CMB- Protein Structure & function

H₂N

Amino group

COOH

Carboxyl group

Amino Acids

Building blocks of proteins. Common structure: an amino group and a carboxyl group connected to the alpha carbon and a side chain (R group).

20

How many common maino acids are there ?

R groups

Amino Acids are classified into 4 groups based on their _____

Basic Side Chains, Acidic Side Chains, Uncharged Polar Side Chains, and Nonpolar side chains

What are the four families of Amino Acids?

Polar Amino Acids, positive

Basic Side chains are ______ Amino Acids and are _______

Arginine, Lysine, Histidine

What are the 3 Basic Side Chains?

Basic, Arg, R

Arginine is a ____ side chain and can be abbreviated as ___ or _

Basic, Lys, K

Lysine is a ____ side chain and can be abbreviated as ___ or _

Basic, His, H

Histidine is a ____ side chain and can be abbreviated as ___ or _

Polar amino acids, negative

Acidic Side chains are ______ Amino Acids and are _______

Aspartic acid, Glutamic acid

What are the two acidic side chains?

Acidic, Asp, D

Aspartic acid is ____ side chain and can be abbreviated as ___ or _

Acidic, Glu, E

Glutamic acid is a ____ side chain and can be abbreviated as ___ or _

Polar, uncharged polar

Uncharged Polar side chain are ____ Amino Acids and are ______

Asparagine, Glutamine, Serine, Threonine, and Tyrosine

What are the 5 Uncharged polar side chains?

Uncharged polar, Asn, N

Asparagine is a ____ side chain and can be abbreviated as ___ or _

Uncharged Polar, Gln, Q

Gutamine is a ____ side chain and can be abbreviated as ___ or _

Polar uncharged, Ser, S

Serine is a ____ side chain and can be abbreviated as ___ or _

uncharged polar, Thr, T

Threonine is a ____ side chain and can be abbreviated as ___ or _

Uncharged polar, Tyr, Y

Tyrosine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Nonpolar

Nonpolar side chains are _____ Amino acids that are______

Alanine, Glycine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan and Cysteine.

What are the 10 nonpolar side chains?

Nonpolar, Ala, A

Alanine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Gly, G

Glycine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Val, V

Valine is a ____ side chain and can be abbreviated as ___ or _

Leu, L, nonpolar

Leucine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Ile,I

Isoleucine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Pro, P

Proline is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Phe, F

Phenylalanine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Met, M

Methionine is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Trp, W

Tryptophan is a ____ side chain and can be abbreviated as ___ or _

Nonpolar, Cys, C

Cysteine is a ____ side chain and can be abbreviated as ___ or _

hydrophilic

Polar Amino Acids are ______

Hydrophobic

Nonpolar Amino Acids are

Peptide Bonds

The bonds between amino acids are formed by dehydration (polymerization)

Hydrogen Bonds, Ionic bonding, Van der Waals attraction, hydrophobic force, and covalent bonds between sulfurs in cystine.

What are the four internal forces that determine protein structure?

The forces between amino acids

What determines the 3D structure of a protein?

Hydrogen Bonding

Covalent bonding between sulfurs in cysteine

Ionic Bonding

Van Der Waals attraction

Hydrophobic exclusion

Primary Structure 1^o

Amino acid sequence

Secondary Structure 2^o

α helix and β helix

α helix

Hydrogen bonds in the backbone elements between the 1^st and 4^th amino acids

β helix

Hydrogen bonds in the backbone elements are parallel and anti-parallel

Motif or Super 2^o

Multiple 2^nd structures but in one domain

Tertiary Structure 3^o

Final folded shape of a polypeptide (or protein), usually a molecule made up of multiple domains.

Domain

A segment of a polypeptide chain that can fold independently into a compact, stable structure usually has a special function.

Quaternary Structure 4^o

Combination of multiple protein units

3-D configuration

Protein function is determined by its _________

Denatured protein

Renaturing

Molecular Chaperones

Assist protein folding in the cell

prion protein

Special misfolded proteins can cause Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans.

Hetrodimer

homodimer

Protein Aggregate

Enzymes, structural proteins, motor proteins, receptors, signal transduction and special functions.

What are the 6 functions of intracellular proteins?

Catalase

Example(s) of Intracellular Proteins Function: Enzyme

Actin filament and sceptrin

Example(s) of Intracellular Proteins Function: Structural Proteins

Myosin, kinesin, dynein

Example(s) of Intracellular Proteins Function: Motor Proteins

hormone receptors

Example(s) of Intracellular Proteins Function: Receptors

Kinase

Example(s) of Intracellular Proteins Function: Signal transduction

DNA binding protiens

Example(s) of Intracellular Proteins Function: Special functions

Transporters, anchors, receptors, enzymes, and recognition

What are the 5 functions of membrane proteins?

ion channels

Example(s) of Membrane Proteins Function: Transporters

Integrins

Example(s) of Membrane Proteins Function: anchors

growth factor receptors

Example(s) of Membrane Proteins Function: receptors

adenylyl cyclase

Example(s) of Membrane Proteins Function: Enzymes

glycoproteins

Example(s) of Membrane Proteins Function: Recognition

Structural proteins, enzymes, growth factor, and immune response

What are the four functions of extracellular proteins?

collagen

Example(s) of Extracellular Proteins Function: Structural Proteins

lysozyme

Example(s) of Extracellular Proteins Function: Enzyme

Fibroblast growth factor (FGF)

Example(s) of Extracellular Proteins Function: Growth Factor

Antibodies

Example(s) of Extracellular Proteins Function: Immune Response

lysozyme & polysaccharide

Enzyme & Substrate

Growth factor & growth factor receptor

ligand & receptor

antigen

antibody

Antibody (immunoglobulin (Ig))

Tetramer composed of two heavy and two light chains. They form a unique Y shape by many intra- and intermolecular S-S disulfide bonds. The variable domain binds a specific antigen.

Homogenization

The mechanical procedure allows the plasma membranes of cells to be ruptured and cell contents to be released.

Breaking cells with high-frequency sounds (ultrasound), using mild detergents to make holes in the plasma membrane, forcing cells through a small hole using high pressure, and shearing/grinding cells by plunger i a tight-fit tube.

What are the four common ways of Homogenization?

Homogenate or extract

The resulting thick “soup” from homogenization contains large and small molecules.

Differential Centrifugation

Repeated centrifugation at progressively higher speeds will fractionate cell homogenates into their components. Does so based on size and density. Bigger components form a pellet at the bottom. Smaller components remain in the suspension.

Supernatant

In Differential centrifugation, the smaller components of the cell remain in the suspension above.

whole cells, Nuclei, cytoskeltons

What fractionates at a low-speed centrifugation?

mitochondria, lysosomes, and peroxisomes

What fractionates at a medium-speed centrifugation?

Microsomes and other small vesicles

What fractionates at a high-speed centrifugation?

ribosomes, viruses and large macromolecules

What fractionates at very high-speed centrifugation?

Column chromatography

A way of separating proteins. A mixture of proteins in a solution is applied to a column filled with a permeable solid matrix. Then a large amount of solvent is pumped through the column. Based on how it reacts to the matric proteins will bind to certain chemical groups.

Ion exchange chromatography

Columns packed with small beads carrying either postive of negativle charges. Proteins of opposite charges are attracted to the beads.

Gel-Filtration Chromatography

The matrix is full of porous beads. Proteins that are small enough to enter the holes in the beads travel more slowly through the column.

Affinity Chromatography

A chromatography that separates proteins by the binding capacity to the packed protein.