Proteins and Enzymes IB Bio HL

What are the parts of an amino acid?

Amino Group, Carboxyl Group,

R Group (changes)

How many amino acids are there?

20 (9 are essential)

Chemical diversity in R groups

R groups can be...

- positive or negatively charged

- acidic or basic

- polar or non-polar

What does it mean if an amino acid is "essential"?

Essential: they cannot be synthesized and must be obtained from food

Non-essential: can be made from other amino acids

How are amino acid chains created?

Condensation Reaction (water OUT to combine) which forms a peptide bond

Where do amino acids connect to form dipeptides?

the amine group of one amino acid connects to the carboxyl group of another

Why is there an infinite combination peptide chains?

- proteins can be ANY length of amino acids

-20 amino acids

Denaturation

changing of a protein's 3D shape (irreversible)

What temperatures are animal proteins stable at (unstable = denaturation)?

animal proteins are stable at body temperatures

What temperatures are plant proteins stable at (unstable = denaturation)?

plant proteins are stable at air temperatures

How does HEAT cause denaturation?

vibrations within the molecule breaks intermolecular bonds or interactions

How do EXTREMES OF pH cause denaturation?

disrupts ionic bonds in proteins

How does COLD cause denaturation?

It doesn't.

Cold does not denature proteins.

Primary Structure

Sequence of amino acids (like a beaded bracelet) produced as result of gene sequence

Secondary Structure

Amine and Carbonyl groups will interact to form Hydrogen bonds

two types:

- 𝞪- helix will form a spiral structure

- 𝜷-pleated sheets form

Tertiary Structure

3 dimensional folding as a result of side chain interactions

R group chemistry will matter!

What are examples of side chain interactions (tertiary structure)?

- hydrogen bonds

- ionic bonds

- hydrophobic interactions

- disulfide bridge

Cysteine in Tertiary Structure

cysteine = amino acid w/sulfur

disulfide bridges (side chain interaction) are critical to lots of tertiary structure

Hydrophobic Amino Acids in Globular Proteins are...

clustered in the middle

Hydrophobic Amino Acids in Integral Membrane Proteins are...

closest to the lipids

Quaternary structure of proteins

multiple polypeptide chains bonded together

Conjugated Proteins...

have another molecule in their quaternary structure

ex: hemoglobin (has iron!)

Non-Conjugated Proteins...

are purely protein in their quaternary structure

exs: insulin and collagen

Collagen (Shape and Function)

Shape: long and fibrous

Function: forms fibers that run through tissues (it makes your bones strong and skin "tight")

Actin and Myosin (Shape and Function)

Shape: long and fibrous

Function: form cellular cytoskeleton and muscle fibers

Insulin (Shape and Function)

Shape: globular

Function: when insulin binds to the receptor on the membrane, the glucose channel opens (allows glucose to leave blood and enter cells)

Enzyme (Shape and Function)

Shape: globular with a specific 3D shape that can bind other molecules at a specific active site

Function: they can change shape to catalyze reactions

Fibrous vs Globular Proteins

SHAPE

Fibrous: long and narrow

Globular: rounded/spherical

Fibrous vs Globular Proteins

ROLE

Fibrous: structural (strength and support)

Globular: functional (active in cell membrane)

Fibrous vs Globular Proteins

SOLUBILITY (generally)

Fibrous: insoluble in water

Globular: soluble in water

Fibrous vs Globular Proteins

SEQUENCE

Fibrous: repetitive amino acid sequence

Globular: irregular amino acid sequence

Fibrous vs Globular Proteins

STABILITY

Fibrous: LESS sensitive to changes in heat and pH

Globular: MORE sensitive to changes in heat and pH

Fibrous Protein EXAMPLES

collagen, keratin, elastin, actin, myosin

Globular Protein EXAMPLES

insulin, immunoglobin, catalase (enzymes end in -ase!)

Usage of Proteins

- catalysis (enzymes catalyze reactions)

- muscle contraction

- cytoskeletons

- tensile strengthening

- blood clotting

- transport (of nutrients and gas)

- membrane transport

- hormones

- receptors

- packing of dna (histone)

- immunity (antibodies) most diverse group

Active Site

region on enzyme where substrate binds

Activation Energy

energy needed to initiate a chemical reaction

Activation Energy GRAPH shows...

the activation energy needed to do the reaction with and without an enzyme

HOW do enzymes lower the activation energy of a reaction?

In the active site, substrates can chemically change.

- A substrate binding to an enzyme stresses certain bonds, making them less stable (unstable bonds are easier to break)

Enzymes changes bonds and lowers energy needed to make the product

Lock and Key Enzyme Model

substrates must fit enzymes EXACTLY

Induced Fit Enzyme Model

enzyme changes shape to fit substrate during binding

Brownian Motion and it's Connection to Enzymes

all particles move randomly!

in order for enzymes to work, they must collide with their substrates in exactly the right position

Immobilized Enzymes

enzymes fixed in place for reuse and stability

Example of Immobilized Enzymes

Lactose-Free Milk

How is Lactose-Free Milk made?

Milk is filtered through lactase in alginate beads ("locks" the enzyme in)

Effect: the lactose is split into glucose and galactose

Factors Affecting the Rate of Enzyme Activity

- temperature

- pH

- substrate concentration

Temperature x Enzyme Activity Graph

as heat increase, collisions increase

pH x Enzyme Activity Graph

enzymes each have an ideal pH

exs:

- pepsin (in stomach) with an ideal pH of 2

- salivary amylase (in mouth) with an ideal pH of 7.2

Substrate Concentration x Enzyme Activity Graph

as substrate concentration increases, rate of reaction will increase until Vmax

Substrate Concentration

amount of substrate available for enzyme reactions

What is "Vmax"?

maximum rate of reaction (the point where every enzyme is working)

Glycolysis

Intracellular

linear pathway for glucose breakdown

Krebs Cycle

Intracellular

cyclic pathway for energy production

Calvin Cycle

Intracellular

cyclic pathway for carbon fixation (plants photosynthesizing)

Digestion

Extracellular: uses enzymes outside the cell in the lumen (space) of the digestive tract

What enzymes does digestion use to break down CARBS?

amylase, maltase, lactase

What enzyme does digestion use to break down FATS?

lipase (think lipids)

What enzyme does digestion use to break down PROTEINS?

pepsin, trypsin, peptidase

Heat Generation

metabolic reactions produce heat due to inefficiency

Why is heat generation important sometimes?

some animals depend on heat generated from metabolic reactions to maintain body temperature

Allosteric Site

site on enzyme where non-substrate molecules bind

Non-Competitive Inhibition

inhibitor binds away from active site (on allosteric site), which prevents the enzyme from working (catalysis)

Antabuse

Drug that treat alcoholism by non-competitive inhibition

Impact: acetaldehyde builds up and causes extreme symptoms

Competitive Inhibition

inhibitor competes with substrate for active site

Statins

Drugs that inhibit cholesterol synthesis by competitive inhibition

Feedback Inhibition

end product inhibits an earlier enzyme in the pathway

Mechanism-Based Inhibition

irreversible binding of inhibitor (alters active site)