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Bio 209 > Lecture 1 - AA & Proteins > Flashcards

Lecture 1 - AA & Proteins Flashcards

Need to memorize AA separately

1
Q

Acidic amino acid mnemonic

A

Erectile Dysfunction is a NEGATIVE thing to have

E = Glutamic Acid
D = Aspartic Acid

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2
Q

Basic amino acid mnemonic

A

RHK

R = Arginine
H = Histidine
K = Lysine

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3
Q

Neutral polar amino acid mnemonic

A

Polar bears are STNQY

S = Serine
T = Threonine
N = Asparagine
Q = Glutamine
Y = Tyrosine

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4
Q

Nonpolar amino acid mnemonic

A

LIMPVAG For Winner Cock

L = Leucine
I = Isoleucine
M = Methionine
P = Proline
V = Valine
A = Alanine
G = Glycine

F = Phenylalanine

W = Tryptophan

C = Cysteine

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5
Q

Most commonly phosphorylated amino acids mnemonic

A

Suck Your Toes

S = Serine
Y = Tyrosine
T = Threonine

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6
Q

Peptide Bond Structure and Chemical Features

A

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)

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7
Q

Covalent forces that stabilize protein structure + function

A

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

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8
Q

Noncovalent forces that stabilize protein structure + function

A

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

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9
Q

Polarity of polypeptides meaning? Direction of protein synthesis?

A

Proteins are read and synthesized from amino N to carboxyl C terminus

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10
Q

The four levels of protein structure and examples of each covered in class

A

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)

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11
Q

Alpha-helix general structure

A
  • 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)
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12
Q

How are alpha-helices stabilized? What is the “n+4” rule? Which amino acids sit on opposite sides of the helix?

A

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

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13
Q

Alpha-helical supermolecular structures

A
  • 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

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14
Q

Helix content varies significantly from protein to protein - hemoglobin vs chymotrypsin a-helix content?

A

Hemoglobin is high is a-helix content
Chymotrypsin lacks a-helix

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15
Q

Beta-pleated sheet general structure

A
  • Extended polypeptide chains
  • Adjacent chains can run “parallel” (same direction), “antiparallel” (opposite direction), or “mixed” (strands running parallel and antiparallel)
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16
Q

How are beta-pleated sheets formed?

A

Hydrogen bonding between NH and CO groups of same/different chains

17
Q

Definition & importance of protein domains. Discuss related proteins

A

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

18
Q

What are homeodomains?

A

DNA-binding domains, conserved b/t species separated by a billion years of evolution

19
Q

Some of the features governing protein-protein interactions (disulfide bonding, sheets/tubes, binding strength/specificity, proximity of AA binding, antibodies)

A
  • 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
20
Q

What does the structure of a protein depend on during protein assemblies?

A

The exact structure depends on orientation of binding sites on each subunit (ex: different binding sites could assemble dimers, helices, or rings)

21
Q

Another name for assemblies?

A

Polymer

22
Q

Some polymeric structures exhibit polarity (not electrical)? If true, give example?

A

True

Ex: actin microfilaments have a plus and minus end

23
Q

What type of structure is collagen?

A

Rigid

24
Q

What type of structure is elastin?

A

Elastic

25
Q

What are covalent modifications of proteins? Most common example?

A

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

26
Q

Kinetic properties of enzymes

A
  • 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
27
Q

All chemical reactions can be described in terms of _________.

A

Equilibrium

28
Q

What is equilibrium in the context of enzymes and reactions?

A

The degree to which a reaction will proceed forward to yield a product or backwards to the starting point

29
Q

What are reaction equilibria linked to? What are reaction rates linked to?

A

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

30
Q

What is the relationship between K’eq and ΔG’o?

A

Inverse -> As K’eq increases, ΔG’o decreases

31
Q

Endergonic vs Exergonic reaction: ΔG and reaction progression plots

A

Endergonic: + ΔG, substrate energy < product energy

Exergonic: -ΔG, substrate energy > product energy

32
Q

Is it better to have an enzyme complementary to substrate or an enzyme complementary to transition state? Explain

A

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

33
Q

Features of the enzyme active/catalytic site?

A
  • 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)
34
Q

Catalytic sites form clefts or crevices - elaborate

A
  • 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)
35
Q

Michaelis Menten saturation kinetics: what this means, what it says about how enzymes work

A
  • 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
36
Q

What are factors affecting enzyme activity? What are we focused on?

A

Can have transcriptional, translational, posttranscriptional,, and posttranslational control

Posttranslational Regulation: discussed in class

  • Allosteric Regulation
  • Covalent Modification
  • Proteolytic Modification
37
Q

What is allosteric regulation? Feedback inhibition?

A

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

38
Q

What is covalent modification?

A

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

39
Q

What is proteolytic modification? Example?

A

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

Bio 209 (10 decks)

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