Biochem 507: Exam 1 Lectures

Front 1

What is the "Progenote"?

Back 1

A breakthrough organism which gave rise to everything; LUCA - last universal common ancestor

Front 2

What were the prebiotic energy sources?

Back 2

- Radiation from sun
- Electric discharge (lightning)
- Radioactivity
- Volcanoes

Front 3

What were the initial raw materials on Earth?

Back 3

CO2, CH4, N2, H2, H2O, NH3

Front 4

What molecule is abundant in many structures which are necessary for life? Why?

Back 4

Adenine - When concentrated HCN is refluxed, the major product is adenine; therefore abundant prebiotically

Front 5

How do new enzymes/proteins begin?

Back 5

Gene duplication yields an extra copy that can evolve with a new function

Front 6

What is phosphotriesterase?

Back 6

A molecule which is found in bacteria that hydrolyzes pesticides and nerve toxins; evidence of the quick evolution of enzymes

Front 7

Evo-Devo stands for what?

Back 7

Evolutionary development

Front 8

What percent of the typical cell is water?

Back 8

70%

Front 9

What leads to Hydrogen Bonding in water?

Back 9

Electrical asymmetry; partial positive on hydrogens, partial negative on oxygen

Front 10

How does hydrogen bonding affect melting points?

Back 10

More hydrogen bonds, higher melting point

Front 11

Which is the H-bond donor?
H-bond acceptor?

Back 11

Donor = Hydrogen involved
Acceptor = Atom bonded to Hydrogen

Front 12

The hydrophobic effect causes what change in entropy?

Back 12

ΔS = Positive, because H bond potential is disrupted by hydrophobic molecules

Front 13

What are Van der Waals interactions?

Back 13

Weak interactions which operate at close range between transient dipoles induced in each atom by the other

Front 14

The stronger the acid, the ______ the pKa; why?

Back 14

Stronger acids = lower pKa = lower pH --- higher likelihood to ionize

Front 15

What is the Henderson Hasselbalch Equation?

Back 15

pH = pKa + log [A-]/[HA]

Front 16

How does the Greek lettering system work for R groups?

Back 16

αC = carbon attached to amino and carboxyl group
β, γ, δ, ε, etc carbons go consecutively downwards

Front 17

What is the difference between configuration and conformation?

Back 17

- Configurations - can be interconverted only by breaking and reforming one or more covalent bonds
- Conformation - Interconverted by rotation about a bond without breaking a covalent bond

Front 18

What are stereoisomers which are nonsuperimposable?

Back 18

Enantiomers

Front 19

Which enantiomer of amino acids is found in proteins?

Back 19

L-amino acids

Front 20

Which amino acids absorb UV light?

Back 20

Tryptophan**
Tyrosine*
Phenylalanine

Front 21

The isoelectric point is the pH when the amino acid is?

Back 21

at a neutral charge

Front 22

Which amino acids were found in the prebiotic atmosphere?

Back 22

Glycine, Alanine, valine, leucine, isoleucine, proline, serine, threonine, aspartate, glutamate

Front 23

Which amino acid kinks protein structure?

Back 23

Proline

Front 24

Which amino acid has a neutral pKa and is involved in H+ transfers?

Back 24

Histidine

Front 25

Which nonstandard amino acid is involved in blood clotting?

Back 25

γ-Carboxyglutamate

Front 26

Which nonstandard amino acid is a pre-cursor for arginine?

Back 26

Ornithine

Front 27

What is the average pKa of COOH on amino acids?

Back 27

~2

Front 28

What is the average pKa of NH2 on amino acids?

Back 28

~9-10

Front 29

How are peptide bonds formed in vitro (test tube)?

Back 29

1) Attachment to resin
2) Removal of protecting group (Fmoc)
3) Activation of next amino acid
4) Peptide bond formation
5) Removal of polypeptide from resin

Front 30

What is the purpose of Fmoc?

Back 30

It is a protecting group which prevents unwanted reactions at the α-amino group of the residue

Front 31

How does chemical synthesis (in vitro) of proteins differ from that done naturally (in vivo)?

Back 31

In vitro - synthesis proceeds from the C-terminus to the N-terminus; reverse of the In vivo method (N-->C)

Front 32

When naming peptides, start at which end?

Back 32

N-terminus

Front 33

If the molecular weight of a peptide is <10,000 it is designated as?
>10,000 is what?

Back 33

<10,000 = Polypeptide
>10,000 = Protein

Front 34

What is the average weight of an amino acid (adjusted for the percentage at which the amino acid occurs in proteins)

Back 34

MW = 110

Front 35

What are some functions of proteins?

Back 35

- Catalysis
- Transport
- Nutrient / Storage
- Motion
- Structure
- Defense
- Regulation
- Many other miscellaneous

Front 36

99.9% of reactions have what?

Back 36

An enzyme catalyst

Front 37

What are two examples of transport proteins?

Back 37

Ex: O2 doesn't diffuse very quickly; hemoglobin provides transport
Ex: Lipoproteins

Front 38

What are the main components for motion in muscle?

Back 38

Action / Myosin

Front 39

What is the main protein involved in structure?

Back 39

Collagen

Front 40

What are examples of kinds of proteins involved in defense?

Back 40

Immunoglobins
Venoms/Toxins

Front 41

What kind of proteins are involved in regulation?

Back 41

Hormones with extracellular signals

Front 42

Why do some proteins have carbohydrates attached? Name?

Back 42

Glycoproteins - used to identify cells

Front 43

Why do some proteins contain metal cofactors? Name?

Back 43

Metallo-enzymes - 1/3 of enzymes have metal cofactors

Front 44

Why are lipids sometimes on proteins?

Back 44

Helpful to embed in membrane

Front 45

What are two ways to detect proteins?

Back 45

1) UV Absorption (tryptophan especially)
2) Colorimetric Assays
- Lowry Blue Complex
- Bradford Blue Dye (Coomassie)
(Color intensity proportional to amount of protein)

Front 46

Why is the Bradford Blue Dye (Coomassie) better than Lowry Blue Complex?

Back 46

Coomassie doesn't destroy the proteins in the process?

Front 47

What is the reaction rate proportional to?

Back 47

The amount of enzyme present

Front 48

What is the "international enzyme unit"?

Back 48

The amount of enzyme that will convert one μmol of substrate to product in one minute at 30˚C

Front 49

What are the units of activity?

Back 49

Units (of desired protein) per mL of solution

Front 50

What are the units of specific activity?

Back 50

Units (of desired protein) per mg of protein total

Front 51

What is the measure of purity of a protein?

Back 51

The specific activity

Front 52

How can proteins be precipitated?

Back 52

1) Salt (NH4SO4) - best, most gentle
2) pH Extremes - can kill proteins
3) Heat - can kill proteins

Front 53

How does Ion-Exchange Chromatography work?

Back 53

- Beads in column have charged particles, either all positive or all negative
- Liquids w/ proteins going through will go through at different rates depending on charge or proteins
- Fractions will contain different proteins w/ different charges

Front 54

How does Size-Exclusion Chromatography work? What is its other name?

Back 54

Gel Filtration
- Bigger proteins go through column faster than small because small proteins get stuck in the porous polymer beads

Front 55

How does Affinity Chromatography work?

Back 55

- Polymer bound ligand (with affinity for protein of interest) is placed in column
- Protein mixture is poured through
- Unwanted proteins wash through column
- Protein of interest is eluted by ligand solution

Front 56

How do you determine when the protein is pure?

Back 56

- When further fractionation does not increase the specific activity
- Electrophoresis

Front 57

What does electrophoresis take place in?

Back 57

Polyacrylamide which allows the proteins to go through based on their molecular weights

Front 58

What is the function of Sodium Dodecyl Sulfate (SDS)?

Back 58

SDS binds to proteins in amounts proportional to their length, partially denatures the structures, as well as gives them all an overwhelming negative charge; this allows the proteins to move through proportional to their MW

Front 59

How do proteins get visualized after they have gone through electrophoresis?

Back 59

Coomassie blue dye which binds to the proteins but not to the gel

Front 60

What trends should be seen in a Purification Table?

Back 60

- Decrease in total protein (mg)
- Total enzyme (units) stays as high as possible
- Specific Activity (units/mg) increases

Front 61

What kind of bonds make up the primary structure of proteins?

Back 61

Covalent bonds: peptide bonds and disulfide bonds

Front 62

How can the N-terminus be determined?

Back 62

Using Sanger's method for direct protein sequencing;
- FDNB attacks the N-terminus and adds to end
- Strong Acid is added which removes the N-terminal A.A. with the FDNB leaving the remaining peptide chain

Front 63

What are proteases? What are 4 we learned about?

Back 63

Enzymes that catalyze the hydrolysis of peptide bonds
1) Trypsin**
2) Chymotrypsin**
3) Pepsin
4) Elastae

Front 64

What does Trypsin do?

Back 64

Protease which cleaves on the carboxyl side of Lysine or Arginine

Front 65

What does Chymotrypsin do?

Back 65

Protease which cleaves on the carboxyl side of Tyrosine, Tryptophan, and Phenylalanine

Front 66

How does CNBr cleave peptides?

Back 66

It hydrolyzes peptide bonds at the C-terminus of methionine residues

Front 67

How are Disulfide Bonds cleaved?

Back 67

1) Oxidation by Performic Acid

OR

1) Reduction by Dithiothreitol
2) Carboxymethylation by Iodoacetate (important or the previous step will revert to a sulfide bond

Front 68

What reactant is used in sequencing by the Edman Degradation?

Back 68

1) Phenylisothiocyanate w/ OH-
(Benz-N=C=S)
2) H+
=> Phenylthiohydantoin Derivative (determine A.A. from this compound) and then continue on remaining peptide chain

Front 69

How can large polypeptides be sequenced?

Back 69

Breaking them down into smaller fragments and piecing it together

Front 70

Specifically, what is the process for sequencing large polypeptides?

Back 70

1) Hydrolyze to separate amino acids
2) Determine # of each A.A.
3) Conclude which protease(s) would be useful based on # of A.A. / # of breaks
4) Determine N-Terminus of Polypeptide (w/ Sanger Method: FDNB + HCl)
5) Reduce Disulfide Bonds
6) Cleave w/ proteases, establish sequence via overlaps

Front 71

Why can't large polypeptides be sequenced solely by the Edman Degradation?

Back 71

The longer the polypeptide chain the lower the overall accuracy of the sequencing; thus they must be broken down into smaller fractions.

Front 72

How are Disulfide Bonds located (specifically which Cysteine residues are linked together)?

Back 72

- Two samples, one cleave disulfide bonds, one leave them
- Cleave with protease
- Electrophoresis
- Compare fragments on a gel
- The run w/o disulfide bond cleavage should have larger bands; that w/ disulfide bond cleavage will have 2+ bands missing which is replaced by larger band

Front 73

What is a Consensus Sequence?

Back 73

A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences
- use cool letter graph
- use symbols, [ ] = these A.A. could be present, x(#) = a lot of options could be here, { } = any AA except for these

Front 74

The C-O bond is _____ than expected in peptide linkages.
The C-N bond is _____ than expected in peptide linkages.

Back 74

C-O is longer than expected (not always "double" bond)
C-N is shorter than expected (not always "single" bond)

Front 75

Because the peptide bond is not solely composed of a C=O and C-N bond... what effect does this have on the rotation of the peptide backbone?

Back 75

There is not free rotation in the backbone of the peptide bond

Front 76

Around which bonds is there free rotation in the peptide backbone?

Back 76

N-C(alpha) and C(alpha)-C bonds have free rotation

Front 77

Which rotation angle is referred to by ϕ (phi)?

Back 77

C - Cα - N - C dihedral / torsion bond angle
(180° means N trans; 0° is cis)

Front 78

Which rotation angle is referred to by ψ (psi)?

Back 78

N - Cα - C - N dihedral / torsion bond angle
(180° means N trans; 0° is cis)

Front 79

In an α-helix, are the R groups on the inside of the helix or outside?

Back 79

Outside of helix

Front 80

How far is one turn of the α-helix? How many amino acid residues is that?

Back 80

0.54 nm
3.6 residues

Front 81

In which direction do α-helices rotate?

Back 81

Right-handed

Front 82

Why are α-helices such stable conformations?

Back 82

It makes optimal use of internal hydrogen bonds; the N-H is lined up with the C=O of the 4th A.A. on the N-terminal side

Front 83

Why is Proline very rarely found in α-helices?

Back 83

Its nitrogen atom is part of a rigid ring, making N-Cα bond rotation impossible, resulting in destabilizing kinks

Front 84

What's the difference between Parallel and Anti-Parallel β sheets?

Back 84

- Parallel - same amino-to-carboxyl orientations
- Anti-Parallel - opposite amino-to-carboxyl orientations

Front 85

Are Parallel or Anti-Parallel β sheets more stable/common?

Back 85

Anti-Parallel is more stable and more common (more direct H-bond alignment between N-H and C=O)

Front 86

Why is silk so slippery?

Back 86

Anti-parallel β sheets with small R groups (glycine and alanine)

Front 87

How are the ends of anti-parallel β-sheets linked?

Back 87

β Turns: 180 deg turn involving 4 A.A. residues w/ a H-bond between the 1st and 4th A.A. involved

Front 88

How are the two types of β turns different?

Back 88

- Type 1 - often includes Proline due to readily assumed cis configuration which is amenable to a tight turn
- Type 2 - includes glycine which is small and flexible (less steric hindrance)

Front 89

What does a Ramachandran Plot show?

Back 89

The possible and likelihood of different combinations of dihedral / torsion angles in proteins (ψ vs ϕ
- dark blue = most favored
- non blue = doesn't happen

Front 90

Which type of dihedral band angle combination is suspected to be possible, but no one has ever found a long enough chain of it?

Back 90

Left-handed α-helix

Front 91

Which amino acid residue can fall outside of the Ramachandran Plot expected values?

Back 91

Glycine due to its small H side-chain which allows it to take part in many conformations that are sterically forbidden for other a.a.

Front 92

What is distinct about Fibrous proteins compared to Globular proteins?

Back 92

- Fibrous usually have just one type of secondary structure with a simple tertiary structure
- Globular usually have multiple types of secondary structure

Front 93

What are the typical functions of Fibrous proteins?

Back 93

Provide support, shape, and external protection

Front 94

What are the typical functions of Globular proteins?

Back 94

Enzymes and regulatory functions

Front 95

When two α-helices are twisted together what is it called? What is known about the handedness?

Back 95

Superhelix
- Handedness is opposite that of the individual helices

Front 96

In perms, what are the main steps?

Back 96

1) Break disulfide bonds in hair with Thioglycolate
2) Curl hair
3) Oxidize sulfide bonds again; different linkages occur causing hair to curl

Front 97

α-Keratin is an example of what kind of protein?

Back 97

Fibrous protein - hair - made up of many superhelices - protofilaments - protofibril

Front 98

What is the most abundant protein in the body?

Back 98

Collagen

Front 99

What is the structure of collagen?

Back 99

Single L-handed helix (not an α-helix) w/ 3 A.A. residues per turn; 3 α chains (separate polypeptides) are supertwisted about each other (right-handed)

Front 100

Collagen is constructed of a repeating tripeptide made of what?

Back 100

Gly-X-Y where X and Y = Proline or 4-Hydroxyproline
- Proline prefers C-endo conformation
- Y prefers to be in C-exo conformation which is less stable, but it is reinforced by the hydroxylation

Front 101

How is Proline hydrolyzed to 4-hydroxyproline (the preferred conformation for c-exo in the Y position of the collagen tripeptide)?

Back 101

Prolyl Hydroxylase hydrolyzes Proline; requires vitamin C (ascorbic acid)

Front 102

What is it called when there are Vitamin C deficiencies? What happens?

Back 102

Scurvy - collagen defects - gums bleed, sore joints, nose bleeds, die

Front 103

How are collagen α chains cross-linked?

Back 103

With unusual amino acid residues - dehydrohydroxylysinonorleucine - lysine residues covalently bonded to hylysine residues

Front 104

What are two genetic defects involving collagen?

Back 104

- Osteogenesis Imperfecta: affects bone formation in babies - Gly to Cis mutation (doesn't fit tightly)
- Ehlers-Danlos Syndrome: loose joints, soft skin, eye problems and bone deformations - Gly to Ser mutation

Front 105

Why is gelatin (a protein) not a good source of protein?

Back 105

Lacks many essential amino acids; primarily consists of glycine (35%), alanine (11%), and proline/hydroxyproline (21%)

Front 106

What stabilizes the 3-D structure of globular proteins?

Back 106

- Electrostatic Forces (ionic interactions / salt bridges)
- Hydrogen Bonds (small contribution, however unpaired donor or acceptor is detrimental to stability)
- Hydrophobic Forces (most important, increases entropy)
- Disulfide bonds

Front 107

What are two pictorial ways to represent protein 3-D structure?

Back 107

- Surface contour conformation (shows reaction sites)
- Ribbon representation (shows secondary structures)

Front 108

What was the protein on which the preliminary understanding of tertiary structure was discovered? How?

Back 108

Myoglobin by John Kendrew (1950s) with x-ray diffraction

Front 109

What are the functions of myoglobin?

Back 109

- Stores oxygen
- Facilitates oxygen diffusion in rapidly contracting muscle tissues
- Underwater mammals have a lot of this so they can stay under a long time

Front 110

How does X-Ray diffraction give the structure of a protein?

Back 110

- Protein is crystallized
- X-Ray beams diffracted through
- Pattern of spots is used to reconstruct the image of protein (e- density)
- Model structure into e- density map
- Answer of where atoms in protein are

Front 111

How can scientists determine the structure of a protein?

Back 111

- NMR (only for smaller molecules)
- X-Ray Diffraction

Front 112

What did scientists learn about protein structure from myoglobin?

Back 112

- Predicted secondary structure exists
- Very compact
- Hydrophobic residues buried
- Proline often found at bends
- All species similar; 3-D structure conserved over evolution

Front 113

Are β sheets typically planar?

Back 113

No, they tend to twist slightly in a right-handed fashion

Front 114

How are two antiparallel β sheets connected?

Back 114

β bends

Front 115

What types of connections are more common between β strands?

Back 115

Right-handed connections

Front 116

What is a motif in protein structure?

Back 116

A recognizable folding pattern involving two or more elements of secondary structure and the connections between them; may or may not be independently stable

Front 117

What are some examples of motifs in protein structure?

Back 117

- β barrel
- β-α-β loop --> α/β barrel (made up of many loops, much more stable than individual loop)

Front 118

What is a domain in protein structure?

Back 118

Part of a polypeptide chain that is independently stable; usually each domain has a specific, discrete function

Front 119

How many domains are in a protein?

Back 119

Depends on individual protein; some have multiple domains, some have just one

Front 120

What are the 4 classes of motifs/folds?

Back 120

1) All α
2) All β
3) α / β (interspersed)
4) α + β (segregated)

Front 121

Serum albumin is in all α protein, what is it's function?

Back 121

Carries many things, regulates osmotic pressure, found in bloodstream

Front 122

Bacterioferritin (cytochorome b1) is an all α protein, what is its function?

Back 122

E- carrier which binds Fe atom or cofactor

Front 123

How is UDP N-acetylglucosamine acyltransferase's structure critical to its function?

Back 123

It is an all β structure (parallel) which forms long deep pockets to synthesize long lipids in.

Front 124

What is the purpose of Collagenase-3?

Back 124

All β structure which looks like it has four bladed β propellers; used to get rid of collagen in places it does not belong

Front 125

Alcohol dehydrogenase has which kind of fold structure?

Back 125

α/β

Front 126

The green fluorescent protein found in jellyfish for glowing has what kind of fold structure?

Back 126

α +β
(β barrel w/ α parts)

Front 127

What stabilizes quaternary structure?

Back 127

The same factors which stabilized individual subunits (hydrophobic effects, hydrogen bonding, van der waals...)

Front 128

How does a protein know which way to fold?

Back 128

** it does not randomly sample all possible conformations **
- Formation of short stretches of secondary structure
- Formations of stable subdomains and domains
- Some proteins have loose "molten globule" intermediate
- Enzymes catalyze some steps (disulfide bond formation and proline isomerization)
** Chaperones **

Front 129

What are chaperones and why are they useful?

Back 129

Large protein complexes with huge chambers which allow proteins to fold up to proper structure

Front 130

What ways can proteins be denatured?

Back 130

- Heat (disrupts H-bonds and others)
- Urea (disrupts hydrophobic interactions)
- pH Extremes (disrupts ionic interactions)
- High [Salt] (disrupts ionic interactions)
- Detergents (disrupts hydrophobic interactions)
- HS-CH2-CH2-OH (mercaptoethanol, reduces disulfide bonds)

Front 131

What does the term "denaturation" mean?

Back 131

Loss of activity, not loss of ALL structure; just enough loss of structure so that protein loses its function

Front 132

What lesson was learned from Anfinsen's experiment? How?

Back 132

** Primary structure determines tertiary structure
- EXP: ribonuclease treated with urea and mercaptoethanol = denatured; when removed, the protein refolded precisely and regained activity = renaturation

Front 133

What are Ligands?

Back 133

Molecules that are bound reversibly to a protein; transient in nature

Front 134

Where do ligands bind to proteins?

Back 134

Binding sites which are complementary to the specific protein-ligand interaction

Front 135

How flexible are proteins?

Back 135

- Not rigid
- Undergo conformational changes (big or small)
- Breathing - molecular vibrations

Front 136

What usually happens when a ligand binds to the specific binding site on a protein?

Back 136

- Coupled with conformation change, causing an induced fit which is more complementary to the ligand

Front 137

How are myoglobin and hemoglobin related/similar/different?

Back 137

Myoglobin (Mb)
- 1 subunit, MW = 16,700
- Found in muscle for oxygen storage
Hemoglobin
- 4 subunits (α2β2), MW = 64,500 (4x myoglobin)
- Found in blood for oxygen transport

Front 138

What does Oxygen bind to?

Back 138

- Transition metals: Fe2+ is suitable for reversible binding
- Found in heme

Front 139

Why do globins need heme / Fe2+ to bind oxygen?

Back 139

No amino acid is suitable for reversible binding of Oxygen

Front 140

Why must free iron in organisms be controlled / bound? How is this taken care of?

Back 140

It can be very damaging to DNA and other macromolecules; It is sequestered, to make it less reactive, within a protein-bound prosthetic group called heme

Front 141

When iron is sequestered in heme, what is the structure that directly surrounds the iron?

Back 141

Porphyrin ring which prevents Fe2+ from changing to Fe3+ (does not bind oxygen)

Front 142

Where is the heme located in heme-containing proteins?

Back 142

Deep within the protein structure

Front 143

The Fe2+ within the porphyrin ring has two open coordination bonds; what is attached to them?

Back 143

1) Histidine residue - attached at N
2) Binding site for O2

Front 144

Why is CO highly toxic to aerobic organisms?

Back 144

It is coordinated to heme iron with greater affinity than O2; therefore O2 would be excluded and organism would die

Front 145

What is the structure of myoglobin?

Back 145

Single polypeptide with a heme molecule; made up of eight α-helical segments connected by bends

Front 146

What is the equilibrium expression, which describes the reversible binding of a protein (P) to a ligand (L)?

Back 146

P + L <-- --> PL
Ka = [PL] / [P][L] = 1/Kd
Ka = association constant [M^-1]
Kd = dissociation constant [M]

Front 147

What does Ka (the association constant) measure?

Back 147

The affinity of the ligand, L, for the protein, P.

Front 148

What is the Binding Equilibrium equations?

Back 148

Θ = Binding sites occupied / Total binding sites = [PL] / [PL]+[P]
Rearranged: Θ=Ka[L] / Ka[L]+1 = [L] / [L] + Kd

Front 149

How does Kd related to binding?

Back 149

Increase Kd= weaker binding
Decrease Kd= stronger binding

Front 150

What is the relationship when half of the binding sites are occupied, Θ=1/2?

Back 150

Dissociation constant Kd = concentration of the ligand

Front 151

What is the specific equation for ligand/protein when Oxygen is the ligand?

Back 151

Θ = [O2] / [O2]+[O2]_0.5
[O2]_0.5 = concentration at 1/2 saturated

Front 152

What are the strong interactions holding hemoglobin together?

Back 152

Strong interactions between "unlike" subunits (α to β, β to α); also hydrophobic interactions, H-bonds, and ionic pairs

Front 153

Oxygen induces conformational changes in hemoglobin; what are the two states?

Back 153

- T = "tense" - low oxygen affinity; predominates in absence of oxygen
- R = "relaxed" - high oxygen affinity
- oxygen binding triggers T to R transition

Front 154

Why is a hyperbolic binding curve inappropriate for the binding of oxygen with myoglobin/protein that binds oxygen?

Back 154

- If it was high-affinity, the protein would pick up oxygen well in the lungs (high pressure) but not release it in the tissues (low pressure)
- If it was low-affinity, it would be able to release the oxygen in the tissues, but wouldn't pick up much from the lungs

Front 155

What is the appropriate binding curve for oxygen binding to proteins (myoglobin)? Why?

Back 155

- A sigmoid cooperative binding curve
- Lower affinity for oxygen in lower pressures (tissues) allows it to release oxygen to tissues
- Higher affinity for oxygen in higher pressures (lungs) allows it to pick up oxygen in lungs

Front 156

What does allosteric binding refer to?

Back 156

The binding of one ligand affects the binding of others

Front 157

What is the Hill equation?

Back 157

log (Θ / 1-Θ) = n log [L] - log (Kd)

Front 158

What is plotted on the coordinates of the Hill Plot?

Back 158

y = log (Θ / 1-Θ)
x = log [L] ((log pO2))
b = - log (Kd)
m = n (Hill coefficient)

Front 159

What does the slope of the Hill plot represent (n)?

Back 159

When n = 1, ligand binding is not cooperative
When n>1, positive cooperation in ligand binding

Front 160

There are two models of cooperative binding, what are they?

Back 160

1) Symmetry model - subunits of a cooperatively binding protein are functionally identical; two conformations possible, all subunits undergo transition simultaneously
2) Sequential model - ligand binding can induce a change of conformation in individual subunits which increases the likelihood of nearby subunits transitioning

Front 161

What can hemoglobin transport besides O2?

Back 161

H+ and CO2 (inverse of O2 binding)

Front 162

What state do H+ and CO2 prefer for hemoglobin?

Back 162

T state = tense = low oxygen affinity

Front 163

What is the Bohr effect?

Back 163

- At low pH (high H+), high CO2, affinity of hemoglobin for oxygen is low and O2 is released in tissues
- At high pH (low H+), low CO2, affinity of hemoglobin for oxygen increases and more O2 is bound for transport

Front 164

How does BPG affect oxygen binding?

Back 164

Binding of BPG stabilizes the T (tense) state which decreases Oxygen binding... causing more oxygen to be released into the tissues

Front 165

When does Sickle Cell Anemia occur?

Back 165

Caused by mutation in hemoglobin (Glu to Val at pos. 6)
- Leads to fewer erythrocytes, unusual shape, weakness and pain

Front 166

What are three principles of enzymatic catalysis?

Back 166

1) Enzymes effect rates, not equilibria
2) Enzyme-transition state complementarity
3) Many parts of a substrate contribute

Front 167

What are Ribozymes involved in?

Back 167

- Mainly in RNA metabolism
- Exception: synthesis of proteins on ribosomes

Front 168

What is a prosthetic group?

Back 168

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein.

Front 169

Where do enzyme-catalyzed reactions take place?

Back 169

Active Site
- analogous to ligand binding site (except that a reaction is facilitated)
- usually a cleft or pocket on the enzyme, lined w/ amino acid residues and cofactors positioned to optimally facilitate reaction

Front 170

How is the standard free-energy change in biochemistry regulated?

Back 170

pH = 7

Front 171

What is binding energy used for?

Back 171

- Entropy reduction - hold substrates in proper orientation to react
- Desolvation - replace H-bonds to H2O
- Strain - facilitates any geometric or electrostatic distortion required
- Induced Fit - bring reactive groups on enzyme into proper orientation for catalysis

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What is heterolytic cleavage? Homolytic?

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E- pair ends up entirely on one atom (most often)
E- pair split between two atoms to produce radicals (very reactive)

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What is the most common reaction?

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Proton transfer

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What are cofactors?

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Groups or molecules (other than AA residues) which are important to catalysis
i.e., metals (metalloenzymes), coenzymes (from vitamins)

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What is an enzyme without a prosthetic group? With?

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W/O: Apoenzyme
W/: Holenzyme - active

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What are metals used for in enzymes?

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Metals bind to substrate to orient them; mediate redox rxns; electrostatic shielding or stabilization of neg. charge

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What does Mg2+ do for ATP?

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Shields the negative charges; very highly charged is not ideal biologically, hard to go through membranes...

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How do covalent catalysts occur?

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- Formation of covalent complex w/ nucleophilic attack
- Catalyst must be linked to substrate transiently

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What are some requirements of covalent catalysts?

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- Catalyst (imidazole) must be better nucleophile than acyl acceptor (H2O)
- Intermediate must be more reactive than substrate
- Intermediate must be less stable than product