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DARAGA COMMUNITY COLLEGE

PROTEIN STRUCTURE AND


FUNCTION
BY: Warren Aycocho Norminda Marcellana
IV- BSED BIOLOGICAL SCIENCE

PROTEINS PLAY KEY ROLES IN A LIVING


SYSTEM

OVERVIEW
Make

up about 15% of the cell Have many functions in the cell


Enzymes Structural Transport Motor Storage Signaling Receptors Gene regulation Special functions

AMINO ACIDS CONTAIN AN AMINO GROUP, A CARBOXYL GROUP, - CARBON AND A UNIQUE R GROUP

Summary of 20 proteinaceous AA

Essential (unexpendable) organism is not able to synthesize these AA but accept from food. Nonessential (expendable) organism produced from essential AA by transamination.

Nonessential AA Alanine Asparagine Aspartate

Essential AA
Valin Leucin Isoleucine Threonine Lysin Methionin Phenylalanine Tryptophan Arginine

Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine

Histidine

Besides basic 20 proteinaceous AA more AA exist found only in some organisms. Essential AA are different for variety of animal species and plants are able to synthesize all 20 AA.

20 AMINO ACIDS
Glycine (G)
Alanine (A) Valine (V) Isoleucine (I) Leucine (L)

Proline (P)

Methionine (M)

Phenylalanine (F)

Tryptophan (W)

Asparagine (N)

Glutamine (Q)

Serine (S)

Threonine (T)

Tyrosine (Y)

Cysteine (C)

Asparatic acid (D) Glutamic acid (E)

Lysine (K)

Arginine (R)

Histidine (H)

White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

Amino acids- with non- polar side or hydrophobic- chain that not bind or give up off the protons or participate in hydrogen or ionic bonds. The side chains of these be thought of as oily or lipid like .Amino acids with uncharged polar side chains or hydrophilicThese amino acids have zero net charge at neutral pH, although the side chains of cysteine and tyrosine can lose a proton at alkaline Ph.

1. Disulfide bond: The side chain of cysteine contains a sulfhydryl group (-SH), which is an important component of the active site of many enzymes. In proteins the SH groups of two cysteines can become oxidized to form a dimer, cysteine, which contains a covalent cross-link called a disulfide bond formation.

2. Side chains as sites of attachment for other compounds: Serine, threonine, and, rarely, tyrosine contain a polar hydroxyl group that can participate or serve as a site of attachment, for example, for a phosphate group. (Note: The side chain of serine is an important component of the active site of many enzymes). In addition, the amide group of asparagine, as well as the hydroxyl group of serine of threonine, can serve as a site of attachment of oligosaccharide chains in glycoproteins.

C. AMINO ACIDS WITH ACIDIC SIDE CHAIN

The amino acid aspartic and glutamic acid are the proton donors. At neutral pH the side chain of these amino acids are fully ionized, containing a negative charged carboxylate group (-COO). They are therefore called aspartate or glutamate to emphasize that these amino acids are negatively charged at physiologic pH.

D. AMINO ACIDS WITH BASIC SITE CHAINS

The side chains of the basic amino acids accept protons. At physiologic pH the side chains of lysine and arginine are fully ionized and positively charged. In contrast, histidine is weakly basic and the free amino acid is largely uncharged at physiologic pH. However, when histidine is incorporated into a protein, its side chain can be either positively charged or neutral, depending on the ionic environment provided by the polypeptide chains of the protein. (Note: this is an important property of histidine that contributes to the role it plays in the functioning of proteins such as myoglobin.

E. ABBREVIATIONS AND SYMBOLS FOR THE


COMMON OCCURRING AMINO ACIDS 1. Unique first letter: if only one amino acid begins with a particular letter, then that letter is used as its symbol. For example, I=isoleucine Cysteine Histidine Isoleucine Methionine Serine Valine = = = = = = Val Cys His Ile Met Ser = = = = = = V C H I M S

2. Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbols. For example, glycine is more common than glutamate, so G=glycine consist . Alanine = Ala = A Glycine = Gly = G Leucene = Leu = L Proline = P = P Threonine = Thr = T

3. Similar sounding names: Some one- letter symbols sound like the amino acid they represent for example,F= phenylalanine, or W= ( Twyptophan as Elmer Fudd would say.) Arginine = Arg = R ( aRginine) Asparagine = Asn = N ( contains N) Aspartate = Asp =D (asparDic) Glutamate = Glu =E (glutEmate) Glutamine = Gln =(Q- tamine)

Peptide Bonds join amino acids Its a condensation reaction (meaning that H20 is released when the bond is formed).

Two amino acids form a DI-PEPTIDE

POLYPEPTIDES are formed from more than two amino acids bonded together

PROTEINS HAVE FOUR LEVELS


OF ORGANIZATION

PRIMARY STRUCTURE IS
THE AMINO ACID SEQUENCE

THE AMINO ACID SEQUENCE IS CODED FOR BY DNA AND IS UNIQUE FOR
EACH KIND OF PROTEIN

AMINO ACID SEQUENCE IS ENCODED BY DNA BASE


SEQUENCE IN A GENE
T
T
TTT TTC TTA TTG CTT CTC CTA CTG ATT ATC ATA ATG GTT GTC GTA GTG Phe Leu

C
TCT TCC TCA TCG CCT CCC CCA CCG ACT ACC ACA ACG GCT GCC GCA GCG

Second letter A
Ser TAT TAC TAA TAG CAT CAC CAA CAG AAT AAC AAA AAG GAT GAC GAA GAG Tyr Stop His Gln Asn Lys Asp Glu

G
TGT TGC TGA TGG CGT CGC CGA CGG AGT AGC AGA AGG GGT GGC GGA GGG Cys Stop Trp Arg T C A G T C A G T C A G T C A G

Third letter

Leu

Pro

First letter

Ile Met Val

Ser Arg

Thr

Ala

Gly

EVEN A SLIGHT CHANGE IN THE AMINO


ACID SEQUENCE CAN CAUSE THE PROTEIN TO MALFUNCTION

For example, mis-formed hemoglobin causes sickle cell disease

PROTEINS HAVE FOUR LEVELS


OF ORGANIZATION

SECONDARY STRUCTURE RESULTS FROM HYDROGEN


BONDING BETWEEN THE OXYGEN OF ONE AMINO ACID AND THE HYDROGEN OF ANOTHER

- COILED SECONDARY STRUCTURE DUE TO A


HYDROGEN BOND EVERY FOURTH AMINO ACID

BASIC STRUCTURAL UNITS OF PROTEINS: SECONDARY STRUCTURE

Secondary structure- polypeptide chains folded into regular repeating structural patterns.

1. -helix or alpha helix


- Consists of tightly coiled polypeptide chain. - The chain is held in this helical shape by hydrogen bonds between the nitrogen of one amino acid and the oxygen of another beyond it in polypeptide chain.

- Formed by a H-bond between every 4th peptide bond C=O to N-H - Usually in proteins that span a membrane - The helix can either coil to the right or the left - Can also coil around each other coiled-coil shape a framework for structural proteins such as nails and skin

2. Beta pleated sheet


- Many side by side hydrogen bonds between the chains. - hydrogen bonds that stabilize the pleated sheet pattern are between different polypeptide chain. - Pleated sheet arrangement is flexible and strong but resists stretching.

THE BETA PLEATED SHEET IS FORMED BY HYDROGEN


BONDS BETWEEN PARALLEL PARTS OF THE PROTEIN

Sheets
Core of many proteins is the sheet Form rigid structures with the H-bond Can be of 2 types
Anti-parallel run in an opposite direction of its neighbor (A) Parallel run in the same direction with longer looping sections between them (B)

PROTEINS HAVE FOUR LEVELS


OF ORGANIZATION

TERTIARY STRUCTURE DEPENDS ON THE INTERACTIONS AMONG THE R GROUP SIDE CHAINS

TYPES OF INTERACTIONS

Hydrophobic interactions: amino acids with nonpolar side chains cluster in the core of the protein, out of contact with water

= charged

= hydrophobic

TYPES OF INTERACTIONS

Hydrogen bonds between polar side chains

TYPES OF INTERACTIONS

Ionic bonds between positively and negatively charged side chains

TYPES OF INTERACTIONS

Disulfide bridge (strong covalent bonds) between sulfur atoms in the amino acid cysteine

Link to video

PROTEINS HAVE FOUR LEVELS


OF ORGANIZATION

QUATERNARY STRUCTURE RESULTS FROM


INTERACTIONS AMONG SEPARATE POLYPEPTIDE CHAINS.

For example, hemoglobin is composed of 4 polypeptide chains

Link to video

DENATURATION MAY BE DUE TO CHANGES IN PH,


TEMPERATURE OR VARIOUS CHEMICALS

PROTEIN FUNCTION IS LOST DURING DENATURATION, WHICH IS OFTEN IRREVERSIBLE

Proteins can be fibrous or globular


Lets explore the diversity of protein structure and function by investigating some examples

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PROTEINS.
If there is a job to be done in the molecular world of our cells, usually that job is done by a protein.
A protein hormone which helps to regulate your blood sugar levels

CATALASE

An enzyme which removes Hydrogen peroxide from your body so it does not become toxic

Examples of proteins include hormones acting as messengers; enzymes speeding up reactions; cell receptors acting as antennae; antibodies fighting foreign invaders; membrane channels allowing specific molecules to enter or leave a cell; they make up the muscles for moving; let you grow hair, ligaments and fingernails; and let you see (the lens of your eye is pure crystalised protein).
Source: http://courses.washington.edu/conj/protein/insulin2.gif http://www.biochem.ucl.ac.uk/bsm/pdbsum/1gwf/main.html

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1. -Keratins

Fibrous Proteins

Found in: mammals, provide strength Hair, wool, nails, claws, quills, horns, hooves, skin

Strengthened by: Disulfide bonds

Fibrous Proteins

-Keratins
Permanent waving of hair 1. Reduce disulfide bonds 2. Moist heat breaks H-bonds and causes uncoiling of helix 3. Remove reducing agent, add oxidizing agent, new S-S bonds

Fibrous Proteins

2. Collagen
helices, left-handed helix with 3 amino acids per turn 35% Gly, 11% Ala, 21% Pro/4-Hyp (Gly-X-Y) repeat with X as Pro and Y as 4-Hyp Coiled-coil, three separate polypeptides called chains are supertwisted Provide strength (stronger than ??) Connective tissue (tendons, cartilage, organic matrix of bone, cornea)

Fibrous Proteins

Collagen
Rigid and brittle bones caused by: Crosslinks in collagen fibrils over time Gly-X-Y repeat important - single change results in disease Osteogenesis imperfecta - abnormal bone formation in babies Ehlers-Danlos syndrome - loose joints Both diseases involve: mutation of Gly to a different amino acid

Fibrous Proteins

Silk
Fibrous protein of silk = Fibroin Secondary structure present: sheets Forces involved: H-bonds between different sheets Made by: insects and spiders Silk does not stretch because it is already highly extended

Globular Proteins Variety of Tertiary Structures

Disulfide bond

Heme Disulfide bond

Respiratory chain in mitochondria

Egg white and human tears Cleaves polysaccharides

Enzyme secreted by pancreas Hydrolyzes RNA

FOLDED PROTEINS ARE PLACED INTO TWO


GENERAL CATEGORIES

FIBROUS PROTEINS HAVE POLYPEPTIDE CHAINS


ORGANIZED IN LONG FIBERS OR SHEETS
Water insoluble Very tough physically, may be stretchy

FUNCTIONS OF FIBROUS PROTEINS

Structural proteins function in support


Insects and spiders use silk fibers to make cocoons and webs Collagen and elastin are used in animal tendons and ligaments Keratin is the protein in hairs, horns and feathers

FUNCTIONS OF FIBROUS PROTEINS

Contractile proteins function in movement

Actin and myosin contract to create the cleavage furrow and to move muscles Contractile proteins move cilia and flagella

GLOBULAR PROTEINS HAVE THEIR CHAINS FOLDED INTO COMPACT, ROUNDED SHAPES

Easily water soluble

FUNCTIONS OF GLOBULAR PROTEINS

Storage proteins function in the storage of amino acids

Ovalbumin is the protein in egg whites Casein is the protein in milk, source of amino acids for baby mammals

FUNCTIONS OF GLOBULAR PROTEINS

Transport proteins function in the movement of other substances

Hemoglobin, the iron containing protein in blood, transport oxygen from lungs to other parts of the body (C3032H4816O872N780S9Fe4)
Membrane transport proteins such as channels for potassium and water

FUNCTIONS OF GLOBULAR PROTEINS

Hormone proteins function as cellular messenger molecules that help maintain homeostasis

Insulin: sends message allow sugar into cells (when blood glucose levels are high, cells will transport glucose into the cells for use or storage) Glucagon: sends message we need more sugar in the blood (when blood glucose is too low, cells will release glucose)

FUNCTIONS OF GLOBULAR PROTEINS

Receptor proteins allow cells to respond to chemical stimuli

Growth factor receptors initiate the signal transduction pathway when a growth hormone attaches

FUNCTIONS OF GLOBULAR PROTEINS

Cholesterol receptors on the cell membrane allow LDL to be endocytosed into the cell

FUNCTIONS OF GLOBULAR PROTEINS

Protective proteins function as protection against disease

Antibodies combat bacteria and viruses

FUNCTIONS OF GLOBULAR PROTEINS

Enzymes speed up chemical reactions

Amylase and other digestive enzymes hydrolyze polymers in food Catalase converts hydrogen peroxide H2O2 into water and oxygen gas during cellular respiration

PROTEINS
Chains

of amino acids

AA AA

Many

proteins are enzymes


AA

AA AA

Enzymes

catalyze chemical reactions

AA

ENZYMES AS CATALYSTS
Catalyst

- Speeds up chemical reactions in living organisms by decreasing the energy needed to start the Energy reaction (activation energy)

Without a catalyst

With a catalyst

Time

DEFINITIONS
Substrate-

monomers that bind to the active site of an enzyme Active site- area on enzyme where substrate binds Product- what the enzyme produces

LOCK AND KEY MODEL


Two substrates

Enzyme Active site of the enzyme

LOCK AND KEY MODEL


The substrates fit like a key in a lock

Enzyme The active site is like a lock

LOCK AND KEY MODEL


The activation energy for these substrates to bind together has been lowered by the enzyme.

Chemical reaction!!!

Enzyme

BASIC ENZYME DIAGRAM


The substrates have reacted and changed into the product

Enzyme is unchanged Active site

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