List potential modifications to amino acids and describe how they may impact the protein
function.
List and name the 20 amino acids that commonly occur in proteins and classify them according to polarity, size, and charge
Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin
and myoglobin (Figure 7.10 and 7.11)
Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin
and myoglobin (Figure 7.10 and 7.11)
Define and explain pH, pKa, and the dissociation constant Ka
Explanation: The pKa of most carboxylic acids is between 2 and 5, therefore at pH 7.4
these acids are nearly fully dissociated.
Explanation: Hydrogen bonding is the primary stabilizing force in both secondary structures.
In alpha helices the hydrogen bond is between the carbonyl oxygen group from one peptide
bond and that amide hydrogen from a different peptide bond approximately amide 4 resides
down in the helix. In beta sheets, the hydrogen bonding is between the carbonyl oxygen and
the amide hydrogen from different peptide strands.
Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
Calculate the [OH] OR [H+] concentration if given the molarity of a solution of strong acid or base
The pH is the negative log of the hydrogen ion concentration, [H+]. At a pH of 7.0 [H+] is 10-7; and at pH
6.0[H+] is 10-6. The [H+] has changed by a factor of 10-6/10-7 which is 10. A decrease in 1 pH units is a
10 fold increase in [H+].
Objectives:
1. Describe the importance of water in biological systems and summarize the characteristics of the molecule
1. 60% of body, 25L ICF and 15L ECF, maintains homeostasis
2. Completely dissolves shit due to dipole interactions and weak H20 binding creates H bonding (Na, Cl)
3. Neutral with small Kd and constant molarity of 55.5M. multiplied, get ion product, tells us how much H+ and hydroxide there are in
solution. In water, it’s equal because H+ and HO make H2O
2. Evaluate the flow of water between intracellular and extracellular compartments based on osmolality
1. Water moves from least concentrated to more concentrated via ion channels, IC to EC.
3. List the components of a buffer
1. Weak acid, conjugate base.
4. Define and explain pH, pKa, and the dissociation constant Ka
1. pH – Concentration of H+ ions in a solution
2. Dissociation Constant – expresses the relationship between the H+ ion concentration, the OH- concentration, and the
concentration of H20 at equilibrium.
3. Ka – Tendency for an acid to dissociate and done a hydrogen ion to solution.
4. pKa is inverse log of that rhythm.
,5. Calculate the [OH] OR [H+] concentration if given the molarity of a solution of strong acid or base
1.
6. Define zwitterions.
1. A molecule with multiple groups with varying charges. Amino acids have carboxyl groups, anide groups, H+’s etc.
7. List potential modifications to amino acids and describe how they may impact the protein function.
1. GLycosylation – protects cell from proteolysis or immune attack.
2. Fatty Acylation/Prenylation – interact hydrophobically.
3. Regulatory Mods
Phosphorylation – adds bulky neg charged group that alters activity.
Acetylation – On chromosome, changes lysine interactions with neg charged phosphate groups of DNA
ADP-Ribosylation –regulates activity of proteins.
4. Posttranslational Mods
Carboxylation – attaching clots to surfaces
5. Selenocystein
Found in enzymes that need it for activity.
8. List and name the 20 amino acids that commonly occur in proteins and classify them according to polarity, size, and charge
1. NonPolar, Alipathic
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
2. Aromatic
Phenylalanine, nonpolar
Tyrosine, polar
Tryptophan, polar
3. Polar, uncharged
Asparagine
, Glutamine
Serine
Threonine
4. Sulfur Containing
Methionine, nonpolar
Cysteine, polar
5. Charged
Aspartate, -, acidic
Glutamate, -, acidic
Arginine, +, basic
Lysine, +, basic
Histidine, +, basic
9. Know the pKas for the amino acids in Figure 6.9
1. Aspartate – 3.9
2. Glutamate – 4.1
3. Histidine – 6.0
4. Cysteine – 8.4
5. Tyrosine – 10.5
6. Lysine – 10.5
7. Arginine – 12.5
10. Calculate the net charge on a molecule using the pKa(s) of ionizable groups (See Figure 6.8)
1. Just know pKa’s for groups of amino acids, decide if it will be ionized, or protonated.
2. N group pKa = 8
3. C group pKa = 3.1
11. Discriminate between primary, secondary, tertiary, and quaternary protein structure (Overview Figure 7.1)
1. Primary – peptide backbone, bonds between carboxyl group and amide group.
2. Secondary
Alfa Helix
o H-bonds between carbonyl Oxygen atoms and H of an amide residue 4 amino acid residues before it.
, Beta Sheet
o Parralel or antiparallel depending on orientation. Same bonding but parallel
Tertiary
o Folding of secondary structure into 3D shape.
Quat
o Association of 2 or more polypeptide chains joined together.
12. Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
1. Done
13. Define motif.
1. Common arrangements of secondary structure, help characterize proteins by fxn
Beta, alpha, beta, alpha, beta.
14. Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin and myoglobin
(Figure 7.10 and 7.11)
1. Myoglobin
Within heat and skeletal muscle
Same tertiary as Hgb.
High Affinity for O2, very saturated enzyme even at low affinity.
Noncooperative
2. Hgb
At same O2 concentration, affinity is less than Mgb.
Cooperative binding. T vs R state.
More efficient for delivery, will retain O2 it has until sat’s are low, then releases, because this area is usually in tissues.
Session 2 Objectives
Students will be able to:
1. Describe the 6 major enzyme classifications and the basic type of reaction catalyzed, including: oxidoreductases, transferases, hydrolases,
lyases, isomerases, and ligases
1. Oxidoreductases
One substrate gains electrons (reduced) while another gains electrons (oxidized)
2. Transferases
function.
List and name the 20 amino acids that commonly occur in proteins and classify them according to polarity, size, and charge
Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin
and myoglobin (Figure 7.10 and 7.11)
Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin
and myoglobin (Figure 7.10 and 7.11)
Define and explain pH, pKa, and the dissociation constant Ka
Explanation: The pKa of most carboxylic acids is between 2 and 5, therefore at pH 7.4
these acids are nearly fully dissociated.
Explanation: Hydrogen bonding is the primary stabilizing force in both secondary structures.
In alpha helices the hydrogen bond is between the carbonyl oxygen group from one peptide
bond and that amide hydrogen from a different peptide bond approximately amide 4 resides
down in the helix. In beta sheets, the hydrogen bonding is between the carbonyl oxygen and
the amide hydrogen from different peptide strands.
Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
Calculate the [OH] OR [H+] concentration if given the molarity of a solution of strong acid or base
The pH is the negative log of the hydrogen ion concentration, [H+]. At a pH of 7.0 [H+] is 10-7; and at pH
6.0[H+] is 10-6. The [H+] has changed by a factor of 10-6/10-7 which is 10. A decrease in 1 pH units is a
10 fold increase in [H+].
Objectives:
1. Describe the importance of water in biological systems and summarize the characteristics of the molecule
1. 60% of body, 25L ICF and 15L ECF, maintains homeostasis
2. Completely dissolves shit due to dipole interactions and weak H20 binding creates H bonding (Na, Cl)
3. Neutral with small Kd and constant molarity of 55.5M. multiplied, get ion product, tells us how much H+ and hydroxide there are in
solution. In water, it’s equal because H+ and HO make H2O
2. Evaluate the flow of water between intracellular and extracellular compartments based on osmolality
1. Water moves from least concentrated to more concentrated via ion channels, IC to EC.
3. List the components of a buffer
1. Weak acid, conjugate base.
4. Define and explain pH, pKa, and the dissociation constant Ka
1. pH – Concentration of H+ ions in a solution
2. Dissociation Constant – expresses the relationship between the H+ ion concentration, the OH- concentration, and the
concentration of H20 at equilibrium.
3. Ka – Tendency for an acid to dissociate and done a hydrogen ion to solution.
4. pKa is inverse log of that rhythm.
,5. Calculate the [OH] OR [H+] concentration if given the molarity of a solution of strong acid or base
1.
6. Define zwitterions.
1. A molecule with multiple groups with varying charges. Amino acids have carboxyl groups, anide groups, H+’s etc.
7. List potential modifications to amino acids and describe how they may impact the protein function.
1. GLycosylation – protects cell from proteolysis or immune attack.
2. Fatty Acylation/Prenylation – interact hydrophobically.
3. Regulatory Mods
Phosphorylation – adds bulky neg charged group that alters activity.
Acetylation – On chromosome, changes lysine interactions with neg charged phosphate groups of DNA
ADP-Ribosylation –regulates activity of proteins.
4. Posttranslational Mods
Carboxylation – attaching clots to surfaces
5. Selenocystein
Found in enzymes that need it for activity.
8. List and name the 20 amino acids that commonly occur in proteins and classify them according to polarity, size, and charge
1. NonPolar, Alipathic
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
2. Aromatic
Phenylalanine, nonpolar
Tyrosine, polar
Tryptophan, polar
3. Polar, uncharged
Asparagine
, Glutamine
Serine
Threonine
4. Sulfur Containing
Methionine, nonpolar
Cysteine, polar
5. Charged
Aspartate, -, acidic
Glutamate, -, acidic
Arginine, +, basic
Lysine, +, basic
Histidine, +, basic
9. Know the pKas for the amino acids in Figure 6.9
1. Aspartate – 3.9
2. Glutamate – 4.1
3. Histidine – 6.0
4. Cysteine – 8.4
5. Tyrosine – 10.5
6. Lysine – 10.5
7. Arginine – 12.5
10. Calculate the net charge on a molecule using the pKa(s) of ionizable groups (See Figure 6.8)
1. Just know pKa’s for groups of amino acids, decide if it will be ionized, or protonated.
2. N group pKa = 8
3. C group pKa = 3.1
11. Discriminate between primary, secondary, tertiary, and quaternary protein structure (Overview Figure 7.1)
1. Primary – peptide backbone, bonds between carboxyl group and amide group.
2. Secondary
Alfa Helix
o H-bonds between carbonyl Oxygen atoms and H of an amide residue 4 amino acid residues before it.
, Beta Sheet
o Parralel or antiparallel depending on orientation. Same bonding but parallel
Tertiary
o Folding of secondary structure into 3D shape.
Quat
o Association of 2 or more polypeptide chains joined together.
12. Compare and contrast beta sheets and alpha helical formations. (Figure 7.3 vs. 7.5)
1. Done
13. Define motif.
1. Common arrangements of secondary structure, help characterize proteins by fxn
Beta, alpha, beta, alpha, beta.
14. Describe the structural difference between hemoglobin and myoglobin and compare O2 binding properties of hemoglobin and myoglobin
(Figure 7.10 and 7.11)
1. Myoglobin
Within heat and skeletal muscle
Same tertiary as Hgb.
High Affinity for O2, very saturated enzyme even at low affinity.
Noncooperative
2. Hgb
At same O2 concentration, affinity is less than Mgb.
Cooperative binding. T vs R state.
More efficient for delivery, will retain O2 it has until sat’s are low, then releases, because this area is usually in tissues.
Session 2 Objectives
Students will be able to:
1. Describe the 6 major enzyme classifications and the basic type of reaction catalyzed, including: oxidoreductases, transferases, hydrolases,
lyases, isomerases, and ligases
1. Oxidoreductases
One substrate gains electrons (reduced) while another gains electrons (oxidized)
2. Transferases
