AP Bio #5 - Proteins and Enzymes

Proteins do it all!

Big Questions:

How do living systems control their metabolism?

How do living systems carry out a wide variety of specific chemical reactions?

Regulation:

Proteins

Enzymatic function can be stimulated or inhibited by factors in the cell.

Amino Acids

Protein Structure

General info:

Competitive Interactions

Non-Competitive Interactions

vs.

Because of the diversity of amino acids, proteins have very complex 3-D structures.

Generally, we can consider 4 levels of protein structure:

• There are 21 known amino acids used in biological systems.
• All amino acids contain an amino (basic) & carboxyl (acidic) group, bonded to a central "alpha" carbon.
• Every amino acid differs in the structure of a variable group (symbolized as R) bonded to the alpha carbon.
• The structure of the R-group varies widely.

Primary structure of Transthyretin:

Primary Structure

Secondary Structure

What it is:

Regular, repeating 3D structures found in all polypeptide chains.

• The most complex biological molecules.
• Made of C, H, O, N & a little S
• Used to accomplish all life functions
• All proteins are polymers of amino acid monomers
• Amino acids are joined by "peptide bonds"

What it is:

The sequence of amino acids in one polypeptide chain

"Alpha helix"

How it happens:

Hydrogen bonding between atoms in the CN backbone of the polypeptide (no R-groups involved)

"Beta Pleated Sheet"

How it happens:

Peptide bonds between amino acids.

How does the cell "know" the order of amino acids?

"-ase"

Why do all proteins have similar secondary structures?

Chains of amino acids have a directionality, with an amino end ("N-terminus") & a carboxyl end ("C-terminus")

A molecule other than the substrate binds to the active site.

Regulation is accomplished without occupying the active site.

Tertiary Structure

Quartenary Structure

What it is:

The specific 3D shape of any protein that is made of more than one polypeptide chain (many are).

The only "optional" level of structure.

What it is:

The specific 3D shape of a particular polypeptide chain (aka the "conformation")

Quaternary structure of Transthyretin (four identical subunits):

Tertiary structure of 1 Transthyretin unit:

Enzymes!

How it happens:

Interactions between R-group atoms with other R-groups and the local environments of the cell

How it happens:

The overall structure when multiple chains form a functional protein.

Why do some proteins consist of more than 1 polypeptide chain?

Nonpolar AA's tend to end up on the interior of the protein!

A common nomenclature suffix for enzymes.

prefix: usually refers to enzyme's substrate

What kinds of interactions can occur to determine tertiary structure?

Protein Function

An Illustrative Example

Sickle cell anemia: One example of the relationship between protein structure and organismal physiology (not the only one, by any means!)

What do proteins do?

Generally speaking: Proteins are responsible for all life activities of the cell (and by extension, the organism, population, etc.)

Your book gives a pretty good overview:

Biological catalysts.

Proteins and some RNA molecules (examples?)

This is Hemoglobin!

It carries oxygen in your red blood cells

This change in the structure of hemoglobin affects the function.

Sickle-cell hemoglobin gets clumpy, and the red blood cells change shape.

They don't carry as much oxygen, and get stuck in blood vessels.

Sickle-cell anemic people die at a young age from the disease.

IT IS

CRAZY

IMPORTANT!

Some unlucky folks have a mutation that results valine (hydrophobic) replacing glutamic acid (hydrophilic) in the beta chains of hemoglobin

Allosteric Interactions

Binding of a substrate molecule to on active subunit of an enzyme can also trigger stabilization of the active conformation in all subunits ("cooperativity")

OOPS!

Activation:

Binding of an activator molecule can stabilize the enzyme in an active conformation.

How do they do it?

"Other-site"

Ex. Caspase

Activator

Active

Denaturation

Induced Fit - Ball & Glove

Reactants

Amino Acid Properties

Stimulate or inhibit enzyme activity by causing a conformational change in the enzyme.

How can you predict the characteristics of an amino acid? Here's some rules:

Important enzymes for cell death (apoptosis and necrosis).

Data from an experiment to determine if caspase enzymes can have an allosteric site.

The active and inactive forms of caspase 1 were already known.

Hypothesis: Allosteric inhibition of caspase 1 will lock the enzyme in an inactive conformation.

Constant Oscillation

Enzyme-Substrate

Complex

Inhibition:

If your R Group has:

Binding of an inhibitor molecule can stabilize the enzyme in an inactive conformation.

There is a direct relationship between a protein's conformation and its function.

If the conformation is altered, the function of the protein will also be altered.

Denaturation: Change in the structure of a protein.

Denatured proteins do not work well (if at all). It generally messes up all levels except primary.

What sorts of conditions can denature proteins?

R Group

Nitrogen then you're likely basic

Enzymes interact with reactants ("substrate")

Cause breaking/formation of particular atomic bonds to be more energetically favorable.

This work is localized to an area of the enzyme called the "active site".

Carboxylic Acid (COOH) then you're likely acidic.

R Group

Denaturation

The shape of the active site of an enzyme is shape-specific for a particular substrate.

The binding of a substrate to the active site induces the necessary conformational change of the enzyme to catalyze the reaction.

Only C's and H's then you're likely nonpolar (hydrophobic)

R Group

Enzyme

Inhibitor

The active site is localized to a small area of the enzyme

O, N, or an acid group then you're likely polar.

Inactive

Renaturation

R Group

Organization:

Examples:

Topoisomerase:

Evolutionary Considerations:

Compartmentalization

Environmental Infuence:

Feedback:

Products

Involved in minimizing mechanical stress on DNA during replication.

Makes a temporary cut in the helix.

Many metabolites have regulatory effects on enzymes that catalyze the metabolic pathways that result in the production of those metabolites.

• Blue: 2 polypeptide chains.
• Orange: DNA Double-Helix
• Purple: Active site.

Localization of specific enzymes (and the reactions they mediate) within compartments of the cell allow for more control over when and where particular metabolic reactions occur in eukaryotes

Evolution plays a central role in enzyme structure and function.

Various studies have been conducted to investigate the effect of evolution on enzymes.

These include:

• analysis of enzyme genes (sequence comparison).
• Artificial selection of enzyme activity in laboratory settings.
• Ethnographic/Demographic studies of enzyme genotypes and enzymatically determined phenotypes.

Rubisco!

Attaches carbon dioxide to sugar precursor molecules in photosynthesis.

50% of all protein found in a chloroplast.

Co-factors

Like all proteins, enzyme structure (and therefore function) can be effected by the conditions of the enzyme's enviornment.

There are three major environmental conditions that effect enzyme structure and function

Most enzymes require accessory compounds many of which you are familiar with as ("vitamins") or metal ions (aka "minerals") in order to be functional.

Variation + Natural Selection = Adaptation

Magnesium ion (green) associated with rubisco's active site.

A manganese ion (dark green) is visible in the topoisomerase active site.

1. Temperature 2. pH

3. Concentration (enzyme, substrate, cofactors)

Make Sure You Can:

Explain how enzymes function as catalysts.

Explain the induced fit model of enzyme function.

Provide examples of enzyme-catalyzed reactions in biological systems.

Explain the relationship between enzyme structure and function.

Explain the major modes of regulation of enzyme activity.