Lecture 1 - AA & Proteins Flashcards
Need to memorize AA separately
Acidic amino acid mnemonic
Erectile Dysfunction is a NEGATIVE thing to have
E = Glutamic Acid
D = Aspartic Acid
Basic amino acid mnemonic
RHK
R = Arginine
H = Histidine
K = Lysine
Neutral polar amino acid mnemonic
Polar bears are STNQY
S = Serine
T = Threonine
N = Asparagine
Q = Glutamine
Y = Tyrosine
Nonpolar amino acid mnemonic
LIMPVAG For Winner Cock
L = Leucine
I = Isoleucine
M = Methionine
P = Proline
V = Valine
A = Alanine
G = Glycine
F = Phenylalanine
W = Tryptophan
C = Cysteine
Most commonly phosphorylated amino acids mnemonic
Suck Your Toes
S = Serine
Y = Tyrosine
T = Threonine
Peptide Bond Structure and Chemical Features
Structure:
- Rigid
- Planar
- Little freedom of movement
Chemical Features:
- Covalent bond b/t nitrogen of one amino acid and carboxylic acid of adjacent amino acid
- Resonance (causes little freedom of movement)
Covalent forces that stabilize protein structure + function
Structure:
- Covalent peptide bond b/t nitrogen of one amino acid and carboxylic acid of adjacent amino acid
- Disulfide bonds b/t cysteine R group sulfurs
Function:
Enzymes change covalent bonds
Noncovalent forces that stabilize protein structure + function
Structure:
- Hydrogen bonds (b/t neutral groups or b/t peptide bonds)
- Ionic interactions (attraction or repulsion depending on charges)
- Hydrophobic interactions (behavior in aqueous solvent like water)
- van der Waals interactions (any two atoms in close proximity)
Function:
- Protein folding
- Membranes
- Transport
- Substrate binding
Polarity of polypeptides meaning? Direction of protein synthesis?
Proteins are read and synthesized from amino N to carboxyl C terminus
The four levels of protein structure and examples of each covered in class
Primary: Amino acid sequence
Secondary: interactions b/t atoms of the backbone (alpha-helix, beta-pleated sheet)
Tertiary: 3D structure resulting from interactions b/t R groups of the amino acids that make up the protein
Quaternary: Interaction between 2 or more proteins (subunits)
Alpha-helix general structure
- Tightly coiled
- Rod-like arrangement of amino acids
- “Backbone” consists of repeating units of amino group N-C
- R groups radiate OUTWARD
- All/most are “right handed” b/c energetically favored (less steric hindrance)
How are alpha-helices stabilized? What is the “n+4” rule? Which amino acids sit on opposite sides of the helix?
Stabilized by extensive H bonding between the NH and CO groups
“n+4” rule -> 3.6 AA per turn: AA 3-4 residues apart in the linear sequence are spatially close to one another
AA two apart sit on opposite sides of the helix
Alpha-helical supermolecular structures
- 2 or more a-helices can intertwine => “coiled coils”
- Found in keratin (hair), myosin (muscle), and fibrin (blood clots)
a-helix -> two-chained coiled coil -> protofilament -> protofibril
Helix content varies significantly from protein to protein - hemoglobin vs chymotrypsin a-helix content?
Hemoglobin is high is a-helix content
Chymotrypsin lacks a-helix
Beta-pleated sheet general structure
- Extended polypeptide chains
- Adjacent chains can run “parallel” (same direction), “antiparallel” (opposite direction), or “mixed” (strands running parallel and antiparallel)
How are beta-pleated sheets formed?
Hydrogen bonding between NH and CO groups of same/different chains
Definition & importance of protein domains. Discuss related proteins
Protein domain: functional structures formed from folded proteins (ex: catalytic function), typically in 3D/tertiary structure
Families of related proteins share conformational features such as similar domains and sequences (but may differ in substrate specificity), which implies similar/identical functions
What are homeodomains?
DNA-binding domains, conserved b/t species separated by a billion years of evolution
Some of the features governing protein-protein interactions (disulfide bonding, sheets/tubes, binding strength/specificity, proximity of AA binding, antibodies)
- Interchain disulfide bonding is more common than intrachain disulfide bonding (b/t cysteines) n/c extracellular environment is oxidizing
- Some protein subunits can form sheets or tubes through multiple points of contact w/ other subunits (ex: viral capsids)
- Interactions b/t two proteins or another molecule type and a protein involve specific non-covalent interactions that determine the specificity and strength of binding
- AA involved in binding are often far from one another in unfolded protein, but close together in folded state
- Modular approach of antibodies: when antibodies are generated, they assemble different genes together => different constant and variable region genes => light chains + heavy chains that provide specificity
What does the structure of a protein depend on during protein assemblies?
The exact structure depends on orientation of binding sites on each subunit (ex: different binding sites could assemble dimers, helices, or rings)
Another name for assemblies?
Polymer
Some polymeric structures exhibit polarity (not electrical)? If true, give example?
True
Ex: actin microfilaments have a plus and minus end
What type of structure is collagen?
Rigid
What type of structure is elastin?
Elastic
What are covalent modifications of proteins? Most common example?
The covalent attachment of a molecule(s) to proteins that can modify its function
Ex: phosphorylation -> attaching phosphate group covalently to a protein -> activate or deactivate
Kinetic properties of enzymes
- Increase rate of biological reaction w/o altering reaction equilibria
- Decrease activation energy of a reaction
- Accelerate reactions through stabilization of transition states i.e. lower activation energy (Ea)
- The enzyme active site
All chemical reactions can be described in terms of _________.
Equilibrium
What is equilibrium in the context of enzymes and reactions?
The degree to which a reaction will proceed forward to yield a product or backwards to the starting point
What are reaction equilibria linked to? What are reaction rates linked to?
Reaction equilibria are linked to the standard free energy change (ΔG’o)
- Energy states of reactants and products remain unchanged in uncatalyzed vs enzyme-catalyzed reactions
Reaction rates are linked to the activation energy, Ea
-Enzymes increase reaction rate by decreasing Ea
*refer to slide 68 lecture 1
What is the relationship between K’eq and ΔG’o?
Inverse -> As K’eq increases, ΔG’o decreases
Endergonic vs Exergonic reaction: ΔG and reaction progression plots
Endergonic: + ΔG, substrate energy < product energy
Exergonic: -ΔG, substrate energy > product energy
Is it better to have an enzyme complementary to substrate or an enzyme complementary to transition state? Explain
It is better to have an enzyme complementary to transition state. Otherwise, the enzyme-substrate complex would be more stable (has less free energy versus substrate alone), which results in an increased activation energy
*refer to slide 70 lecture 1
Features of the enzyme active/catalytic site?
- The catalytic site is relatively small and recessed compared with the rest of the enzyme to increase substrate specificity
- Enzyme may also be big because of regulation and the presence of regulatory sites (allosteric effects, covalent modification, etc.)
- The catalytic site is a three-dimensional entity
- Substrates are bound to enzymes by multiple weak, non-covalent interactions (electrostatic bonds, hydrogen bonds, van der Waals forces, hydrophobic interactions)
Catalytic sites form clefts or crevices - elaborate
- Substrate molecules bound within cleft
- Water (unless involved in catalysis) is normally excluded
- Overall nonpolar character of cleft can enhance binding of substrate
- May also contain polar residues which may take on catalytic properties w/in this nonpolar environment (exception to the rule regarding hydrophobic “core” present in many globular proteins)
Michaelis Menten saturation kinetics: what this means, what it says about how enzymes work
- At constant [enzyme], the rate of a reaction increases w/ increasing [S] until a Vmax is achieved => this saturation effect is an important distinction versus uncatalyzed reactions
- Interpretation of enzyme kinetic curve: ES complexes formed until substrate saturation (Vmax) occurs at which point no more substrate binding sites (i.e. enzymes) are available
What are factors affecting enzyme activity? What are we focused on?
Can have transcriptional, translational, posttranscriptional,, and posttranslational control
Posttranslational Regulation: discussed in class
- Allosteric Regulation
- Covalent Modification
- Proteolytic Modification
What is allosteric regulation? Feedback inhibition?
Allosteric Regulation: When a positive/negative modulator binds to allosteric site of an enzyme, the enzyme conformationally change to become more/less active
Feedback Inhibition: When a downstream product acts as a negative modulator, binds the allosteric site, making enzyme less active => way of regulating levels of synthesized endproduct
What is covalent modification?
The covalent attachment of a molecule(s) to proteins that can modify its function
Ex: phosphorylation -> attaching phosphate group covalently to a protein -> activate or deactivate
What is proteolytic modification? Example?
The breakdown of proteins into smaller polypeptides or amino acids through the hydrolysis of peptide bonds by a protease => activating/deactivating
Protease: enzyme that cleaves peptide bonds on other proteins
Ex: Digestive enzymes
