Proteins

Fall Biology

Table of contents

Amino Acids and Their Polymerization
What Do Proteins Look Like?
Folding and Function
1. Normal Folding is Crucial to Function
2. Protein Shape is Flexible
  1. Protein Folding is Often Regulated
  2. Folding Can Be Infectious
Protein Functions Are as Diverse as Protein Structures
1. Why Are Enzymes Good Catalysts?
  1. Lock and Key Model
2. Did Life Arise from a Self-Replicating Enzyme?
Protein Structure
Protein Functions and Types

Amino Acids and Their Polymerization

Modern cells produce tens of thousands of distinct proteins.
Most molecules are composed of just 20 different building bocks: amino acids.
- Share a common structure.

The Structure of Amino Acids

Carbon atoms have a valence of four.
- They can form up to 4 covalent bonds.
In all 20 amino acids, a central carbon atom bonds covalently to 4 different groups of atoms:
- H - hydrogen atom.
- NH2 - amino functional group.
- COOH - carboxyl functional group.
- R-group ('side chain').
Combination of amino and carboxyl groups is key to how these molecules behave.
- In water (pH=7), amino acids ionize.
  - Concentration of protons at this pH causes amino group to act as a base.
  - Attracts proton.
- Carboxyl group acts as an acid.
  - Highly electronegative oxygen atoms pull electron away from hydrogen atom.
  - It is easy for this group to lose a proton.
- The charges on these functional groups:
  - Keep amino acids in solution, where they can interact with each other.
  - Affect amino acid’s chemical reactivity.

The Nature of Side Chains

R-group or side chain represents part of amino acid core structure that makes each of the 20 amino acids unique.
- R-grops vary from single hydrogen atom to large structures.
Properties of amino acids vary because R-groups vary.

Functional Groups Affect Reactivity

Several of side chains in amino acids contain carboxyl, sulfhydryl, hydroxyl, or amino functional groups.
- Functional groups can participate in chemical reactions.
Example: amino acids with sulfhydryl group (-SH) in their side chains can form disulfide (S-S) bonds that help link different parts of large proteins.
- Bonds form between proteins in hair.
Some amino acids contain side chains with no functional groups.
- Consist of only C and H atoms.
- Rarely participate in chemical reactions.
Influence of amino acids on protein function determined primarily by size and shape rather than reactivity.

Polarity and Charge of R-Groups Affect Solubility

Nature of R-group affects solubility of an amino acid.
- Polar and electrically charged R-groups interact with water and are hydrophilic.
- Nonpolar R-groups lack charged or highly electronegative atoms to form hydrogen bonds withw ater. These are hydrophobic.

Categorizing Amino Acid R-Groups

Amino acid R-groups are divided into three types:
charged, acidic and basic;
uncharged polar;
nonpolar.
Ask these four questions:
1. Does the R-group have a negative charge? If so, it is acidic and has lost a proton.
2. Does the R-group have a positive charge? If so, it is basic and has gained a proton.
3. If the R-group is uncharged, does it have an oxygen atom? If so, the electronegative oxygen will form polar covalent bond in the R-group, making it uncharged polar.
4. If the R-group does not have a charge or an oxygen atom, it is nonpolar.

How Amino Acids Link to Form Proteins

Amino acids polymerize when a bond forms between carboxyl group of one amino acid and amino group of another.
C-N covalent bond that results from condensation reaction is peptide bond.
- Water molecule is removed from condensation reaction, carboxyl group converted to carbonyl functional group (C=O) and amino group becomes N-H.

The Peptide Bond

Peptide bonds are very stable.
Nitrogen can intermitantly donate its pair of unshared valence electrons to carbon in C-N, forming C=N.
- Pair of electrons pushed from the carbonyl (C=0) to the oyxgen atom, forming a single bond with oxygen anion.
Amino acids linked by peptide bonds in a chain are referred to as residues.
- Distinguishes from free amino acid monomers.
Three points to note about the peptide-bonded backbone:
- Regroup orientation. Side chains of each residue extend from the backbone. Makes it easier to interact with each other and water.
- Directionality. An amino group on one end (N-terminus) and a carboxyl group on the other (C-terminus).
- Flexibility. Single bonds on either side of the peptide bond can rotate. Structure as a whole is flexible.

Term	Definition
oligopeptide/peptide	Means ‘few-peptides’. Name for polymers with 50 or less amino acids.
polypeptide	Means ‘many-peptides’. Name for polymers with 50 or more amino acids.
protein	Any chain of amino acid residues. Formal use: ‘protein’ as the complete functional form of a molecule.

Polymerization of Proteins in Early Earth

Process of linking together amino acids required other cellular factors.
If rpoteins were responsible for start of life in chemical evolution, must have occurred without cellular factors.
Can amino acids spontaneously assemble into proteins?
Several mechanisms could have led to self-polymerization:
- Researchers have been able to generate stable polymers by mixing free amino acids with a source of chemical energy & mineral particles. Growing macromolecules are protected from hydrolysis if they cling to a mineral surface.
- Conditions that simulate hot, metal-rich environments of undersea volcanoes, researchers observe amino acids formed and polymerized.
- Amino acids joined into polymers in cooler water if energy rich carbon and sulfar-containing gas is present.

What Do Proteins Look Like?

Structure gives rise to function.
- Protein size and shape variability means there is a wide diversity in function.

Primary Structure

Each protein has a unique sequence of amino acids.
Unique sequence of amino acids in protein is primary structure.
20 types of amino acids and tens of thousands of amino acid residues, number of primary structures that are possible almost limitless.
R-groups represent size, shape, chemical reactivity, and solubility.

Secondary Structure

Generated by interactions between functional groups and peptide-bonded backbone.
Distinctively shaped sections of lienar sequence stabilized by hydrogen bonding that occurs between oxygen and carbonyl group of one amino acid and hydrogen on amino group of another.
Hydrogen bonding between sections of the backbone is possible only when polypeptide bends in a way that brings C=O and N-H groups close together.
- Polar groups are aligned when backbone forms:
- alpha-helix; polypeptide’s backbone is coiled.
- beta-pleated sheet; segments of the peptide chain bend 180 degrees and fold in the same plane.
Formation due to specific geometry of side chains.
Each hydrogen bond is weak compared to a covalent bond, but in large numbers it can make polypeptides very stable.

Tertiary Structure

Distinctive overall three-dimensional shape is its tertiary structure.
Results from interactions between residues brought together as the backbone bends and folds in space.
Residues interact with one another and fold in space.

Five Important R-Group Interactions

Hydrogen Bonding. Hydrogen bonds form polar side chains and opposite partial charges either on the peptide backbone or other R-groups.
Hydrophobic Interactions. In an aqueous solution, water molecules interact with the hydrophillic polar side chains, forcing hydrophobic polar side chains to group in the middle.
van der Waals Interactions. Once nonpolar side chains are close to each other via hydrophobic interactions, they are stabilized by van der Waals interactions.
Covalent Bonding. Covalent bonds cna form between sde chains of two cysteines through reactions of sulfhydryl groups. Disulfide bonds referred to as bridges because they create strong links between regions of the same polypeptide.
Ionic Bonding. Ionic bonds form between groups that have full and opposing charges, like ionized acidic and basic side chains.

Quaternary Structure

Some proteins contain multiple polypeptides that interact to form a single functional structure.
Combination of polypeptides gives some proteins quaternary structure.
Cells contain macromolecular machines - complexes of multiple proteins that assemble to carry out a particular function.
- Ribosome contains several nucleic acid molecules as well as >50 proteins.

Important Messages About Structures

Combination of primary, secondary, tertiary, and quarternary levels is responsible for diversity of sizes and shpaes.
Protein folding is directed by the sequence of amino acids present in primary structure.
Most elements of protein structure are the result of folding polypeptide chains.

Summary of Levels of Structures in Tabular Form

Level	Description	Stabilized by
Primary	Sequence of amino acids in a polypeptide	Peptide bonds
Secondary	Formation of alpha-helices and beta-pleated sheets in a polypeptide (dependent on primary structure)	Hydrogen bonding between groups along the peptide-bonded backbone
Tertiary	Overall 3-dimensional shape of polypeptide, based on contribution from secondary structures	Bonds and other interactions between R-groups or between R-groups and a peptide-bonded backbone.
Quaternary	Shape produced by combinations of polypeptides (combinations of tertiary structures)	Bonds and toher interactions between R-groups and between different polypeptides.

Key idea: levels of structure are __hierarchical.__

Folding and Function

Folding is spontaneous in many cases because chemical bonds and interactions that occur release enough energy to overcome a decrease in entropy.
- Folded molecule has less potential energy and is more stable than the unfolded molecule.

Normal Folding is Crucial to Function

Ribonuclease can be unfolded or denatured by treating it with compounds that break hydrogen and disulfied bonds.
- Denatured ribonuclease unable to function normally.
- Could no longer degrade nucleic acids.
When chemical denaturing agents removed, nuclease folded spontaneously and functioned normally.
- Primary sequence contained all information necessary for folding, and that it was essential for function.
Cells contain proteins called molecular chaperones.
- These facilitate protein folding.
- Molecular chaperones belong to a family of molecules called heat-shock proteins.
  - Produced in large quantities after cells experience denaturing effects of high tempratures.
Nonpolar side chains of unfolded polypeptides can clmp together and disrumpt normal folding process.
- Molecular chaperones attach to hydrophobic patches before aggregates can form.

Protein Shape is Flexible

Although each protein has a characteristic folded shape necessary for function, must proteins are flexible and dynamic when they are not actively performing that function.
Over half of proteins have disordered regions lacking apparent structure.
- Each protein will exist in several shapes until they need to adopt a single folded and functional form.

Protein Folding is Often Regulated

Function of a protein is dependent on its shape.
Controlling when or where it is folded regulates its activity.
Interactions induce proteins to fold into an ordered, active conformation.
Regulated folding plays a major role in controlling and coordinating cellular activities.

Folding Can Be Infectious

Certain normal proteins can be induced to fold into infectious, disease-causing agents.
Proteins: prions, or prteinaceous infectious particles.
Infectious prions: alternately folded forms of normal proteins present in healthy individuals.
- Versions of a protein have the same primary structure but have different shapes.

Protein Functions Are as Diverse as Protein Structures

Proteins perform more types of cell functions than any other molecule.
Proteins are crucial to most tasks for cells and organisms:
- Catalysis. Many proteins are specialized to catalyze, or speed up, chemical reactions. A protein that functions as a catalyst is an enzyme.
- Structure. Structural proteins make up body components.
- Movement. Motor proteins and contractile proteins are responsible for moving the cell itself.
- Signaling. Proteins involved in carrying and recieving signals from cell to cell inside the body.
- Transport. Proteins allow particular molecules to enter and exit cells or carry them throughout the body.
- Defense. Proteins called antibodies attack and destroy viruses and bacteria.
Catalysis may be the most important function. Speed. Life consists of chemical reactions.
- Doesn’t occur fast enough unless a catalyst is present.

Why Are Enzymes Good Catalysts?

Catalyzed reactions involve one or more reactants: substrates.
Enzymes are effective catalysts because they hold substrates in a precise orientation to react.

Lock and Key Model

Hypothesis by Emil Fischer in 1894.
Enzymes are analogous to the lock; keys are substrates that fit into the lock and react.
Location where substrates bind and react is the enzyme’s active site.
No other class of macromolecules can match proteins for catalytic potential.

Did Life Arise from a Self-Replicating Enzyme?

Could be argued that a protein catalyst was the first molecule capable of replication.
Amino acids were likely abundant during chemical evolution.
- Could have polymerized to form small proteins.
Most researchers are skeptical that life could have begun with a protein.
- Proteins would need to possess information, replicate, and evolve to achieve attributes of life.
- Information carried in proteins is necessary for function but cannot be used as a template or mold for replication.

Protein Structure

Most proteins are folded into a complex, globular shape.
Each protein consists of one or more chains of amino acid minomers.
- Linked by peptide bonds.
- Protein polymer often known as polypeptides.
Proteins are very complex, so described in 4 layers of structure.

Primary Structure

Each protein has a unique primary structure.
- Number and sequence of amino acids, making up the polypeptide chain.
- 20 amino acids are used to build proteins.
- Various amino acids could be linked in almost any sequence.
Structure of a single amino acid:
- Same backbone: amino group, C, H, carboxyl group
- R group that projects out from the backbone unique.
  - This makes each of the 20 amino acids unique.
  - Affects folding of the protein.

Secondary Structure

Parts of the polypeptide chain are folded or coiled.
Examples:
- Alpha helix - chain twists forms a helix.
- Beta pleated - chain folds back on itself, or two regions lie parallel.
Results from hydrogen bonding between atoms of the polypeptide backbone.
- O and N along the backbone are highly electronegativity.
- Bound to H; are attracted to each other at regular intervals.
- Part of the protein twists on itself.

Tertiary Structure

Superimposed on primary and secondary structure: irregular loops and folds that give the protein its 3d shape.
Results from interactions along R groups.
- Basic & Acidic groups ionize.
  - Can form ionic bonds.
- Hydrophilic or polar R-groups may hydrogen bond with each other or turn outwards and bond with surrounding water.
- Hydrophobic or nonpolar R groups cluster on the inside of the protein, away from water.
- Furhter stabalized by sulfur-containing strong covalent bonds.

Quaternary Structure

Some proteins are made up multiple polypeptide chains.
Results from combination of two or more polypeptide subunites.
Stabilized by same interactions that stabalize tertiary structure.
For example: hemoglobin (oxygen carrying protein of blood)
- 2 Alpha chains
- 2 Beta chains

Protein Functions and Types

Proteins are the most complicated molecules known.
A cell contains thousands of types of proteins.
- These carry out different functions.
Each protein’s function is determined by its 3-dimensional structure.
- Function depends on shape and changes in shape.

Structural Proteins

Anchor cell parts
Serve as tracks along which cell parts can move
Bind cells together to form muscles, ligaments, etc.
Examples:
- Major Ampullate Spidroin Protein makes the black widow spider web.
- Collagen strengthens bones, cartilage, tendons, ligaments, and skin.

Signal Proteins

Hormonal proteins that coordinate an organism’s activity by acting as a signal between cells.
Insulin signals an animal’s cells to take in sugar.
Hormone receptor is also a protein.
Signal molecules bond with receptor proteins to deliver messages.
Some signal molecules are also proteins.
Examples
- Adrenergic receptor activated by non-protein hormone (adrenaline) in times of stress. Signals heart cells to beat faster and liver cells to release glucose.
- Insulin released into blood stream after meal. Activates insular receptor, which signals muscle and fat cells to store blood sugar.

Transport Proteins

Carry molecules from place to place.
Allows certain solute molecules to enter the cell.
Examples:
Cytochrome C proteins form one protein complex to another, generating energy to power the cell.
- Hemoglobin is the transport protein that carries oxygen in the blood.

Sensory Proteins

Detect environmental signals like light.
Respond by emitting signals to call for a response.
Examples:
- TRPA1 Protein in rattlesnake’s pit organ senses body heat.
- Cryptochrome proteins in monarch butterflies sense Earth’s magnetic field.

Enzyme Proteins

A protein that changes the rate of a chemical reaction without itself being changed into a different molecule in the process.
Control and regulate all chemical reactions.
Build and break down molecules.
Critical for growth, digestion, and other processes.
- Without enzymes, chemical reactions would happen to slowly to sustain life.
Examples:
- Lactase helps infants digest lactose.
- Luciferase makes fireflies grow and controls a chemical reaction that gives off light.
- DNA polymerase builds DNA molecules. Reads old DNA strand and inserts correct nucleotides into the new strand.

Storage Proteins

Stockpile materials used to make other proteins. Store nutrient and energy-rich molecules for later use.
Examples:
- Main substance in egg white (Ovalbumin) serves as a storage protein for developing chicken embryos.
- Glucose is a storage protein in seeds of wheat, barley, and rye.

Contractile (Motor) Proteins

Move parts of a cell.
Proteins working together in muscle groups can move an entire animal.
Examples:
- To contract muscle cells, millions of myosin motors slide along chains of actin proteins.

Gene Regulatory Proteins

Bind to DNA in particular locations and control whether certain genes will be read.
Allows cells to be specialized to certain functions.
Examples:
- p53 protein prevents cell from dividing when DNA is damaged.
- Androgen and estrogen receptors control genes that trigger puberty.

Defensive Proteins

Defensive proteins help organisms fight infection, heal damaged tissue, and evade predators.
Examples:
- Antibodies bind to invaders like viruses and mark foreign objects for destruction.
- Fibrin proteins form blood clots and scabs at the wound site. Plugs a wound and stops bleeding.