Cell Biology Chapter 3

Structural components of a proteins

Amino acids held together by peptide bonds created by condensation reactions

What influences protein shape?

Side chain amino acids

Protein folding

Steric hindrance limits bond angles

Peptide bonds are planer

Effected by non covalent bonds ( electrostatic, hydrogen, van der waals )

Protein folding affecters

Distribution of polar and nonpolar side chains

Non polar - hydrophobic

Polar - hydrophobic

Conformation

Final folding structure

Urea denatures protein due to polar hydrogen bonds being stronger then water

Hsp

Heat shock proteins (molecular chaperone)

Shared by all cells

Induced by exposure to stress

Aid in protein folding

These chaperone proteins bind to hydrophobic residues to prevent from clumping and sticking to unwanted things, offer safe way to fold correctly

Secondary structure

Alpha helix

Alpha keratin is a fibrous structural proteins

Stabilized by N-H and C=O 4 bonds away from each other

Beta sheets

Silk fibroid is a fibrous structural proteins

Stabilized by hydrogen bonds with alternating R groups

Beta sheets

Can be anti parallel or parallel

Tertiary Structure - coiled coil

Several alpha helices wrapped around each other, hydrophobic toward center and hydrophilic outward

3-D structures

Combinations of alpha and beta make globular proteins, example is Src Kinase

Quaternary structure

Large proteins can contain more than 1 polypeptide chain or subunit

Protein domain

A distinct region of the protein that could fold independently into its own structure containing about 40 to 350 amino acids and has a specific function

Example - src kinase a globular protein with 4 domains

Protein families

Similar conformations and structures have similar functions

Protein sequence homology

Used as tool to determine functions - homeodomains

Example is yeast and fruit fly homology to test

Collagen

Fibrous, elongated, protein in extracellular matrix

What stabilizes enzymes

Covalent cross linkages

Active sites

Folding creates cavities/pockets

Cavity containing, amino acid side that make nonchalant bonds with specific ligands

Cyclic AMP

Used as a ligand that binds to active sites

Active site reactivity

Determined by amino acid side chains and orientation

Catalytic Triad

3 AA used for catalysts

Protein to protein interactions

Surface string - string (loop of aa), surface rubs against and recognizes spot

Helix helix - coiled coil

Surface surface - large proteins fit together forming many weak interactions

Antibody and antigen bonding

Antibodies bind antigens through loops in the variable domains of their heavy and light chains. Variation in the amino acid sequences and shapes.

Enzymes catalysis

Bind to the substrate, reduction of activation energy (stabilizing), bringing reactive groups together.

Co enzymes

A small molecule that helps an enzyme carry out a chemical reaction

Some enzymes don’t work without a co enzymes

Feedback inhibition

Most common type of negative regulation

Positive regulation

Accumulation of activates glycolytic enzymes

Allosteric effects

Binding to another location, change shape, effects binding of substrate at active site.

Positive regulation

Inactive molecule binds to substrate allowing molecule to bing what it wants until all molecules are bound when molecule x is present 100% active.

Negative regulation

Active cell binds to molecule to release continents when molecule x is present cell is not active

Enzymes regulation

Phosphorylation by kinase activity activating and inhibiting utilizing protein kinase and protein phosphatase.

GTP binding molecular switches

GTP have higher binding affinity so it moves faster.

Receptor associated trimeric G proteins

Involved in cell signaling, signal comes in and G protein delivers the message

Proteins regulating intercellular traffic of vesicles

Tiny bubbles carrying things around

Proteins that bind to transfer RNA

Protein synthesis - tRNA carries amino acids to the ribosome, where proteins are made.

GTP/GDP binding activating or inactivating proteins

RAS PLUS GTP is active and RAS plus GDP is inactive

GAP

GTPase activating protein is analogous to protein phosphatase

Promotes the removal of the terminal phosphate from GTP by hydrolysis

GEF

Guanine nucleotide exchange factor

Protein that helps GTP binding protein exchange GDP with GTP turning the protein on

Allosteric motor proteins

Utilize ATP hydrolysis for large movement

Allosteric Membrane bound transporter proteins

ABC = ATP binding cassette

Pumps large hydrophobic molecules across the membrane

Energy of ATP hydrolysis, ion gradient, electron transport used to pump ions or small molecules across membrane.

Protein machines

Several proteins come together to create a multi protein complex

Yeast two-hybrid = method used to detect protein to protein interactions