Biochem - Exam 2

Biological Functions of Proteins
* Signaling Compounds and Receptors
* Structural Proteins
* Immunoproteins
* Transport Proteins
* Enzymes
* Fluid Balance
* Buffers
* Other (e.g. storage proteins)
Peptide Hormones
> 100 amino acids (e.g. Glucagon, Parathyroid Hormone, Calcitonin, Insulin, Oxytocin).
AA (Amino Acid) Derivative
1 amino acid (e.g. Tyrosine, Histidine, Tryptophan).
Tyrosine (Derivatives)
Thyroid hormones (thyroxine), catecholamines (dopamine, epinephrine, and norepinephrine) are derived from what amino acid derivative?
Histidine (Derivatives)
Histamine (immune response associated with allergies) is derived from what amino acid derivative?
Tryptophan (Derivatives)
Serotonin (neurotransmitter regulating mood, sleep, appetite), melatonin (regulates sleep-wake cycle) are derived from what amino acid derivative?
Small proteins that act as regulators of growth and differentiation (e.g. Interleukin-1 (IL-1), tumor necrosis factor-alpha (TNF-α), IL-6, C-reactive protein (CRP), and IL-10).
Anti-inflammatory cytokine produced during exercise.
C-reactive Protein (CRP)
The cytokine that is the best indicator of inflammation.

* good < 1 mg/dL
* mid 1-3 mg/dL
* high > 3 mg/dL
* rheumatoid arthritis > 60 mg/dL
Baseline Inflammation
25% of {this} is due to phagocytes trapped in our adipose tissue.
Fibrous Proteins
Collagen, Elastin, Keratin
Contractile Proteins
(65% of muscles) Actin, Myosin
(Immunoglobulins, Antibodies) Y-shaped proteins containing 4 peptides that bind to antigens and inactivate (e.g. five classes: IgG, IgA, IgM, IgE, and IgD).
Immunoprotein class responsible for allergies.
Transport Proteins
Proteins that combine with other substances and acts as a mode of transport through the body (e.g. albumin, hemoglobin, transferrin, and vitamin d-binding protein).
Albumin (Transport Protein)
Transport protein that transports calcium, zinc, and vitamin B₆. Maintains osmotic pressure. Three-quarters of all protein in the plasma. Can be used to measure protein status, but is slow to change (~2 weeks).
Hemoglobin (Transport Protein)
Transport protein that transports oxygen.
Transferrin (Transport Protein)
Transport protein that transports iron.
Vitamin D-binding Protein (Transport Protein)
Transport protein that transports Vitamin D.
Biological catalysts that speed up reactions by lowering energy needed for reaction to occur and are not used up in the process.
Fluid Balance
Water interacts with several groups on proteins: charged residues, peptide backbone, and hydroxyl groups. Water is attracted to protein. A protein deficiency can cause edema.
Protein malnutrition.
A compound that prevents a change in pH (e.g. hemoglobin in RBCs).
Amino Acids
Building blocks of proteins. 9 essential (i.e. need in our diet (exogenous)), 11 nonessential (i.e. our body can make (endogenous)).
AA (Amino Acid) Structure
Positively charged amino group (NH₃⁺), side chain, negatively charged carboxyl group (COO⁻) all attached to an α-carbon.
AA (Amino Acids) Metabolized in Liver
20% of amino acids in the liver are used to make new proteins and N-containing compounds. New proteins made: enzymes (remain in liver), plasma proteins, acute phase proteins (inflammatory response).
Branched Chain (Amino Acids Metabolized)
{These} types of amino acids are metabolized in muscles.
A transport protein with a half-life of 2 days. Best biomarker for protein.
* Nonessential
* Nonpolar
* Glucogenic
* Found in high concentrations in collagen
* Simplest amino acid
* Nonessential
* Nonpolar
* Glucogenic
* Found in high concentrations in collagen
* Nonpolar
* Glucogenic
* Essential
* Nonpolar
* Glucogenic
* Branched Chain
* Essential
* Nonpolar
* Glucogenic
* Precursor for SAMe
* Essential
* Nonpolar
* Both Glucogenic and Ketogenic
* Aromatic
* Essential
* Nonpolar
* Both Glucogenic and Ketogenic
* Branched Chain
* Essential
* Nonpolar
* Both Glucogenic and Ketogenic
* Aromatic
* Precursor for Serotonin, Melatonin, Niacin
* Essential
* Nonpolar
* Ketogenic
* Branched Chain
* Precursor for Cholesterol
* Nonessential
* Polar
* Glucogenic
* Important for cross-linking proteins through disulfide bonds (i.e. Disulfide Bridge)
* Nonessential
* Polar
* Glucogenic
* Nonessential
* Polar
* Glucogenic
* Main N Carrier
* Nonessential
* Polar
* Glucogenic
* Able to H-bond
Aspartic Acid
* Nonessential
* Polar
* Glucogenic
* Acidic
Glutamic Acid
* Nonessential
* Polar
* Glucogenic
* Acidic
* Precursor for GABA (gamma-amino butyric acid)
* Nonessential
* Polar
* Glucogenic
* Basic
* Precursor for Nitric Oxide (NO) (a vasodilator)
* Essential
* Polar
* Glucogenic
* Basic
* Precursor for Histamine
* Essential
* Polar
* Both Glucogenic and Ketogenic
* Nonessential
* Polar
* Both Glucogenic and Ketogenic
* Aromatic
* Precursor for Thyroid Hormones, Melanin, Catecholamines
* Essential
* Polar
* Ketogenic
* Basic
* Important for collagen formation
Essential AA (Amino Acids)
PVT MT HILL: Phenylalanine, Valine, Tryptophan, Methionine, Threonine, Histidine, Isoleucine, Lysine, Leucine
Amino acid is used to make glucose if necessary (product: pyruvate).
Amino acid is turned into Kreb's cycle intermediate, ketone bodies, or fatty acids if in excess (product: acetyl CoA).
Ketogenic Only
Leucine and Lysine
Glucogenic and Ketogenic
Phenylalanine, Isoleucine, Tryptophan, Threonine, and Tyrosine
Branched Chain AA (Amino Acids)
Valine, Isoleucine, and Leucine
Aromatic AA (Amino Acids)
Phenylalanine, Tryptophan, and Tyrosine
Acidic AA (Amino Acids)
Aspartic Acid and Glutamic Acid
Basic AA (Amino Acids)
Arginine, Histidine, and Lysine
Sickle Cell Anemia
* Genetic disorder
* Valine (nonpolar) replaces Glutamate (polar) in hemoglobin
* Protein folds incorrectly
Maple Syrup Urine Disease
* Genetic deficiency of enzymes required to metabolize branched chain amino acids (valine, leucine, isoleucine)
* Symptoms: urine with color, odor and viscosity of maple syrup
* Untreated: brain damage and death
* Treatment: avoid high protein food
Phenylketonuria (PKU)
* Genetic disorder that lacks enzyme necessary to metabolize phenylalanine
* Causes brain damage
* Phenylalanine found in Nutrasweet and anything with protein
* Treatment: avoid phenylalanine
Cystic Fibrosis
* Genetic disorder affecting 1 in 2000
* Missing 1 phenylalanine in protein that regulates transport of chloride ions across cell membranes
* Protein does not fold correctly, protein is degraded
* Causes mucus to build up (lung and digestion issues)
Coenzymes/Cofactors (in AA Metabolism)
Vitamin C, Vitamin B₆, Folic Acid, Iron, Niacin function as {these} in AA metabolism.
The acid dissociation constant.
The removal of H from the carboxyl group acid dissociation constant.
The removal of H from the amino group acid dissociation constant.
The removal of H from the R group acid dissociation constant.
Has hydrogen (H) attached (e.g. pH < pK).
Hydrogen (H) lost (e.g. pH > pK).
Isoelectric Point (pI)
* The point where an AA or protein is neutral (zwitterion)
* when pH < pI, then protein has a net positive charge
* when pH > pI, then protein has a net negative charge
pI (Calculation)
* average of pK₁ and pK₂ (AA without any loss from R-group)
* average of pK-R and the closest pK (AA with loss from potential from R-group(s))
Physiologic pH
Compound that can act as an acid and a base.
* Chains of AA
* Formed via condensation/dehydration reactions
* Bonds trans in nature
2 amino acid peptide.
Peptide of 10-100 amino acids.
Peptide of > 100 amino acids.
Primary (1°) (Protein Structure)
* Sequence of amino acids
* Includes covalent bonding (peptide bonds)
* Sequence determines other structural levels and acts as signals
* Does not change during denaturation
Secondary (2°) (Protein Structure)
* Spatial arrangement of atoms around a polypeptide backbone
* Stabilized by noncovalent interactions (IMF, mostly H-bonding)
* α-helices, β-pleated sheets, and β-bends
Repeat units of protein structure stabilized by H-bonding every 4 amino acids. H-bond between H on amide and O on carboxyl group of another amino acid.
Polypeptide H-bonded to another polypeptide aligned in parallel or antiparallel fashion.
Reverse direction of polypeptide chain to fold compactly in globular structures (4 AA per turn). H-bond between carboxyl group on AA₁ and amide group on AA₄.
Tertiary (3°) (Protein Structure)
* 3-D arrangement
* Folding of peptide chains
* Influenced by R-groups
- Covalent Bonds (Disulfide Bonds between Cysteines)
- Non-covalent Bonds (IMF)
Quaternary (4°) (Protein Structure)
* Grouping of 2+ peptide chains
* Non-covalent bonding (IMF)
* Polar outside, nonpolar inside (so it can travel through aqueous liquids (blood))
Globular (Protein Shape)
* Highly folded, water-soluble proteins
* Dense, hydrophobic core
* Hydrophilic outside
* Easily denatured
* Hemoglobin, Myoglobin, Peptide Hormones (e.g. insulin, glucagon, oxytocin), Enzymes
Fibrous (Protein Shape)
* Long strands of proteins, highly cross-linked
* Insoluble
* Structural role of the body
* Hard to denature
* Keratin (hair, nails), Elastin (connective tissue), Collagen (connective tissue)
* Triple helix
* Extracellular matrix of bone and connective tissue
* One-third of total protein in the body
* Glycine - Proline - Y and Glycine - X - Hydroxyproline
- X and Y can be any amino acid; often hydroxylysine
- Vitamin C required to hydroxylate proline and lysine
Nomenclature prefix denoting the addition of a hydroxyl (-OH) group. The addition of which adds a H donor and acceptor key to H-bonding.
* Vitamin C deficiency
* Symptoms: corkscrew hairs, bleeding gums
Complete Proteins
* Foods that contain all essential AA
* Animal proteins (e.g. human milk, eggs, meat, poultry, seafood, dairy; EXPECT gelatin)
* Plant proteins: soy, amaranth, quinoa
Incomplete Proteins
* Foods that do not contain all essential AA
* Corn - deficient in lysine and tryptophan
* Wheat - deficient in lysine
* Rice - deficient in lysine
* Legumes (beans, peanuts, peas) - deficient in methionine
Complimentary Proteins
Combining 2 incomplete proteins that together provide all 9 essential AA.
4 kcal / gram
Caloric value of protein per gram.
(Protein Digestion in) Mouth
No protein digestion occurs here (before stomach).
(Protein Digestion in) Stomach
* HCl is released from parietal cells in response to gastrin (which is released due to organ distention, smell, thought, and/or sight of food)
- Denatures 2°, 3°, and 4° structured proteins
- Converts pepsinogen (inactive enzyme released by chief cells) to pepsin (active)
An endopeptidase found in the stomach.
An enzyme that breaks internal peptide bonds in a peptide chain which results in polypeptides, oligopeptides (maximum 3 AA long), and free AA.
An anzyme that breaks the terminal peptide bond in a peptide chain resulting in free AA only.
(Protein Digestion in) Small Intestine
* Chyme released {here} stimulates release of secretin and CCK (cholecystokinin)
* Secretin and CCK stimulate release of bicarbonate, water, electrolytes, and zymogens from pancreas
Pancreatic zymogen of Trypsin. Activated by Enterokinase or Trypsin.
Pancreatic zymogen of Chymotrypsin. Activated by Trypsin.
Pancreatic zymogen of Carboxypeptidase. Activated by Trypsin.
Pancreatic zymogen of Elastase. Activated by Trypsin.
Pancreatic Endopeptidases
Trypsin, Chymotrypsin, Elastase, and Collagenase
Pancreatic endopeptidase that digests protein in elastin.
Pancreatic endopeptidase that digests protein in collagen.
Pancreatic Exopeptidase
Pancreatic exopeptidase that digests protein from the carboxy terminal and is zinc dependent.
Brush Border Endopeptidase
Brush border endopeptidase that activates trypsin.
Brush Border Exopeptidases
Aminopeptidase, Dipeptidase
Brush border exopeptidase that digests protein from the amino terminal.
Brush border exopeptidase that digests peptide bond between 2 amino acids in a dipeptide and is magnesium dependent.
(Protein Digestion in) Large Intestine (Colon)
No digestion occurs here (after small intestine).
Free AA (Absorption)
* Absorbed via active transport utilizing AA Transporter, Na⁺, K⁺, and ATP
* Sodium binds carrier protein → AA binds carrier protein → carrier protein release sodium and AA inside enterocyte → sodium is pumped out of enterocyte and potassium is pumped in using ATP
Peptide (Absorption)
* Absorbed via active transport utilizing PEPT1 transport protein, H⁺, Na⁺, K⁺, and ATP
* Hydrogen binds to PEPT1 → di/tri peptide binds to PEPT1 → PEPT1 release hydrogen and di/tri peptide inside enterocyte → hydrogen is pumped back into the SI lumen in exchange for sodium → sodium is pumped out of enterocyte and potassium is pumped in using ATP → peptidase (enzyme in the cytoplasm) digests di/tri peptides to free AA so they can cross the basolateral membrane
(AA in) Enterocytes
* AA are used for energy or protein synthesis
* AA {here} are necessary to make:
- Proteins for new {these}
- Nucleotides
- Apoproteins for lipoproteins
- New digestive enzymes
- Hormones
- N-containing compounds
AA Transport Out of Enterocyte
Free AA not needed by the enterocyte are transported through the basolateral membrane into the interstitial fluid by passive diffusion and facilitated diffusion (AA Transporter).