What is Proteomics?

The large-scale study of proteins

What is a polypeptide?

A polymer of amino acids.

What is a protein?

A biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific three-dimensional structure.

What are the 7 jobs of proteins?

1. Transport 2. Enzymes 3. Signal Transduction 4. Cell-cell recognition 5. Intercellular joining 6. Attachment to the cytoskeleton 7. Formation of the cytoskeleton

What is an amino acid?

The monomer for proteins.

What 3 parts does an amino acid contain?

1. An amino group 2. A carboxyl group 3. A side chain

What is the name of the carbon onto which the side chain is attached?

The Alpha Carbon

How many different amino acids are there?

20, hence 20 different side chains.

How do side chains differ in chemical properties?

1. Hydrophilic Basic 2. Hydrophilic Acidic 3. Hydrophilic Neutral 4. Hydrophobic

How do side chains differ in physical properties?

1. Big 2. Small 3. Linear 4. Ringed

How are proteins formed?

1. A dehydration reaction occurs between two amino acids to start building a polypeptide 2. A peptide bond is formed 3. Ribosomes create dehydration reactions. Ribosomes can either be in the cytosol or the endoplasmic reticulum. 4. Ribosomes get the instructions to make the proteins from the DNA.

What is the most important aspect of a protein?

It's shape

Why is shape the most important aspect of a protein?

A protein's function is dependent upon its shape. If the shape is messed up, then the protein cannot function.

What is primary structure?

The first layer- refers to the order on which amino acids are put together.

How can amino acids be abbreviated?

1. 3 letters, ex: Try 2. 1 Letter code, ex: Y

Primary structure can be affected by mutations:

Sickle-cell disease is caused by a substitution of one amino acid (valine) for the normal one (glutamic acid) at the position of the 6th amino acid.

What is Secondary structure?

The second layer- refers to the alpha helices and beta pleated sheets that occur because of the hydrogen bonding that occurs between the amino acids.

How can secondary structure be disrupted?

1. Heat 2. pH

What is the Tertiary Structure?

The third layer - refers to the actual, physical shape of the protein. Or Folding, folding = Shape.

What interactions occur across amino acids?

1. Hydrogen bonding 2. Covalent bonds 3. S-S bonds (disulfide bridges) 4. Ionic bonds 5. Hydrophobic interactions 6. Van der Waal's interactions

What can disrupt the tertiary structure?

1. Heat 2. pH

What is denaturation?

When a protein unravels and loses its native shape

Can denaturation be fixed?

1. Lightly denatured can be fixed 2. Severely denatured cannot be fixed

What is the Quaternary Structure?

The 4th layer- this is when 2 or more polypeptides come together to create a protein.

What structures does a polypeptide have?

has primary, secondary, and tertiary.

How many amino acids does peptides have?

small chain, 50 or less.

In quaternary structure, polypeptides are often referred to as what?

subunits

What is a motif?

refers to patterns that are seen over and over again in proteins

What is a domain?

refers to a substructure within the tertiary structure. Where the protein physically performs a specific job

What is a chaperone protein?

Helps newly strung together amino acids start to fold into the correct secondary and tertiary structures.

What is a chaperonin?

1. Type of chaperone protein 2. Exists in E. coli bacteria 3. Has a cylindrical container shape

What is a misfolded protein?

A protein which has the wrong shape

How can misfolded proteins occur?

1. Prions 2. Environmental factors, pH and Temp

What is Renaturation?

When a protein refolds after the normal environment is reestablished.

What is dissociation?

when subunits in quaternary structures become unglued from one another

What does an enzyme act as?

As a catalyst. They speed up reactions without actually being used by a reaction.

How do enzymes speed up chemical reactions?

1. Lowering the activation energy of reactions 2. brining 2 substrates together or by stressing particularly chemical bonds of a substrate

What is free energy of activation/activation energy?

The energy required contort the reactant molecules so the bonds can break

What is it called when the substrate binds to the enzyme?

The enzyme-substrate complex

What is the active site?

The specific region of the enzyme that actually binds the substrate. 1. pocket or groove on the surface of the enzyme 2. only a few amino acids big 3. Shape must match the shape of substrate 4. Not rigid

What is an induced fit?

refers to the tightening of the binding between the substrate and active site after initial contact

What is the product?

What comes out of the enzyme, end result of the chemical reaction.

What is saturation?

All of the enzymes will have their active sites engaged. The reaction is now saturated.

Cofactors:

1. nonprotein helper 2. Can be permanently bound or loosely bound 3. some are metal

Coenzymes:

1. A type of cofactor 2. Vitamin B family serves as precursors for coenzymes

Competitive Inhibitors:

Bind to the active site of the enzyme

Noncompetitive Inhibitors/allosteric inhibitors:

Bind to the allosteric site

Allosteric activators:

1. required for an enzyme to work 2. bind to a different allosteric site

What is feedback inhibition?

Where a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway. The prevents the cell of making too much of an end product, thus wasting chemical resources.

What is a multienzyme complex?

When several enzymes catalyzing different steps in a sequence of reactions are associated with one another.

What are the purposes of a multienzyme complex?

1. Helps speed up series of reactions 2. Unwanted side reactions are prevented 3. All of the reactions in that series are controlled as one unit.

What is Metabolism?

The total of all chemical reactions carried out by a living organism

What is Anabolism?

The chemical reactions that expand energy to build up molecules

What is Catabolism?

The chemical reactions that harvest energy by breaking down molecules.

What is a Biochemical Pathway?

Where the product of one reaction becomes the substrate for the next