Chapter 22: Proteins

K. Dunlap Chem 104

Human Proteins• proteins contain C, H, O, and N

• Made up of 20 amino acids

• amino acids written in blue are essential amino acids, meaning they can not be made and must be consumed

Proteins• Proteins serve many functions:

– 1.Structure:1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails.

– 2. Catalysts:2. Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes.

– 3. Movement:3. Movement: muscles are made up of proteins called myosin and actin.

– 4. Transport4. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes.

– 5. Hormones:5. Hormones: many hormones are proteins, among them insulin, oxytocin, and human growth hormone.

Proteins

– 6. Protection:6. Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease.

– 7. Storage:7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron.

– 8. Regulation:8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place.

Amino Acids

•Have an alpha- carbonattached to:

• an amino group

• carboxyl group

• a hydrogen

• an R group

Each R groupdetermines the properties of the amino acid

R groups can be polar, nonpolar,acidic, basic

Each R groupdetermines the properties of an amino acid

R groups can be polar, nonpolar,acidic, basic

Chirality of Amino Acids• With the exception of glycine, all protein-

derived amino acids have at least one stereocenter (the -carbon) and are chiral.– The vast majority of protein-derived amino acids

have the L-configuration

Zwitterions

• amino acids can act as acids and bases• Amino acids exist in solution as dipolar ions (Zwitterions)

• Like buffers, AA’s can act as proton donors or acceptors

– “Amphoteric” compounds or “amphoteric electrolytes”

• Isoelectric point – pH at which all the molecules have equal positive and negative charges

Proteins are made of 20 amino acids

proteins

Peptides: how aa are linked• proteins are long chains of amino acids joined by

amide bonds.

peptide bondpeptide bond:: – amino acids become linked together to form

peptide bonds with the elimination of water– The reaction takes place between the -COOH of

one amino acid and the -NH2

formation of peptide bondsPeptides and proteins are polymers of amino acids

• Two amino acids are covalently joined in condensation reaction

N-terminal C-terminal

Peptides– PeptidePeptide: A short polymer of amino acids joined by

peptide bonds; they are classified by the number of amino acids in the chain.

– DipeptideDipeptide: containing two amino acids joined by a peptide bond.

– TripeptideTripeptide: containing three amino acids joined by peptide bonds.

– PolypeptidePolypeptide: chain containing up to 50 amino acids– ProteinProtein: A biological macromolecule containing at

least 30 to 50 amino acids joined by peptide bonds.

4 levels of protein structure

• Primary – sequence of amino acids• Secondary – interactions between adjacent amino

acids• Tertiary – 3D folding of the polypeptide• Quaternary – arrangements of multiple polypeptides

Levels of Structure• Primary structure:Primary structure: the sequence of amino

acids• Secondary structure:Secondary structure: conformations of amino

acids in localized regions of a polypeptide chain; examples are -helix, -pleated sheet, and random coil.

• Tertiary structure:Tertiary structure: the complete three-dimensional arrangement of atoms of a polypeptide chain.

• Quaternary structure:Quaternary structure: the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain.

1) Primary Structure• the sequence of amino acids in a polypeptide

chain.

• The number peptides possible from the 20 protein-derived amino acids is enormous.

– the number of peptides possible for a chain of nn amino acids is 2020nn.

– for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078

Primary Structure

• The hormone insulin consists of two polypeptide chains held together by two interchain disulfide bonds.

Primary Structure• Just how important is the exact amino acid

sequence?– Human insulin consists of two polypeptide chains

having a total of 51 amino acids.– In the table are differences between four types of

insulin.

Primary Structure– Vasopressin and oxytocin are both nonapeptides

but have quite different biological functions.

– Vasopressin is an antidiuretic hormone.

– Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk.

proteins range in size

2) Secondary Structure• conformations of amino acids in localized

regions of a polypeptide chain.– The most common types of secondary structure

are -helix and -pleated sheet. -Helix:-Helix: a type of secondary structure in which a

section of polypeptide chain coils into a spiral, most commonly a right-handed spiral.

-Pleated sheet:-Pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other

-Helix• The -helix structure: held together by

hydrogen bonds

-Helix• In a section of -helix;

– The C=O group of each peptide bond is hydrogen bonded to the N-H group of the peptide bond four amino acid units away from it.

– All R- groups point outward from the helix.

secondary structure

• Note the position of the purple R groups relative to the backbone of the polypeptide

all α helices are right handed

• But some supramolecular complexes are left handed (keratin, collagen)

right-handed = clockwise

β sheet secondary structure• More extended• H-bonds may occur between amino acids some

distance from one another• Adjacent chains can run parallel or anti-parallel

to each other

-Pleated Sheet

• In a section of -pleated sheet;

– The C=O and N-H groups of peptide bonds from adjacent chains point toward each other so that hydrogen bonding is possible between them.

– All R- groups on any one chain alternate, first above, then below the plane of the sheet, etc.

Pleated Sheet Structure of Proteins

secondary structure and function

3) Tertiary Structure• the overall conformation of an entire

polypeptide chain.

• Tertiary structure is stabilized in four ways:– Covalent bondsCovalent bonds, as for example, the formation of disulfide

bonds between cysteine side chains.– Hydrogen bondingHydrogen bonding between polar groups of side chains, as

for example between the -OH groups of serine and threonine.

– Salt bridgesSalt bridges, as for example, the attraction of the -NH3+

group of lysine and the -COO- group of aspartic acid.– Hydrophobic interactionsHydrophobic interactions, as for example, between the

nonpolar side chains of phenylalanine and isoleucine.

Cysteine• The -SHSH (sulfhydryl) group of cysteine is easily

oxidized to an -S-S--S-S- (disulfide).

the permanent wave that isn’t

New S-S bonds

Heat

+

Tertiary Structure• Forces that stabilize 3° structure of proteins

Tertiary Structures of Proteins• the three dimensional shape of proteins that results from further crosslinking, folding and interaction between R groups

1) disulfide linkages (-S-S-) b/w cysteins2) dipole dipole interactions b/w polar groups3) hydrogen bonding on side chains4) London forces

relative compactness of proteins

• Hypothetical chain length of a protein if it were to appear either as an α helix or β sheet

4) Quaternary Structure• the arrangement of polypeptide chains into a

noncovalently bonded aggregation.– The individual chains are held together by

hydrogen bonds, salt bridges, and hydrophobic interactions.

• Hemoglobin– Adult hemoglobin:Adult hemoglobin: two chains of 141 amino acids

each, and two chains of 146 amino acids each.– Each chain surrounds an iron-containing heme

unit.

Hemoglobin• The 4° structure of hemoglobin: made up of 4

subunits

Denaturation

• the process of destroying the native conformation of a protein by chemical or physical means.

– Some denaturations are reversible, while others permanently damage the protein.

• Protein function often includes reversible binding interactions with other molecules.

• Complementary interactions between proteins and ligands are the basis of self vs non-self recognition by the immune system.

• Specific protein interactions modulated by chemical energy are the basis of muscle movement.

Protein Function

oxygen-binding proteins have a heme prosthetic group

oxygen-binding proteins have a heme prosthetic group

hemoglobin

http://www.youtube.com/watch?v=5LjLFrmKTSA&feature=related

Hemoglobin

Binds O2 is a cooperative process.

Binding affinity of Hb for O2 is increased by the O2 saturation of the molecule with the first O2 bound influencing the shape of the binding sites (conformation change) for the next O2

hemoglobin-O2 binding allosterically modulated by 2,3-bisphosphoglycerate

BPG reduces the affinity of Hb for O2.

BPG binds at a site distant from the O2-binding site and regulates the affinity of Hb for O2.

immune responses are mediated by protein interactions that distinguish self and non-self

Humoral immune response – B cells produce antibodies or immunoglobulins against bacteria, viruses and foreign molecules

Cellular immune response - T cells destroy host cells infected by viruses

Muscle contraction occurs by the sliding of the thick (myosin) and thin (actin) filaments past each other

Conformational changes in the myosin head are coupled to ATP hydrolysis

muscle contraction is also based on protein interactions and conformational changes

http://www.sci.sdsu.edu/movies/actin_myosin_gif.html

1. What 2 functional groups are present in all amino acids?

2. Name the simplest amino acid. Is it a chiral molecule?

3. Approximately how many amino acids are needed to make the proteins found in the body?

4. What element is present in proteins but not in sugars or fats?

5. What is meant by the primary, secondary and tertiary structures of proteins?

6. What type of bonds are responsible for the helix structure of some proteins?