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Cell & Mole Bio - HES > Lecture 2 - Proteins and Enzymes > Flashcards

Lecture 2 - Proteins and Enzymes Flashcards

1
Q

Who were awarded the Nobel Prize for elucidating the structure of proteins?

A

Kendrew and Perutz for the crystallization of myoglobin (which is active in the tertiary structure - hemoglobin has a similar structure but is only active in the quaternary structure)

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2
Q

Functional groups to know (7)

A
  1. Hydroxyl is polar
  2. Aldehyde is very reactive
  3. Keto refers to ketone
  4. Carboxyl is acidic
  5. Amino is basic
  6. Phosphate is acidic
  7. Sulfhydryl forms disulfide bridges
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3
Q

Isomers (2)

A
  • same chemical formula, different atom arrangement
  • 3 types:
    1. structural: differ in how atoms join
    2. cis-trans: differ in sides
    3. optical: mirror image; asymmetric carbon
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4
Q

What are the four kinds of molecules characteristic to living things?

A

proteins, carbs, lipids, and nucleic acids

all except lipids are polymers

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5
Q

Macromolecules are polymers of…

Three examples:

A

monomers.

  1. (20) amino acids = protein
  2. sugars, monosaccharides = carbohydrate
  3. nucleotides = nucleic acid
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6
Q

Macromolecules are polymers formed by… and broken down by…

A

formed by: condensation

  • also called dehydration rxn
  • water is released and covalent bond forms between monomers
  • energy is added

broken down by: hydrolysis

  • water reacts with covalent bond to break in monomers
  • covalent bond is broken; H2O splits into H+ and OH-
  • energy is released
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7
Q

Proteins (3)

A
  • made up of (20) amino acids in different proportions and sequences
  • amino acids are covalently bound to form polypeptide chains
  • each chain folds into 3D shape based on amino acid sequence
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8
Q

Amino Acids (3)

A
  • contain an amino group “N-terminus” and a carboxyl group “C-terminus” at the same carbon “alpha carbon”
  • also attached are hydrogen and side chain, also called R-group
  • the alpha carbon is asymmetrical and therefore amino acids exist as optical isomers. D-amino acids (right) and L-amino acids (left)
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9
Q

Amino Acids (2)

A
  • at pH 7, carboxyl and amino groups are ionized.
    • carboxyl loses a hydrogen COOH -> COO- + H+
    • amino gains a hydrogen NH2 + H+ -> NH3+
  • (20) amino acids are grouped by side chains
    • electrically charged (ionized) attract H2O and oppositely charged ions
    • polar (hydrophilic), uncharged attract other polar or charged molecules
    • nonpolar (hydrophobic) attract other nonpolar molecules
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10
Q

Peptide Linkages (4)

A
  • Also called peptide bonds
  • form backbone of a protein
  • formed between carboxyl and amino groups of two different amino acids
  • formed by condensation (release of H2O).
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11
Q

Peptide bond influences…

A

3D shape.

  • C-N linkage is the peptide bond
    • adjacent alpha carbons are not free to rotate freely.
  • Oxygen bound to carbon (C=O) in carboxyl
    • carries a slight negative charge (delta-)
  • Hydrogen bound to nitrogen (N-H) in amino
    • carries a slight positive charge (delta+)
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12
Q

Primary structure (3)

A
  • sequence of amino acids in polypeptide chain
    • held together by peptide bonds
  • backbone is repeating structure of -N-alphaC-C-
  • 3 letter and single letter abbreviations for each amino acid
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13
Q

Secondary structure (2)

A
  • consists of regular, repeated spacial patterns in different regions of a polypeptide chain.
  • two types determined by hydrogen bonding:
    1. alpha helix: right handed coil
    2. beta pleated sheet
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14
Q

Tertiary structure (2)

A
  • definite 3D shape determined by bending and folding
  • interactions occur between different R-groups and between R-groups and environment via strong (covalent) or weak (hydrogen, hydrophobic, ionic) interactions.
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15
Q

3 Molecular representations of a protein:

A
  1. space-filling model
  2. stick model
  3. ribbon model
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16
Q

Quaternary structure (2)

A
  • contains two or more polypeptide chains (subunits) that interact to form larger proteins
  • example is hemoglobin that has four subunits held together by weak interactions.
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17
Q

Denaturation is utilized to…

A

study and characterize proteins.

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18
Q

Chemical denaturation (2)

A
  • Christian Anfinsen, 1961

- showed that proteins spontaneously fold provided that the primary structure remains intact.

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19
Q

Factors that influence function (2)

A
  1. Shape - fit between 3D shapes

2. Chemistry - exposure of R-groups on surface allow interactions

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20
Q

Factors that disrupt weak interactions (4)

A
  1. Temperature change - break hydrogen bonds; disrupt hydrophobic interactions
  2. pH change - change pattern of ionization of exposed carboxyl and amino group
  3. High concentration of polar substances - disrupt hydrogen bonds (ex. Urea)
  4. Nonpolar substances - disrupt hydrophobic interactions (ex. H2, N2, O2 gases)
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21
Q

Proteins change shape by.. (2)

A
  1. interacting with other molecules
    - form weak interactions
    - disrupt protein
  2. undergo covalent modification
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22
Q

Molecular chaperones…

A

help shape proteins.

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23
Q

Proteins are vulnerable (4)

A
  • after synthesis and before folding is complete
  • following denaturation
  • why? before folding (or refolding), protein may present a surface that binds wrong molecules
  • solution: chaperones
24
Q

Molecular Chaperones (2)

A
  • project 3D structure of proteins

- cage-like structure that pulls in a polypeptide, causes it to fold, then releases.

25
Q

Two types of chemical reactions (release or consume energy):

A
  1. Catabolic reaction
    - break down to small molecules
    - release free energy (negative deltaG)
    - exergonic
  2. Anabolic reaction
    - build up to complex molecules
    - consumes free energy (positive deltaG)
    - endergonic
26
Q

Enzyme structure and specificity (3)

A
  • enzymes (catalysts) increase rate of reaction
  • catalysts are proteins
    • however, some are RNA molecules called riboenzymes
  • enzymes provide: framework within which catalysis occurs, binding site for reactant.
27
Q

Energy barrier…

A

controls rate of chemical reaction

28
Q

Activation energy (2)

A
  • the energy input needed to overcome the energy barrier.
  • once the activation energy is reached, transition state occurs (in other words, activation energy is energy needed to change reactants into unstable molecular forms called “transition-state intermediates”.
29
Q

Transition state intermediates (3)

A
  • have higher free energy than either reactants or products.
  • their bonds may be stretched and therefore unstable
  • activation energy added to start the reaction is recovered during ensuing “downhill” phase. It isn’t part of the net free energy change (deltaG)
30
Q

Heat vs. Enzyme: Both can catalyze a reaction but enzymes are used as the main catalysts in the human body. Why?

A

Because temperature is not a factor that can be changed drastically within the human body.

31
Q

Substrate binds at the _____ ____ of an enzyme

A

active site.

32
Q

Enzyme (2)

A
  • contains a specific active site
    • reactants bind based on 3D shape, functional groups present in active site.
    • usually 6-12 amino acids
  • most end in -ase
    • name often reflects function.
    • eg. sucrase enzyme catalyzes hydrolysis of sucrose.
33
Q

Substrate (S)

A
  • in enzyme catalyzed reaction, reactants are called substrates and are typically smaller than enzymes.
  • enzymes and active site changes shape when bound to substrate: this is called an induced fit.
34
Q

Enzyme “rxn”:

A

E + S -> ES complex -> E + P

35
Q

Lower activation energy =

A

faster reaction rate

- enzymes don’t change difference in deltaG between reactants and products.

36
Q

Enzymes orient substrate

A
  • part of activation energy to start reaction is used to bring atoms together
    ex. oxaloacetate (4C) binds first, which induces enzyme conformation changes to allow Acetyl CoA (2C) binding to catalyze formation of citric acid (6C).
37
Q

Enzymes induce physical strain

A
  • once ES has formed, enzyme causes substrate bonds to stretch, causing unstable transition state.
38
Q

Enzymes add chemical group

A
  • temporary addition of chemical group to substrate: R-groups of enzyme’s amino acid participate to make substrate more chemically reactive.
39
Q

Temporary addition of chemical groups to substrates (3)

A
  • acid-base catalysis: acid or base side chains (R-groups) of enzyme transfer H+ to/from substrate
  • covalent catalysis: functional groups in side chain forms temporary covalent bond with substrate
  • Metal ion catalysis: ex. Cu+, Fe+, Mn+ ions lose/gain electrons without detaching from enzyme.
40
Q

Some enzymes require other molecules for function (4)

A

All non-protein chemical “partners”

  1. Prosthetic Group: distinct, atoms/molecules that are permanently bound to enzymes
  2. Inorganic Cofactor: ions, such as copper, zinc, or iron that are permanently bound to enzymes
  3. Coenzyme: carbon-containing and moves from enzyme to enzyme adding or removing chemical groups from substrate.
41
Q

Substrates are NOT _____

A

porteins.

42
Q

The concentration of substrate affects the… (A+2)

A

reaction rate.

  • reaction rate of enzyme-catalyzed reaction initially increases, but then levels off (enzyme/active site saturation)
  • the rate stays the same when more substrate is added when enzyme is saturated.
43
Q

Maximum rate of a catalyzed reaction…

A

can be used to measure how efficient enzyme is.

44
Q

Turnover number is maximum…

A

number of substrate molecules that can convert to product per unit of time.

45
Q

Michaelis-Menten (MM) Kinetics (2)

A
  • reaction rate depends on concentration of enzyme and substrate.
  • Km, which is the MM constant, implies that half of enzyme active sites are occupied by substrate
    • influenced by pH, temperature, ionic strength, nature of substrate.
46
Q

To estimate Km and Vmax:

A
  • Vmax is the maximum rate of enzyme catalysis when substrate is saturated
  • Km is substrate concentration at which reaction rate is half Vmax
    • most cellular enzymes function near Km
47
Q

Enzyme Regulation (3)

A
  • metabolic pathways contain reactions, each catalyzed by a specific enzyme.
  • level of enzyme production is controlled by gene expression.
  • computer algorithms model pathways and show interdependent system (systems bio).
48
Q

Enzymes are regulated by…

A

inhibitors

  • natural: regulate metabolism
  • artificial: used to treat disease, kills pests, or study enzyme function.
49
Q

Irreversible inhibition (3)

A
  • occur if inhibitor binds covalently to side chains of active site, permanently inactive enzyme.
  • not common in cells
  • DIPF is an example of an inhibitor (nerve gas)
50
Q

Reversible inhibition is common in cells (3)

A
  • competitive inhibitor: binds to active site noncovalently
  • uncompetitive inhibitor: when bound, product doesn’t release
  • noncompetitive inhibitor: binds to site other than active site (allosteric site), changing enzyme structure
51
Q

Allosteric regulation

A

change in enzyme shape due to noncompetitive inhibitor - alters affinity of active site for substrate.

52
Q

concentration of substrate X reaction rate of nonallosteric enzyme vs. multi-subunit allosteric enzyme:

A

nonallosteric enzyme : hyperbolic

multi-subunit allosteric enzyme: sigmoid

53
Q

Enzymes are affected by…

A

environmental conditions such as pH and temperature.

54
Q

pH and enzyme activity (2)

A
  • each enzyme is most active at a certain pH

- there is always an optimal pH

55
Q

Temperature and enzyme activity (3)

A
  • in general, heat increases rate - reactant molecules have enough kinetic energy to provide activation energy.
  • enzyme catalyzed reactions are similar
  • however, high temperature breaks down noncovalent bonds.

Cell & Mole Bio - HES (11 decks)

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