Enzymes + Protiens [B]

Grawr~
Here's what I've gotten down for the subject so far.
Feel free to use this if you've lost your notes!

As always, the word doc is much, much better formatted. ;A;


Biochemistry
VII: Proteins
• Polymers of amino acids
Each has a unique 3D shape, and varies in sequence of amino acids.
Functions:
Transport protein—hemoglobin contains iron and carries oxygen from lungs throughout the body
Structural proteins—collagen is in connective tissues (skin, bone, cartilage), it’s also present in spider silk
Hormonal proteins—insulin regulates concentration of sugar in blood. Extra note: Hormones are involved in coordination of activities. Not to be confused with steroids, which are made from fat.
Defensive proteins—immunoglobulin are antibodies that combat bacteria and viruses
Enzymatic proteins—amylase aids in the hydrolysis of starches in mouth and intestine. Extra note: enzymatic proteins speed up chemical reactions in the body.
VII: Amino Acids
There are 20 amino acids
Review: Amino acid is made of NH2, COOH, carbon, and an additional R group
There are four types of amino acids
Nonpolar: 8 of the 20 essential amino acids are nonpolar. Nonpolar amino acids are hydrophobic, thus, will cluster towards the inside of the protein
Polar: 12 of 20 acids are polar. These amino acids are hydrophilic, and will cluster towards the outside of the protein.
• Polar Charged Acidic
o Negatively charged
o Donates an H+ to the solution
o Water soluble
• Polar Charged Basic
o Positively charged
o Receives H+ from solution
o Water soluble
When trying to differentiate between the two, it’s helpful to look at the R group, and see if any atom is missing a bond, or if there are too many atoms for a particular molecule
VII: Protein Conformation
There are layers to these.
• Primary Structure
o Decides shape of all other levels
 This is because subsequent layers are all due to interactions of the R groups in the primary structure
o Is a sequence of amino acids held together by peptide bonds
o Determined by DNA
• Secondary Structure
o ‘Local’ coiling of the primary chain
o Coils are held together with hydrogen bonds between the polypeptide backbone, NOT between R groups
 Basically, the amino acids are not bonded so that the chain coils, it’s the structure on the outside that’s bonded
o Two types of structures
 Alpha helix
• Hydrophilic
• Coiled up like a spiral (think of DNA)
• Found in hair, wool, feathers
 Beta pleated sheets
• Hydrophobic
• Appears ‘folded’ like a paper fan
• 2 parts of polypeptides lie parallel
• Found in silk
• Tertiary Structure
o Structure determined by interactions between R groups which cases the chain to fold
o Hydrophobic groups will be found towards the middle
o Hydrophilic groups will be found towards the outside
o Mechanisms that hold the structure together:
 Disulfide bridges
 Hydrogen bonds between R groups
 Interactions between ions forming ionic bonds
• Quaternary Structure
o Doesn’t always happen
o These are many polypeptide chains grouped together
o Held together by same mechanisms that hold the tertiary structure together
o Other things can be incorporated, ex: hemoglobin


Types of proteins
1. Fibrous
a. Made by many polypeptide chains in a long narrow shape
b. Insoluble
c. For example: collagen and keratin
2. Globular proteins
a. Are more 3D in shape
b. Soluble
c. For example: hemoglobin, insulin
IX: Enzymes
• A protein catalyst
• Changes the rate of a specific chemical reaction without being consumed in the process
• Ex: Speed up a process that would have normally taken years to mere seconds
Activation energy
This is the initial energy needed for a reaction to happen
An enzyme lowers the activation energy, without changing the free energy between reactants and proteins. There are two types
• Endergonic, where the products end up with more energy than the reactants by taking in energy
• Exergonic, where the products have less energy than the reactants because they released energy
Enzyme-Substrate specificity
• Substrate
o Is the specific reactant that an enzyme acts on
o Envision this as the ‘key’
• Active site
o Region on enzyme where substrate binds
o Think of this as the ‘lock’
• The substrate is the item that needs to be changed by the enzyme. The active site is the area on the enzyme that the substrate comes in contact with when it changes
• Induced-fit
o The active site ‘changes’ in fit so that the substrate are brought into positions where their abilities to react are best
o Think of this as a bowling ball. Your fingers have to bend to pick the ball up

Inhibition
• Competitive Inhibition
o An inhibitor settles into the active site, so that the substrate can’t connect with the enzyme
o This is usually reversible, but toxins/poisons may cause damage that’s irreversible
• Non-competitive inhibition
o The inhibitor binds to another part of the enzyme called the ‘allosteric site’
o This causes the enzyme to change shapes, so the substrate won’t fit anymore
• End-product/Feedback inhibition
o In cases where there is a long metabolical pathway, this method prevents the cell from wasting chemical resources
o The product of the last reaction binds using ‘non-competitive inhibition’ to the first enzyme, causing the metabolical pathway to be shut down.

Other factors that affect enzymatic activity:
1. Substrate type
2. Substrate amount
a. Increasing this will increase the rate of product formation
b. Until the point when all enzymes of that type are saturated
3. Temperature and pH
a. As temperature increases, enzymatic activity also increases
b. There is an optimum temp+pH where enzyme activity is at its peak
c. Bell shaped curve of temp+pH vs. enzyme activity with optimum at its apex
Denaturation
Under extreme temperature, pH, or chemical agents, the proteins of the chain become unraveled or scrambled
Enzyme is no longer able to function.
This is sometimes reversible