[2] PROTEINS

• Proteins

are naturally occurring unbranched polymers made of monomer units known as amino acids

Proteins are generally composed of

C, H, O N, S and some may contain Fe, P, and other metals (specialized structures)

Proteins are polypeptides with atleast ___

40 amino acid residues)

• Proteins are described based on

different structural characteristics

Based on Polypeptide Chain

-monomeric

-multimeric

Monomeric

- contains one polypeptide chain

• Multimeric

- contains two or more polypeptide chains

Homomultimer

- one type chain

Heteromultimer

- two or more type of chains

Hemoglobin is a

heterotetramer

Hetero

- α and β chains

Tetra

- 2 α-chains + 2 β-chains

Based on Chemical Composition

-Simple protein

-Conjugated protein

• Simple protein

- made up of amino acid only

• Conjugated protein

- contain non-amino-acid entities (prosthetic groups) in the structure

-One or more polypeptide chains may be present with an inorganic or organic prosthetic group.

Hemoproteins

Heme

Lipoproteins

Lipid

Glycoproteins

Carbohydrate

Phosphoproteins

Phosphate

Nucleoproteins

Nucleic acids

Metalloproteins

metal ions

Based on Shape

fribrous

globular

Fibrous proteins examples

- α-keratin & collagen

Fibrous proteins

• Polypeptide chains are arranged in long strands or sheets

• Long rod-shaped or string-like molecules intertwine with one another, forming strong fibers that are water-insoluble

Fibrous proteins (function)

Structural functions

Globular proteins examples

- myoglobin & hemoglobin

Globular proteins

• Polypeptide chains are folded into spherical or globular shapes

• Nonpolar AAs are in the interior, polar AAs are on the exterior = water soluble

Globular proteins (functions)

• Dynamic functions

Based on Function

• Catalytic proteins

• Defense proteins

• Transport proteins

• Messenger proteins

• Contractile proteins

• Structural proteins

• Transmembrane proteins

• Storage proteins

• Regulatory proteins

• Nutrient proteins

Catalytic Proteins

Aka enzymes, has varying roles as a biochemical catalysts.

Catalytic Proteins

Proteases, Amylase

Defense Proteins

Aka immunoglobulins / antibodies, are responsible for the body's immune system

Defense Proteins

IgA, IgG, IgE, IgM

Transport Proteins

Facilitates the delivery of small molecules within the body to target locations

Transport Proteins

Hemoglobin, Transferrin, HDL, LDL

Messenger Proteins

Trasmits biochemical signals to coordinate cellular function within the body

Messenger Proteins

Insulin, Glucagon, Human Growth Hormone

Contractile Protein

responsible for all forms of movement

Contractile Protein

Actin, Myosin

Structural Proteins

Provides structural rigidity that results to mechanical strength and protection

Structural Proteins

α-keratin, Collagen

Transmembrane Proteins

Helps control the movement of small ions and molecules through the cell membrane

Transmembrane Proteins

Ligand-gated ion channel, Integrin

Storage Proteins

Binds and store small molecules for future use

Storage Proteins

Ferritin, Myoglobin

Regulatory Proteins

Binds to enzymes to control their "on/off" state and regulate enzymatic action

Regulatory Proteins

Ubiquitin

Nutrient Proteins

serves as source of nutrients during the early stages of life development

Nutrient Proteins

Casein, Ovalbumin

Buffer Protein

Maintains acid-base balance in the body

Buffer Protein

Hemoglobin, Transmembrane proteins

Fluid-Balance Proteins

Maintains fluid balance between blood and tissues

Fluid-Balance Proteins

Albumin, Globulin

Based on Amino Acid Contents

-complete

-incomplete

-complementary

COMPLETE PROTEINS

- contain the essential AA in proper amounts

• Proteins from animal sources

are complete, except gelatin •

INCOMPLETE PROTEINS

- low in one or more of the essential amino acids, usually Lys (K), Trp (W )or Met (M) •

Proteins from vegetable sources

are incomplete, except soy protein

• COMPLEMENTARY PROTEINS

are incomplete proteins which when served together complement each other and provide all the essential amino acids

PRIMARY PROTEIN STRUCTURE

sequence of a chain of amino acids

secondary protein structure

local folding of the polypeptide chain into helices or sheets

tertiary protein structure

three-dimensional folding pattern of a protein due to side chain interactions

quaternary protein structure

protein consisting of more than one amino acid chain

Primary Structure of Proteins

• Order in which amino acids are linked together in a protein through peptide bonds

• It is distinctive of a protein (or polypeptide) and tells its AA composition

• defines the protein's shape and function (dictated by the DNA base sequence in gene)

Primary Structure of Proteins

• Each protein has its own unique AA sequence -

number, kind, and order of attachment are all important.

protein backbone

in a peptide chain, the linkage of each aa makes the protein backbone and the r-grp are all left outside the backbone

Insulin

has 51 AA residues in its structure divided into 2 chains - Chain A & B

1˚ structure of insulin in several species

are alike but identical since there are residues that are different.

Primary Structure of Proteins

• Peptide linkages are essentially _

planar, 6 atoms lie in the same plane (C=O, C-N and N-H)

Planar peptide linkage structure is rigid,

-thus rotation of C-N group is hindered; cis-trans isomerism is possible (the trans being highly favored)

-effect is peptide bond planarity resulting to zigzag arrangement of the protein backbone

Secondary Structure of Proteins

-After the primary level, the polypeptide starts to fold.

-All the information necessary for folding the peptide chain into its "native conformation" is contained in the 1˚ amino acid structure of the peptide.

-The ordered 3D arrangements/regular folding in localized regions of a polypeptide chain

-Spatial arrangement of the atoms in the polypeptide chain

Secondary Structure of Proteins

• Formed and stabilized by

H-bond between the amide (-NH) proton and carbonyl O (C=O).

Secondary Structure of Proteins: dictated by the 1˚ structure based on

the AAs present in the chain.

Secondary Structure of Proteins

types

1) Alpha Helix

2) Beta-pleated Sheets

Alpha Helix

Single protein chain resembling coiled spring (helix)

Alpha Helix Results from

intramolecular H-bonding between AA

Alpha Helix: Rgroup

stay outside the helix because there is not enough space inside the helix

Alpha Helix: The helix is tightly wound that the space in the center is _

too small for solvent molecules to enter

Alpha Helix: • Must have the __ to coil

same conformations (all D or all L)

Beta-pleated sheets

"Pleated" or zigzag pattern

Beta-pleated sheets

• Completely extended protein chain segments governed by

intermolecular (between molecules) or intramolecular (within the molecule) H-bonds

Beta-pleated sheets: R or side chains are

below or above the sheet and backbone is alternating top and bottom position

Beta-pleated sheets: U-turn

__ structure is the most frequently encountered

• Beta-pleated sheets

Intermolecular H-bonding can be

-parallel

-anti-parallel

Parallel

-chains run in the same direction

• Antiparallel

-chains run in opposite direction which makes it more stable because of fully collinear H-bonds.

Unstructured Segments

Structure in the protein that is neither a helix nor a beta-pleated sheet, imparting flexibility to the protein structure to interact with different substances

Tertiary Structure of Proteins

overall 3D shape of a protein that defines the function of the protein.

Tertiary Structure of Proteins Results in

interactions between AA side chains that are widely separated from each other.

Tertiary Structure of Proteins

• fibrous or globular

Proteins may be __ based on shape

Tertiary Structure of Proteins

4 types of interactions

• Disulfide bonding

• Electrostatic interactions

• H-bonding

• Hydrophobic interactions

• Disulfide bonds

• Covalent bonds between cysteine groups (-SH)

• Strongest of the tertiary interacting forces

• Causes chains to twist and bend.

Electrostatic interactions

• AKA Salt bridges

• Interaction between acidic R groups and basic R groups

H-bonding

• Between polar, acidic and/or basic R groups: - OH, - NH2, -COOH, -CONH2

• Relatively weak and easily disrupted by changes in pH and Temperature

Hydrophobic attractions

• Between non-polar R groups orienting inwards avoiding common polar solvents

• Momentary interactions brought by weak forces (London dispersion) that is common with alkyl-aryl R groups

Hydrophobic Interactions

• nature of bonding

Interactions between nonpolar groups

*Hydrophilic Interactions

• nature of bonding

Attractions between polar or ionized groups and water on the surface of tertiary structure

Electrostatic Interactions/Salt Bridges

• nature of bonding

Ionic interactions between ionized acidic and basic amino acids

Hydrogen Bonds

• nature of bonding

Occur between H and O or N

Covalent Disulfide Bonds

• nature of bonding

Strong covalent links between sulfur atoms of two cysteine amino acids