Amino Acids and Proteins

Positively charged amino acids

-3 positively charges amino acids -Have extra amino acid that can be charges

Phenylalanine

Phe

Polar, uncharged amino acids

Polar, uncharged amino acids have other differnet atoms attached, not just hydrogens and carbons.

What is are proteins?

Polymers made of amino acids, which are joined head to to in a long chain that folds into a three dimensional structure that is unique for each type of protein.

Space-filling model

Privides a map of the proteins surface, shows how the protein may look.

Proline

Pro

Serine

Ser

Backbone model

Shows a overall prganization of the polypetide chain and provides a straight forward way to compare tje structures of related proteins

Tertiary Structure

The full three dimensional structure formed by alpha beta abd coils, that go from N to C terminus -Held by hydrogen bonds, ionic bonds, disulfied bonds and hydro phobic interactions

Tyroine

Tyr

Valine

Val

Secondary Structure

Folding into alpha helix or beta pleated sheet or random coil -Held by hydrogen binds

Glutamine

Gln

How are peptide bonds formed?

Peptide bonds are formed by condensation reactions that link one amino acid to the next.

Primary structure

A linear sequence held together by amino acids in a polypeptide chain. -Held by covalent peptide bonds

Alanine

Ala

Quaternary Structure

2 or more folded polypeptide chains -Held by the same as tertary structure

Hydrophobic interaction

-4th weak fource, Hydrophobic interaction, also has a a central role in determining the shape of the protein. -An important factor governing the folding of any protien is the disturbution of polar and non polar amino acids. -Non polar (Hydrophobic) part tend to cluster in the interior part of the folded protien. -Polar part arranges outside of the protien, where they can form hydrogen binds with water

Polypeptide backbone

-Each polypepetide chain consists of a backbond that is adorned with a variety of chemical side chains. -This polypeptide backbond is formed from a repeating sequence of the core (N-C-C-) atoms, found in every amino acid.

Keratin Filaments

-Extremely stable: long lived structure such as hair, horns, nails are compised of this protien

Chaperone Proteins

-Protien folding in a living cell is usually assisten by chaperone proteins. -Make the folding process more efficent and reliable -The shape is still specified by its amino sequence.

Aromatic amino acids

-Relatively non-polar -R groups have rings -Grouped together due to rings

Amino Acids

-Small organic molecules with one defining property: they all possess a carboxylic acid group and an amino group, both linked to their alpha- carbon atom. -Each amino acid also had a side chain attached to its alpha carbon -The identity of the side chain (OR R group) is what distinguishes one amino acid from another

Fibrous Proteins

-They proteins form long fibres and mostly consist of repeated sequences of amino acids which are insoluble in water. -Fibrous proteins are abundant outside of the cell where they form the gel like extracellular matrix that helps bind cell together to form tissue. -

What happens when a protein folds inccorecty

-They sometimes form aggregates that can damage nerve cells and even whole tissues. -Misfolded proteins are thought to contribute to alzimers and huntingdon desiase. -Can even lead to death

How are amino acids in proteins held together?

Amino Acids in a protein are held together by a peptide bond

Binding site

Any region on a proteins surface that interacts with another molecule through sets of noncovalent binds is binding site

Protein Domain

Any segment of a polypeptde chain that can fold indedendently into a compact, stable structure. -A protein domain usually consists of 40 and 350 amino acids folded into alpha helices and beta sheets

Arginine

Arg

Asparagine

Asn

Aspartate

Asp

What do cells use to make proteins?

Cells use amino acids to build proteins.

Trptophan

Trp

What is the final folded structure of a protein called?

Conformation

Cysteine

Cys

Renaturation

Denatiruing solvent is removed, the protein often refolds into its orrignal conformation.

Protein families

Each family member has an amino acid sequence and a three dimiensional conformation that closely resemble those of the other family members

Ribbon Model

Empasizes its various folds, which describe in detail shortly

Glutamate

Glu

Glycine

Gly

Example of a amino acid that is not a optical isomer?

Glyciine because it has 2 hygrogen attched.

Histidine

His

Isoleucine

Ile

Wire Model

Includes the postitions of all the amino acids side chains. this view is useful for predicting which amino acid might be invlved in the proteins activity.

How does a protein usually fold?

It folds where the free energy is usually minimized.

What s buffer?

Keeps pH from changing to much

Leucine

Leu

Lysine

Lys

Methionine

Met

Negatively charged amino acids

Negative because they have a extra carboxyl group.

Nonpolar, aliphatic amino acids......

Nonpolar, aliphatic amino acids only have carbons, hydrogens attaches

optical isomers

Optical isomers are two compounds which contain the same number and kinds of atoms, and bonds and different spatial arrangements of the atoms,

Subunit

Subunit is a single protein molecule that assembles (or "coassembles") with other protein molecules to form a protein complex.

What is a peptide bond?

The covalent bond between two adjacent amino acids in a protein chain is called a peptide bond; the chain of amino acids is also known as poly

Threonine

Thr

Coled-coil

When 2 or 3 alpha helices wrap around a protein to make it stable

Intermediate filaments

a component of the cytoskeloten that gives the cell mechanical strength

Like sugars, all amino acids......

exist as a optical isomer in the D AND L forms

What is pK?

pK is the pH at which the hyrogen ion comes off.