to the defense of the body

Against bacterial invasion

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Hormones Thyroxine

Controls growth and metabolism

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Enzymes Urease; Arginase

Catalyses reactions in ornithine cycle and therefore help in protein breakdown and urea formation

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Actin/Myosin Needed for muscle contraction

Ossein Structural support in bone

Collagen Gives strength with flexibility in tendons and

cartilage Elastin

Gives strength and elasticity to ligaments Keratin

Tough for protection Scales; claws; nails; hooves; skin

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Hormomes Insulin/Glucagon

Controls blood sugar level Vasopressin

Controls blood pressure Rhodopson/opsin

Visual pigments in the retina; sensitive to light Phytochromes

Plant pigments important in control and flowering, germination, etc.

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Hormones Prolactin

Induces milk production in mammals Chromatin

Gives structural support to chromosomes Keratin

Forms horns and antlers which may be used for sexual display

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