Class 1 - Biochemistry I Flashcards
4 Biologically Relevant Macromolecules
- Proteins
- Carbohydrates
- Lipids
- Nucleic Acids
The biologically relevant macromolecules are made from…
Polymers (made from monomers)
Enzymes that make biologically relevant macromolecules/ polymers are called…
polymerases
Reactions that make biologically relevant macromolecules/ polymers are called…
polymerization reactions
Within the polymerization reaction that forms biological polymers are what other reactions?
Dehydration Synthesis
Dehydration Synthesis
Two smaller molecules are fused together to make a bigger molecule while getting rid of water
Opposite of a dehydration synthesis reaction
Hydrolysis
Another name for a dehydration synthesis reaction
Condensation
Protein Monomers
Amino Acids
How many biologically relevant Amino Acids are there?
20
Amino Acid general structure
N-C-C Backbone (Amino Nitrogen - Alpha Carbon - Carbonyl Carbon)
Amine Group (NH2) - can get protonated in acidic solution
Acid Group (COOH) - can get de-protonated in basic solution
Hydrogen Group - Alpha Proton (one proton away from alpha carbon)
R-Group - side chain; changes for each amino acid; determines which amino acid it is
The part of the amino acid that changes and determines which amino acid it is
The R-group side chain (KNOW EACH R-GROUP STRUCTURE)
Mutation Notation
ex. R322K
Means R (Arginine) is the original AA, the number is the position of the amino acid in the protein, and the K (Lysine) is what it mutated into
Making a protein out of amino acids involves what sort of reaction?
Dehydration Synthesis
What is the type of bond that links two amino acids together?
Peptide Bond - an amide bond linking AAs
Normal way that proteins are synthesized?
“N-C” synthesis
The N terminus attacks the C of another AA
Primary Protein Structure
Amino Acid Chain/ Sequence
No folding has been done yet
Characteristic bond = Peptide Bond
Secondary Protein Structure
First level of folding
Characteristic bond = Hydrogen bonding between backbone atoms
Alpha Helix
Beta Pleated Sheet
Two Types of Secondary Structure
- Alpha helix
- Beta Pleated Sheet
Tertiary Structure
Folding is due to side-chain interactions WITHIN a polypeptide
Non-covalent and covalent interactions in tertiary structure (and their subtypes)
What is the lowest level of structure a protein can have to be functional?
Tertiary Structure
Two Main Types of Interactions in Tertiary Structure
- Non-Covalent
- Covalent
The types of Non-Covalent Interactions in Tertiary Structure
***describes the types of R-groups interacting with one another
1. nonpolar/nonpolar aka London Dispersion aka Van der Waal
2. polar neutral/polar neutral aka dipole-dipole
3. acid/base (electrostatic) - involve full charges (strongest interaction)
The types of Covalent Interactions in Tertiary Structure
- Disulfide Bridges
-Stronger than non-covalent
-two cystine groups bond together to give disulphide bridge
Where would you expect a nonpolar r-group to fold in tertiary structure?
Inward, away from the water - hydrophobic
Where would you expect a polar r-group to fold in tertiary structure?
Outward, towards the water - hydrophilic
When do Disulfide Bridges form
Occurs when you have 2 cysteine residues and they interact with one another
Quaternary Protein Structure
Folding is due to side-chain interactions BETWEEN DIFFERENT polypeptides
ex. hemoglobin - different subunits coming together to make the protein functional
Examples of Protein Functions
Assembling DNA
Perform Phosphorylation
Cleavage
Catalyze reactions (enzymes
Transport
Signaling
Surface receptors/signaling
Structural roles
Receptors
Assist in making more proteins
Help with folding (chaperoning)
Hormones
Maintain pH
Antibodies
Channels
Can be broken down for energy
*NOT ALL ENCOMPASSING LIST
Monomer for Carbohydrates
Monosaccharides
Monosaccharide formula
CnH2nOn
n = # of Carbons
These are “simple sugars”
3 common monosaccharides
- Glucose - know glucose structure
- Fructose
- Galactose
All have formula C6H12O6 - they are structural isomers
2 monosaccharides used for DNA and RNA
- Ribose - C5H10O5 (simple sugar)
- Deoxyribose - C5H10O4 (deoxy sugar)
Both are 5-Carbon sugars
2 Monosaccharides fused together produce…
Disaccharides
3 Common Disaccharides
- Maltose
- Sucrose
- Lactose
All structural isomers - C12H22O11
What type of reaction forms disaccharides?
Dehydration Synthesis
What are all of the common disaccharides made of?
Glucose + another monosaccharide
Glucose + Glucose =
Maltose
Glucose + Fructose =
Sucrose
Glucose + Galactose =
Lactose
Formula for disaccharides
Two monosaccharides fused together through dehydration synthesis - take out a water (H2O) molecule
C12H22O11
Multiple monosaccharides make up…
Polysaccharides
3 Common Polysaccharides
All 3 are glucose polymers (many glucoses linked together)
- Glycogen
- Starch
- Cellulose
Just know their function
Glycogen function
glucose energy storage for ANIMALs
Starch function
Glucose energy storage for PLANTs
Cellulose function
Plant cell structure; functional component of cell wall
Functions of polysaccharides overall
ENERGY
Structural roles
Cell surface markers - glycolipids and glycoproteins
Adhesion (in unicellular organisms)
Lipids monomer
Hydrocarbon - a carbon only bound to hydrogens
Fatty acid formation
Adding a carboxylic group (OOH) to the end of a hydrocarbon chain
Saturated Fats
fatty acid only has carbon-carbon single bonds; pack together very well; great IMF interactions;
SOLID at room temp
ex. butter, avocado, peanut butter, animal fats
Unsaturated Fats
Has a carbon-carbon double bond, so some of the hydrogens have to be taken out; need at least one double bond in an unsaturated fat (monounsaturated = one C-C double bond, polyunsaturated = more than one C-C double bond);
Bent molecular structure, minimizing IMF interactions, so they don’t pack as well
usually LIQUID at room temp. because melting point is lowered
ex. Olive oil, most other plant oils
4 Forms of Fatty Acids
- Triglycerides
- Phospholipids
- Terpenes
- Steroids
Triglyceride function and formation
***Storage form of fatty acids/ stored form of energy found in adipose tissue
-Insulation (brown fat in babies)
-Padding for internal organs (visceral fat)
3 Fatty acid groups + binding to glycerol = triglycerides - formed through 3 dehydration synthesis reactions (more specifically called an esterification reaction)
Phospholipids Function and Formation
2 Fatty Acids (nonpolar) AND a Phosphate Group (Polar) + binding to a glycerol = a phospholipids - molecule with polar and non polar regions (amphipathic)
***Form phospholipid bilayer (cell membrane lipid bilayer in the body)
Amphoteric
Can act as an acid or a base
ex. Water, bicarbonate
Amphipathic
Has a polar and nonpolar region
ex. phospholipid bilayer
Terpenes Function and Formation
Built from multiple isoprene (C5H10) units
Fully Non-polar
NOT made from dehydration
synthesis (don’t need to know the specific reaction)
Need at leasts 2 isoprenes to make a terpene, but can be longer
***Precursor to cholesterol (which is the precursor to steroid hormones)
-Wax formation (ear wax, desert plants have wax layer to prevent evaporation)
Vitamin A is a terpenoid (like a terpene)
Terpene Classification
Every 2 isoprenes = 1 Terpene “unit”
ex. 6 isoprenes = triterpene
Steroid Function and Formation
All steroids are made from cholesterol (recognize cholesterol structure and its derivatives) (structure = 3 six-carbon rings and 1 five-carbon ring)
***Main function of cholesterol is precursor to steroids
Found in cell membranes
Used to form bile salts
Gibb’s Free Energy Equation
^G = ^H - T^S
^H - Potential Energy in the reaction
T^S - Kinetic Energy in the reaction
(^) means delta
G = Gibbs free energy
H = Enthalpy or bond energy
T = Temperature
S = Entropy
^G > 0
Non-spontaneous, Endergonic
On a graph, reactants lower than products
^G = 0
Equilibrium
Reaction Coupling
Combining non-spontaneous reactions with spontaneous reactions (in the body) to force non-spontaneous reactions to happen, since we can’t increase temp. in the body to power the reaction; the excess free energy from the spontaneous energy powers the non-spontaneous
ex. Most common reaction in the body to do this is ATP hydrolysis
ATP Hydrolysis Formula
ATP -> ADP + Pi
very exergonic
Drives other non-spontaneous reactions in the body
^G of ATP hydrolysis in the body = -12 kCal/mol (very big number)
***SPONTANEITY DOES NOT MEAN SPEED
-spontaneity just means pushing the reaction to happen
Transition State
In between state of reactants turning into products;
High energy, transient (can’t be isolated)
Must be hit in order for reaction to happen
Energy needed to produce the transition state?
Energy of Activation (Ea)
High Ea tells us the reaction rate is…
Slow (Ea and reaction rate have an inverse relationship)
Low Ea tells us the reaction rate is…
Fast (Ea and reaction rate have an inverse relationship)
How can we make the slope from the reactants to the transition state (Ea) smaller to make the reaction faster?
Catalysts
Catalysts Increase the rate of reactions by
- stabilizing the transition state AND
- reducing the Ea
CANNOT MAKE A REACTION MORE SPONTANEOUS WITH CATALYSTS, ONLY FASTER!
^G does not change
Biological/Physiological Catalysts used in the body
Enzymes
3 Defining Characteristics of Enzymes
- Must increase the rate of the reaction/speed up reaction
- Must not be used up in the reaction
- Must be specific to particular reactions
How do you make a reaction more spontaneous in the body?
Reaction coupling (with heat or ATP hydrolysis)
Enzyme Structure
Active site + Allosteric site
Active Site of Enzyme Function
- Where substrate binds
- Where reaction occurs
How do we turn enzymes “on” to accept substrate?
- Phosphorylation - phosphate group comes in and turns enzyme on
- Allosteric regulation - can use any number of chemicals that can bind into a secondary site on the enzyme called the allosteric site
Negative Feedback
Intermediate or product going back in the reaction and inhibiting an enzyme that came before it
**Most common type of feedback in the body
Positive Feedback
**Rare in the body
Intermediate or product going back in the reaction and stimulating an enzyme that came before it, but it requires an external regulator to turn off production
ex. labor - babies head pushes on cervix, releasing oxytocin to stimulate the baby to push more
- baby = external regulator
Michaelis-Menton Graph
Plots V (the rate of product formation) on the Y-axis vs S (substrate concentration) on the X-axis
MUST assume the enzyme concentration is constant (unless told on the MCAT otherwise)
3 Different Conditions on the Michaelis-Menton Graph
- Conc. of Substrate «_space;Conc. of Enzyme (linear up trend) - enzyme excess
- Conc. of Sub. + Conc. of Enzyme (Curve starts to flare, rate of rise decreases) - rate of product formation slows, but product is formed
- Conc. of Sub.»_space; Conc. of Enzyme (rate of product formation really flattens out; we reach maximum rate of product formation (called Vmax - a constant number)
What is the maximum rate of product formation called?
Max
Vmax is a constant that depends on…
- Enzyme Concentration
- Specific enzyme you are using
Changing these will change Vmax
The concentration of substrate required to reach 1/2 Vmax is…
Km
1/2 Vmax = Km
What kind of relationship is there between the affinity the enzyme has for the substrate and the Km?
Inverse Relationship
High affinity = Low Km
Low Affinity = High Km
4 Kinds of Enzyme Inhibitors
- Competitive Inhibition
- Non-Competitive Inhibition
- Uncompetitive Inhibition
- Mixed Inhibition
Always assume reversibility, unless MCAT says it is covalently bound - this is a permanent inhibitor that permanently disables the enzyme
Competitive Inhibition
Binds at: Active Site
Effect on Vmax: NO CHANGE - enzyme is not changing
Effect on Km: INCREASE, Km shifts to the right
Inhibitor is competing with substrate for the enzyme’s active site
Doesn’t change active site or modify the enzyme itself, but takes up the active site position, so Vmax stays same
Affinity between substrate and enzyme decreases, so we need more substrate to reach 1/2 Vmax, so Km increases
Non-Competitive Inhibition
Binds at: Allosteric Site (Enzyme alone), does NOT change the shape of the active site
Effect on Vmax: DECREASE - Enzyme less effective at making product, less product
Effect on Km: No CHANGE - because the shape of the active site is still the same and binds substrate just as effectively
Makes the enzyme less effective at making product, so Vmax decreases
Active Site shape remains the SAME, so no change in affinity, therefore no change in Km
Graphically, Km same, Vmax lower
Uncompetitive Inhibition
Binds at: Allosteric Site of Enzyme-Substrate complex
Effect on Vmax: Decrease - less effective at making product
Effect on Km: Decrease - affinity increases, so Km decreases
Waits for enzyme and substrate to bind and then jumps into allosteric site and locks ES complex together
*Raises the apparent affinity because it locks ES together
Makes the enzyme less effective at producing product - lower Vmax
Grpahically, Lower Vmax, Km shifts to left
Mixed Inhibition
Binds at: Allosteric Site of the Enzyme alone, and DOES change the shape of the active site OR binds to the ES complex
Effect on Vmax: Decreased - less effective at making product
Effect on Km: If ES complex, Km decreases (identical to uncompetitive); If it finds the E alone and changes the shape of the active site, affinity decreases, so Km increases
^H in Gibbs free energy represents what kind of energy?
Potential Energy
T^S in Gibbs free energy represents what kind of energy?
Kinetic Energy
What is the relationship between Ea and reaction rate?
Inverse!
Graphically, what does ^G represent?
The difference between reactants and products
Lineweaver-Burk Plot
Similar to Michaelis-Mention, but inverted
Lineweaver-Burk Plot Axis
1/v (y-axis) vs. 1/[s] (x-axis)
In a Lineweaver-Burk Plot, y-intercept represents…
1/Vmax
V on Michaelis-Menton Graph
Rate of Product formation
Y-axis
[S] on Michaelis-Menton Graph
Substrate concentration
X-axis
Covalently bound inhibitors
Permanent, non-reversible inhibitor
Enzyme permanently disabled
Lineweaver-Burk Plot
Inverse of Michaelis-Menton
1/V vs 1/[S]
Movements on this plot are reverse of Michaelis-Menton
Plot begins in top right corner of graph
**Be able to tell which kind of inhibition is being show based on the shift in the graph
A way to make finding the Vmax easier without using a calculator
Lineweaver-Burk Ploy y-intercept
1/Vmax
When graph touches y-axis, that is your 1/Vmax
Lineweaver-Burk Ploy x-intercept
-1/Km
When graph touches x-axis, that is your -1/Km
Competitive Inhibition Lineweaver-Burk
Shift to the right
Vmax - no change
Km - increase
1/Vmax same on y-intercept
-1/Km increases and shifts to the right towards the origin
Non-Competitive Inhibition Lineweaver-Burk
Vmax - decreases
Km - no change
1/Vmax increases and shifts up on the y-intercept
-1/Km same on x-intercept as uninhibited
Uncompetitive Inhibition Lineweaver-Burk
Vmax - decrease
Km - decrease
1/Vmax increases and shifts up on y-intercept
-1/Km increases and shifts left on the x-intercept
