Proteins

Front 1

Four components of an amino acid

Back 1

1. Amino group
2. Carboxyl group
3. Hydrogen
4. Side chain functional group

Front 2

What is the chirality of amino acids?

Back 2

They are all in the L configuration.

Front 3

Acid

Back 3

A proton donor

Front 4

Base

Back 4

A proton acceptor

Front 5

Henderson-Hasselbalch equation

Back 5

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

Front 6

Titration curves

Back 6

A buffer is only useful over a pH range of pKa +/- 2. The change in pH caused by the addition of a base depends on how far the pH is from the pKa.

Front 7

Peptide bond

Back 7

Planar bond between carboxy and amide groups.

Front 8

Primary structure

Back 8

The order in which the amino acids are connected.

Front 9

Sequence conservation

Back 9

Proteins with a similar function in different organisms often have a similar primary sequence because they have evolved from each other.

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Percent identity

Back 10

Number of residues that are identical when two sequences are compared.

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Percent similarity

Back 11

Number of residues that are identical or of a similar type.

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Conservative Mutation

Back 12

Mutation results in an amino acid from the same class.

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Semi-conservative

Back 13

If you have an uncharged polar it would be like changing it to a nonpolar.

Front 14

Non-conservative

Back 14

Changing charges.

Front 15

Sickle-Cell Anemia

Back 15

Primary Mutation: Glu6Val in beta chain of hemoglobin causes aggregation at low concentrations of oxygen

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Cystic Fibrosis

Back 16

CFTR inactivated by deletion of Phe508.

Front 17

Amyotrophic Lateral Sclerosis

Back 17

Superoxide dismutase, an enzyme that protects against free radicals is inactivated by a point mutation.

Front 18

Severe Combined Immunodeficiency

Back 18

Adenosine deaminase, an enzyme important for immune system function is inactivated by mutation Ala239Val.

Front 19

Hydrophobic interactions

Back 19

Nonpolar molecules, like hydrocarbons interfere with water binding to itself. Does not dissolve in water.

Front 20

Hydrogen Bonds

Back 20

N-H and C=O can interact through hydrogen bond. H bond is weaker in water because there is no net change in stability.

Front 21

Electrostatic Interactions

Back 21

Charge-charge interactions. Contribution to protein stability is weaker because no net change.

Front 22

Van der Waals interactions

Back 22

When atoms approach each other they attract weakly. at shorter distances they repel weakly. Make contacts in the middle of proteins.

Front 23

Molecular Recognition

Back 23

Leads protein to adopt a defined structure, an active site region.

Front 24

Locations of amino acids in proteins

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1. Hydrophobic amino acids are found in interior of protein molecule.
2. Hydrophilic molecules are found on the surface of proteins.
3. Charged residues are found on the surface of proteins.

Front 25

alpha-helix

Back 25

Has 3.6 residues per turn and is right handed. The C=O of the peptide bond forms a hydrogen bond with NH of a peptide bond 4 residues ahead in the sequence.

Front 26

Parallel beta sheets

Back 26

The direction of the sequence N to C is parallel in all strands of the sheet. Hydrogen bonds form between C=O and NH groups in adjacent strands.

Front 27

Antiparallel beta sheets

Back 27

The direction of the sequence N to C alternates between the various strands of the sheet. Hydrogen bonds form between C=O and NH groups in adjacent strands.

Front 28

Type I beta turn

Back 28

Allows protein chain to fold back on itself.

Front 29

Helix turn helix

Back 29

Two alpha helixes are separated by a beta turn introducing a kink.

Front 30

Beta-meander

Back 30

Random beta sheets out of line.

Front 31

Beta alpha beta structure

Back 31

Two antiparallel beta sheets separated by an alpha helix.

Front 32

Secondary structure

Back 32

Secondary structure provides a way for the peptide backbone to fold into structures that allow the formation of H-bonds between C=O and N-H groups.

Front 33

Super-secondary structure

Back 33

Elements of secondary structure stabilized by interactions, usually hydrophobic between individual structural elements.

Front 34

Tertiary structure

Back 34

The 3D structure of a single protein molecule that bring together primary and secondary structures.

Front 35

Quaternary structure

Back 35

Assembly of multiple protein subunits into a functional protein.

Front 36

Why don't proteins need to be super stable?

Back 36

If they were, we might never be able to break them down and recycle them. They need to have flexibility as well.

Front 37

Folding of proteins

Back 37

The primary sequence contains sufficient information to direct the formation of the tertiary and quaternary structures. Some proteins can spontaneously fold back to original form if denatured.

Front 38

Hypothesis for protein folding

Back 38

1. After rapid collapse, secondary structure begins to develop within collapsed state over short segments
2. Secondary elements dock with each other
3. They reattach into native state

Front 39

Molecular chaperones

Back 39

Bind to unfolded proteins and prevent non-specific aggregation and hydrophobic collapse.

Front 40

Protein disulfide isomerase

Back 40

Recognizes correct disulfide bonds during assembly

Front 41

Peptidyl prolyl isomerase

Back 41

Catalyzes cis-trans isomerization of proline residues that can retard the folding of proteins.

Front 42

Posttranslational modification of proteins

Back 42

Can be modified after they are synthesized to control activity, affect stability, or modify structure of protein.

Front 43

Disulfides

Back 43

Formed between two Cys residues stabilizing proteins against denaturation.

Front 44

Phosphorylation

Back 44

Occurs on serine, threonine, and tyrosine (contain hydroxy groups). Phosphorylation occurs by reaction with ATP catalyzed by specific protein kinases.

Front 45

Hydroxylation

Back 45

Proline and lysine can be hydroxylated normally in collagen.

Front 46

Glycosylation

Back 46

Carbohydrates are added to extracellular proteins on asparagine, serine, or threonine residues in specific sequences. This alters stability, assists proteins, and provides recognition by other proteins.

Front 47

Carboxylation

Back 47

Glutamine is carboxylated in blood clotting system to form a Ca2+ binding site in these proteins.

Front 48

Fatty acylation/prenylation

Back 48

Cysteine, Serine, Lysine, N-terminis - a long chain fatty acid or prenyl substituent unit can be added to a protein to increase hydrophobicity and increase tendency to bind to membranes.

Front 49

Proteolysis

Back 49

Cleaving a peptide bond can be used to remove signal sequence or activate an inactive proenzyme. Many are stored as zymogens activated before use.

Front 50

Protonation/Deprotonation

Back 50

Lysines, histidines, glutamic acid, aspartic acid, and cysteine can be affected by changes in pH because they act as acids and bases.

Front 51

Hemoglobin and myoglobin

Back 51

Bind to O2 reversibly. Oxygen binds to an iron atom (Fe2+) which is coordinated to heme prosthetic group that is bound to the globin protein. Amino acid side chains participate in binding of oxygen to heme iron with the proximal histidine coordinating the iron while the distal one interacts with oxygen.

Front 52

Structure of hemoglobin

Back 52

1. Tetramer composed of two copies of two different subunits. The tetrameric structure is essential for cooperative binding of oxygen.
2. There are four beta like chains and 2 alpha like chains.

Front 53

Structure of myoglobin

Back 53

Monomeric protein similar to one of the four subunits of hemoglobin.

Front 54

Cooperativity of hemoglobin

Back 54

1. The binding of oxygen to hemoglobin becomes easier when oxygen is already bound.
2. Oxygen binding causes a change in conformation of subunit it binds to that transmits info between subunits
3. Cooperative binding makes the dependence of the % saturation on oxygen concentration steeper than non-cooperative binding increasing the amount of oxygen transferred from lungs to tissues.

Front 55

The Bohr effect

Back 55

1. Describes the effect of pH on the oxygen carrying of Hb.
2. At lower pH, oxygen binds less tightly to Hb causing release of oxygen (in tissues)
3. At higher pH oxygen binds more tightly (in lungs)

Front 56

Bisphosphoglycerate effects on oxygen binding

Back 56

BPG has a binding site in the center of the deoxyHb tetramer. Once oxygen binds to hemoglobin, this site disappears so BPG can only bind to deoxyHb. This results in weaker binding of oxygen in presence of BPG.

Front 57

Fetal Hemoglobin

Back 57

Has poorer binding site for BPG than adult increasing affinity of fetal Hb for oxygen.

Front 58

Enzymes

Back 58

Accelerate the rates of chemical reactions and are catalysts that are not used up in the reactions.

Front 59

Active sites of enzymes

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1. Regions which interact with substrate specifically and anchor the substrate to the enzyme
2. Catalytic groups (side chains of amino acids) participate in and accelerate the chemical reaction
3. Cleft or pocket on the surface of the enzyme into which the substrate fits

Front 60

Mechanisms to regulate enzyme activity

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1. Control the amount of enzyme, the rate of synthesis and rate of degradation
2. Posttranslational modification - active by phosphorylation
3. Presence of substrates and products. Increase substrate increase rate. Increase product decrease rate.

Front 61

Initial velocity of enzymatic reaction

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1. Velocity is calculated from the slope of the absorbance vs. time graph and is expressed as umols consumed per minute.
2. International unit is the amount of enzyme that will consume one umol of substrate or produce one umol of product per minute.

Front 62

Isoenzymes

Back 62

Enzymes that catalyze the same reaction but are structurally different. Usually encoded by different genes.

Front 63

Lactate dehydrogenase

Back 63

Tetramer of two different subunits, one expressed dominantly in the heart and the other in the muscle and liver.

Front 64

Saturation

Back 64

At high substrate concentration the velocity of the reaction approaches a maximum value

Front 65

Michaelis-Menten equation

Back 65

Relates velocity to substrate concentration.

Front 66

Specific Activity

Back 66

v is divided by the amount of enzyme. Does not vary with enzyme concentration.

Front 67

Km

Back 67

The Michaelis Constant is the concentration of the substrate required to attain a velocity that is one-half Vmax.

Front 68

Lineweaver-Burk treatment

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The Y intercept is 1/Vmax and the slope is Km/Vmax

Front 69

Reversible inhibition

Back 69

Inhibition by filling up active site and preventing substrate from binding in a reversible way.

Front 70

Competitive inhibition

Back 70

An inhibitor combines with the same form of the enzyme as the substrate. An infinite concentration of substrate will prevent inhibition.

Front 71

Non-competitive inhibition

Back 71

An inhibitor combines with both the E-S complex and free enzyme. Effects are seen on both slopes and intercepts.

Front 72

Substrate concentration

Back 72

The physiological concentration of the substrate is usually near or below Km. When it increases it is used faster.

Front 73

Product concentration

Back 73

The product of the reaction can inhibit the overall reaction. When the product concentration goes up it is made slower.

Front 74

Enzyme concentration

Back 74

A slower mechanism of control (hours-days). Increased synthesis of the enyzme will increase the rate of product formation while increased degradation will decrease the amount of enzyme and lower formation of product.

Front 75

Specific activity - changes in activity of the enzyme

Back 75

1. Posttranslational modification
2. Changes in quaternary structure
3. Binding an effector molecule

Front 76

Allosteric enzymes

Back 76

Activity is modulated by a combination of an effector with the enzyme at a site other than the active site influencing the velocity of catalytic reaction through changes in structure of the protein.

Front 77

Heterotrophic effector

Back 77

An effector is a regulatory molecule other than the substrate.

Front 78

Homotrophic effector

Back 78

Effector is the substrate itself.

Front 79

Cooperativity

Back 79

Almost always made up by multiple subunits and multiple active sites. The binding of a substrate to one site changes the properties of the remaining sites on the other subunits.

Front 80

Positive cooperativity

Back 80

Binding of the substrate to one site makes it easier for the substrate to bind at a different site.

Front 81

Negative cooperativity

Back 81

Binding of a substrate at one site makes it harder for the substrate to bind a different site.

Front 82

Sigmoidal kinetics

Back 82

Increasing substrate concentration causes the velocity to change much less at low substrate concentrations and much more at intermediate concentrations of the substrate.

Front 83

Vmax/Km (specificity constant)

Back 83

Describes how enzymes discriminate among various substrates. If an enzyme is presented with two substrates, it will use the substrates in proportion to the Vmax/Km values.

Front 84

Lock and key

Back 84

The substrate fits precisely into the active site.

Front 85

Induced fit

Back 85

The binding of substrate induces a change in the conformation of the enzyme that brings catalytic groups into the right geometry to accelerate the specific reaction that occurs at the active site of this enzyme.

Front 86

Organization of substrates

Back 86

An enzyme may accelerate the reaction by simply aligning the molecules at the active site.

Front 87

Solvation effects

Back 87

An enzyme may provide a microenvironment which is much different from the environment of bulk water.

Front 88

Covalent catalysis

Back 88

Enzymes can accelerate reactions by forming covalent bonds with the substrate.

Front 89

Acid-base catalysis

Back 89

Acidic and basic side chains of amino acids can be used to catalyze proton abstraction and donation to the substrate to avoid the high activation energy due to forming very unstable intermediates.