HL Biology (Interaction & Independence)

Proteins, Enzymes, Cellular Respiration, Photosynthesis

Structure & Function of Non-Polar R-Groups

1. No charge

2. Hydrophobic

They are clusters in the protein’s core to avoid water, becoming a magnet that collapses all other hydrophobic parts. This makes the 3D structure neat and stable (conformation). These are mostly globular proteins, and dissolve well in water because all the hydrophilic parts are left on the exterior.

Structure & Function of Polar R-Groups

1. More electronegative (pull all negative things to one side, making that side slightly negative and the other slightly positive)

2. Form H-Bonds with other polar things (ex. water)

3. Typically on protein’s surface

Function of enzymes

1. Grab target molecule (substrate) and hold onto it so bonds can either break or form

2. Release the finished product once it forms

3. Have active sites for substrates to bind (small pocket specified to a certain substrate)

Bonds in Quaternary Structure

1. Hydrogen bonds (weak bond between R-Groups)

2. Ionic Bonds (attraction between positive and negative)

3. Hydrophobic Interactions (non-polar R-groups crowding together on the inside of the protein)

4. Disulfide bridges (strong/permanent covalent bonds between sulfur-containing amino acids)

Conjugated Quaternary Structure

Have one or more non-protein part that gives it an extra ability that just amino acids don’t have

Non-Conjugated Quaternary Structure

Only made of amino acids and handle most of the essential roles in the human body (ex. structural support, enzymes/catalysts, transport, regulation)

Fibrous Proteins + Example

They have a long and repetitive thread-like structure and provide strength and stability in cells/tissues. They are insoluble due to lots of hydrophobic amino acids, but are very stable, making them resistant to temperature and pH changes.

ex. Collagen (make of 3 polypeptide chains wound together in quaternary structure, becoming a ‘rope’ that can form longer fibres, it’s rigid with tensile strength and resists stretching)

Globular Proteins + Example

They are compact, spherical, and have precise recognition sites. Roles for these are diverse (ex. enzymes, transport), and they are soluble in water due to the hydrophilic amino acids on their exterior and the hydrophobic ones in the interior. They have an irregular sequence and low stability, making them sensitive to denaturation in severe temperature/pH changes.

ex. Insulin (2 polypeptide chains linked by disulfide bonds, stable enough to circulate in the bloodstream and interact with target cells)

Enzymes are effective in ____ amounts

Small

Enzymes are ____ after a reaction

Unchanged

How cells regulate their metabolic pathways

By changing their conditions to choose which enzymes are produced

Molecules invovled in metabolism

Metabolites

Where do metabolites come from?

1. Made inside organisms

2. Brought in from environment (food, water, CO₂, O₂)

Define random collisions

When metabolites (ex. sucrose and water) collide at the wrong angle/speed, causing them to bounce off each other rather than form a product (ex. glucose)

Define enzyme specifity

Each enzyme is specific to a substrate, this is a way of controlling metabolic processes. Enzymes are classified by the type of reaction they catalyse, and are named according to the substrates/reactants they act on. Metabolism has linear sequences and cycles.

Two types of enzyme reactions

1. Anabolic

2. Catabolic

Anabolic reactions + examples

1. Deal with growth and repair

2. Consume more energy than they release (energonic)

3. Form macromolecules from monomers

4. Condensation reactions

ex. protein synthesis, DNA replication, photosynthesis

Catabolic reaction + examples

1. Provide energy for the cell

2. Release more energy than they consume (exergonic)

3. Break down large molecules to small/simple ones

4. Hydrolysis reactions

ex. Digestion, cellular respiration, lipolysis

Metabolism is made up of

Anabolic reactions and catabolic reactions

Enzyme-Substrate Complex

Forms when enzyme and substrate bind together

Active Site

Small ‘pocket’ in enzyme, shaped like the substrate. This is where the substrate binds to it.

Lock & Key Model

The substrate is perfectly fit for the active site’s rigid shape, they click together like lego pieces

Induced Fit Model (Hand in glove)

Substrate and enzyme both change shape slightly as they bind together, which is essential for raising the substrate to its high-energy transition state (so it can react). Some amino acids match certain groupings on the substrate, allowing it to bind. But other amino acids at the site cause the catalytic reaction mechanism. Different enzymes have different aa arrangements at the active sites, so each one catalyses a specific reaction or a few closely related ones.

Kinetic energy creates

Greater chance of collisions (between enzymes and substrates)

EIM

Enzymes embedded in/on cell membrane, because it’s a porous structure

Advantages of EIM

1. Often more stable and better for enzyme activity

2. Recycles the enzyme and strengthens its properties (stability/viability)

3. Product is enzyme-free

Types of Enzyme Immobolization

1. Entrapment

2. Absorption

3. Covalent bonding

4. Cross-linking

5. Affinity

What causes denaturation in enzymes

The breaking of weak intramolecular bonds/interactions in the globular protein, changing the 3D shape and the active site (AS) structure. Peptide bonds are no longer hydrolyzed/broken.

Factors affecting rate of enzyme activity

1. Temperature

2. pH

3. Substrate concentration

How does temperature affect the rate of enzyme activity

As temperature increases, so does the kinetic energy of the molecules. This causes them to move faster, leading to more frequent collisions and reactions. Eventually, the heat is too high for the proteins to withstand, and they begin to denature, leaving less active enzymes behind until the rate finally drops to 0. All enzymes have a preferred/optimum temperature where the rate of activity is highest.

Note for DBQ: hydrolization of starch by amylase makes maltose, in iodine solution starch is blue/black and maltose yellow/brown

How does pH affect the rate of enzyme activity

Enzymes have a limited pH range where they can function efficiently. Protein (and AS) structure are maintained by bonds and weak intermolecular forces. pH changes the pattern of these bonds, but the effects of this on the AS are reversible as long as they’re not too extreme (temperature ones aren’t). The highest point in a graph for this is its optimum range/value.

How does substrate concentration affect the rate of enzyme activity

Effect can be shown with catalase, which breaks down H₂O_2. The rate of the substrate disappearing and the product appearing can both be measured, but only the initial rate is measured because the concentration quickly decreases. At lower concentrations, rate increases with the concentration because there are less substrate molecules so they all quickly find an enzyme and lots are leftover. If there’s more substrate available, there’s more frequent collisions. Eventually there will be more substrates than enzymes, and some substrates will have to ‘wait in line’. At this point, the rate will no longer increase and the graph will flatten out.