Proteins

Biological Importance and Functional Diversity of Proteins

• General Definition and Abundance:

  • Proteins are linear polymers made up of monomeric units called amino acids.

  • They are indispensable biomolecules in living organisms, carrying out a vast array of biological functions essential for sustaining life.

  • Proteins constitute almost $50\%$ of the total cellular dry weight.

• Major Biological Roles:

  • Catalysis: Accelerated chemical reactions mediated by enzymes.

  • Structural Roles: Mechanical support and architectural integrity provided by proteins such as collagen, silk fibroin, and elastin.

  • Movement: Contractile and motile functions facilitated by actin and myosin.

  • Defense and Immunity: Immunological protection mediated by immunoglobulins (antibodies).

  • Regulation: Physiological control and signaling mediated by protein hormones.

  • Transport: Delivery and storage of vital biological substances, such as hemoglobin, myoglobin, and ferritin.

  • Gene Regulation: Chromatin organization and transcriptional control mediated by histones.

Stereochemistry and Molecular Structure of Amino Acids

• Basic Chemical Structure:

  • All amino acids possess a central alpha-carbon ($\text{C}_\alpha$) bound to an amino group ($-\text{NH}_2$ or $-\text{NH}_3^+$), a carboxyl group ($-\text{COOH}$ or $-\text{COO}^-$), a hydrogen atom ($-\text{H}$), and a distinct side-chain functional group ($\text{R}$).

• Chirality:

  • All amino acids found in proteins possess a chiral center at the $\text{C}_\alpha$ position (with the exception of glycine, where the $\text{R}$ group is a hydrogen atom).

  • Although both $\text{D}$ and $\text{L}$ enantiomers exist theoretically, only $\text{L}$-amino acids occur naturally in protein structures.

• Optical Activity:

  • Chiral amino acids exhibit optical activity, rotating plane-polarized light. The specific rotation $[\alpha]_\text{D}^{25}$ values measured at $25\,^\circ\text{C}$ using the sodium D line are:

    • $\text{L-Alanine}$: $+1.8^\circ$

    • $\text{L-Arginine}$: $+12.5^\circ$

    • $\text{L-Aspartic acid}$: $+5.0^\circ$

    • $\text{L-Glutamic acid}$: $+12.0^\circ$

    • $\text{L-Histidine}$: $-38.5^\circ$

    • $\text{L-Isoleucine}$: $+12.4^\circ$

    • $\text{L-Leucine}$: $-11.0^\circ$

    • $\text{L-Lysine}$: $+13.5^\circ$

    • $\text{L-Methionine}$: $-10.0^\circ$

    • $\text{L-Phenylalanine}$: $-34.5^\circ$

    • $\text{L-Proline}$: $-86.2^\circ$

    • $\text{L-Serine}$: $-7.5^\circ$

    • $\text{L-Threonine}$: $-28.5^\circ$

    • $\text{L-Tryptophan}$: $-33.7^\circ$

    • $\text{L-Valine}$: $+5.6^\circ$

Ionization, Zwitterions, and Acid-Base Chemistry

• Zwitterionic State:

  • At physiological $\text{pH } 7$, amino acids exist as dipolar ions known as zwitterions.

  • In a zwitterion, the amino group is protonated and positively charged ($-\text{NH}_3^+$), while the carboxyl group is deprotonated and negatively charged ($-\text{COO}^-$), maintaining a net charge of $0$

• Ionization Behavior of Polyprotic Weak Acids:

  • Amino acids act as weak polyprotic acids. The dislodging of protons ($\text{H}^+$) occurs in a stepwise manner depending on the environmental $\text{pH}$.

  • Protonation states of Glycine across $\text{pH}$ ranges:

    • At $\text{pH } 1$: Exists in cationic form ($\text{Gly}^+$) with a net charge of $+1$

    • At $\text{pH } 7$: Exists as a neutral zwitterion ($\text{Gly}^0$) with a net charge of $0$

    • At $\text{pH } 13$: Exists in anionic form ($\text{Gly}^-$) with a net charge of $-1$

  • Dissociation constants and equilibrium equations for Glycine:

    • Carboxyl dissociation step: $\text{Gly}^+ + \text{H}_2\text{O} \rightleftharpoons \text{Gly}^0 + \text{H}_3\text{O}^+$ with equilibrium constant $K_1 = \frac{[\text{Gly}^0][\text{H}_3\text{O}^+]}{[\text{Gly}^+]}$

    • $\text{pK}_1$ values center in the range of $2.0$ to $2.4$ (with $K_1$ values between $0.4 \times 10^{-2}\,\text{M}$ and $1.0 \times 10^{-2}\,\text{M}$).

    • Amino dissociation step: $\text{Gly}^0 + \text{H}_2\text{O} \rightleftharpoons \text{Gly}^- + \text{H}_3\text{O}^+$ with equilibrium constant $K_2 = \frac{[\text{Gly}^-][\text{H}_3\text{O}^+]}{[\text{Gly}^0]}$

    • $\text{pK}_2$ values center in the range of $9.0$ to $9.8$

• Henderson-Hasselbalch Equation:

  • Determines the solution $\text{pH}$ given the molar concentrations of acid and base conjugate species:

    • $\text{pH} = \text{p}K_a - \log_{10}\left(\frac{[\text{Acid}]}{[\text{Base}]}\right)$

    • $\text{pH} = \text{p}K_a + \log_{10}\left(\frac{[\text{Base}]}{[\text{Acid}]}\right)$

• Amino Acid Titration Curves:

  • Biphasic titration curves occur for monoprotic $\text{R}$-groups (e.g., Glycine), featuring inflection points at $\text{pK}_1$ and $\text{pK}_2$, separated by the Isoelectric Point (pI).

  • Triphasic titration curves occur for ionizable $\text{R}$-groups:

    • Acidic Amino Acids (e.g., Glutamic Acid): Deprotonation sequence progresses through $\text{Glu}^+ \rightarrow \text{Glu}^0 \rightarrow \text{Glu}^- \rightarrow \text{Glu}^{2-}$, governed by $\text{pK}_1$, $\text{pK}_2$ (carboxyl side chain), and $\text{pK}_3$

    • Basic Amino Acids (e.g., Lysine): Deprotonation sequence progresses through $\text{Lys}^{2+} \rightarrow \text{Lys}^+ \rightarrow \text{Lys}^0 \rightarrow \text{Lys}^-$, governed by $\text{pK}_1$, $\text{pK}_2$, and $\text{pK}_3$ (amino side chain).

Physicochemical Classification and Properties of Amino Acids

• Classification Criteria:

  • Amino acids are classified by the physicochemical properties of their side-chain $\text{R}$-groups, including size, structure, polarity, charge, and aqueous solubility.

• Non-Polar (Hydrophobic) Amino Acids:

  • Alanine (Ala, A): Nonpolar aliphatic side chain ($-\text{CH}_3$).

  • Valine (Val, V): Nonpolar branched aliphatic side chain.

  • Leucine (Leu, L): Nonpolar branched aliphatic side chain.

  • Isoleucine (Ile, I): Nonpolar branched aliphatic side chain.

  • Proline (Pro, P): Cyclic imino acid structure restricting conformational flexibility.

  • Methionine (Met, M): Nonpolar sulfur-containing thioether side chain.

  • Phenylalanine (Phe, F): Nonpolar aromatic side chain.

  • Tryptophan (Trp, W): Aromatic indole group; borderline non-polar due to the presence of an ring nitrogen capable of forming hydrogen bonds with water.

  • Cysteine (Cys, C): Thiol-containing side chain grouped with nonpolar amino acids in standard shorthand tables.

• Polar, Uncharged Amino Acids:

  • Glycine (Gly, G): The smallest amino acid; lacks a chiral center. Unique among polar uncharged amino acids in its inability to form side-chain hydrogen bonds with water.

  • Serine (Ser, S): Contains a hydroxyl group ($-\text{OH}$) active in hydrogen bonding.

  • Threonine (Thr, T): Contains a hydroxyl group ($-\text{OH}$) active in hydrogen bonding.

  • Tyrosine (Tyr, Y): Aromatic hydroxylated side chain; exhibits the lowest water solubility among all polar amino acids.

  • Asparagine (Asn, N): Contains an amide side chain that acts as a strong hydrogen-bond donor/acceptor.

  • Glutamine (Gln, Q): Contains an amide side chain that acts as a strong hydrogen-bond donor/acceptor.

• Acidic Amino Acids (Negatively Charged at Neutral $\text{pH}$):

  • Aspartic Acid (Asp, D): Carboxylate side chain ($-\text{COO}^-$).

  • Glutamic Acid (Glu, E): Carboxylate side chain ($-\text{COO}^-$).

  • Functional properties: Highly negatively charged at $\text{pH } 7$; possess strong capacity to bind divalent metal cations and serve as nucleophiles in enzymatic catalytic reactions.

• Basic Amino Acids (Positively Charged at Neutral $\text{pH}$):

  • Lysine (Lys, K): Alkyl amino side chain ($-\text{NH}_3^+$).

  • Arginine (Arg, R): Guanidinium side chain ($-\text{NH}-\text{C}(\text{NH}_2)_2^+$).

  • Histidine (His, H): Imidazolium side chain.

  • Ionization behavior: Lysine and Arginine are fully ionized at neutral $\text{pH}$. Histidine has a $\text{p}K_a$ near physiological $\text{pH}$ and is only $10\%$ ionized at $\text{pH } 7$, allowing it to act as a physiological buffer and acid-base catalyst.

Non-Standard Amino Acids and Derived Metabolites

• Modified Proteinogenic Amino Acids:

  • $5\text{-Hydroxylysine}$: Found in collagen structure.

  • $4\text{-Hydroxyproline}$: Found in collagen structural stability.

  • $\epsilon\text{-N-Methyllysine}$, $\epsilon\text{-N,N,N-Trimethyllysine}$, and $3\text{-Methylhistidine}$: Post-translationally methylated derivatives.

  • $\gamma\text{-Carboxyglutamic acid}$: Found in blood-clotting factors for calcium binding.

  • $Pyroglutamic acid$: Cyclized glutamic acid derivative.

  • $Phosphoserine$, $Phosphothreonine$, and $Phosphotyrosine$: Phosphorylated amino acids critical for metabolic signal transduction.

• Metabolic Intermediates and Non-Protein Amino Acids:

  • $\alpha\text{-Aminoadipic acid}$

  • $Thyroxine$ (iodinated thyroid hormone derivative).

  • $Sarcosine$ ($\text{N-methylglycine}$).

  • $\gamma\text{-Aminobutyric acid}$ (GABA): Primary inhibitory neurotransmitter.

  • $Betaine$ ($\text{N,N,N-trimethylglycine}$).

  • $\beta\text{-Alanine}$: Non-protein $\beta$-amino acid.

  • $Homoserine$ and $Homocysteine$: Sulfur metabolic pathway intermediates.

  • $\text{L-Lanthionine}$,$\text{L-Phenylserine}$, $Cycloserine$, and $\text{L-Chloramphenicol}$.

  • $Ornithine$ and $Citrulline$: Key urea cycle intermediates.

• Biogenic Amines derived from Amino Acids:

  • $Histamine$: Decarboxylation product of Histidine.

  • $Epinephrine$: Catecholamine neurotransmitter derived from Tyrosine.

  • $Serotonin$: Neurotransmitter derived from Tryptophan.

  • $Penicillamine$: Thiol-containing amino acid derivative.

Essential Amino Acids and Nutritional Aspects

• Definition:

  • Essential amino acids cannot be biosynthesized de novo by human metabolism and must be obtained through the diet.

• The Nine Essential Amino Acids:

  • Histidine (His)

  • Isoleucine (Ile)

  • Leucine (Leu)

  • Lysine (Lys)

  • Methionine (Met)

  • Phenylalanine (Phe)

  • Threonine (Thr)

  • Tryptophan (Trp)

  • Valine (Val)

• Dietary Sources and Limiting Amino Acids:

  • Animal Sources: Complete proteins containing all $20$ standard amino acids in adequate proportions.

  • Plant Sources: Incomplete proteins deficient in specific essential amino acids.

  • Rice: Rich in Methionine (Met); limiting in Lysine (Lys).

  • Beans and Legumes: Rich in Lysine (Lys); limiting in Methionine (Met) and Cysteine (Cys).

Primary Structure and Peptide Bond Chemistry

• Peptide Bond Structure:

  • Proteins are linear chains joined by peptide bonds, which are covalent amide linkages formed between the $\alpha\text{-carboxyl}$ group of one amino acid residue and the $\alpha\text{-amino}$ group of another.

  • Individual amino acid units integrated within a peptide chain are termed residues.

  • Chain nomenclature: Dipeptide ($2$ residues), Tripeptide ($3$ residues), Oligopeptide ($12$ to $20$ residues), Polypeptide (long chain), Protein (functional polypeptide macromolecule).

• Planar Geometry and Resonance:

  • The peptide bond exhibits partial double-bond character due to resonance delocalization of the lone pair of electrons on the amide nitrogen to the carbonyl oxygen.

  • The rotation energy barrier around the peptide $\text{C-N}$ bond is approximately $88\,\text{kJ/mol}$, holding the six atoms of the amide group within a single rigid plane.

  • The carbonyl oxygen and amino hydrogen are positioned in a trans conformation relative to each other across the peptide bond.

• Geometric Parameters of the Peptide Bond:

  • $\text{C=O}$ Bond length: $0.123\,\text{nm}$ ($1.24\,\text{\AA}$)

  • $\text{C-N}$ Peptide bond length: $0.133\,\text{nm}$ ($1.33\,\text{\AA}$)

  • $\text{N-C}_\alpha$ Bond length: $0.145\,\text{nm}$ ($1.46\,\text{\AA}$)

  • $\text{C}_\alpha\text{-C}$ Bond length: $0.152\,\text{nm}$ ($1.51\,\text{\AA}$)

  • $\text{N-H}$ Bond length: $0.10\,\text{nm}$ ($1.0\,\text{\AA}$)

  • Bond angles: $\text{C}_\alpha\text{-C=O} = 121.1^\circ$ (or $120.5^\circ$), $\text{O=C-N} = 123.2^\circ$ (or $123.5^\circ$), $\text{C}_\alpha\text{-C-N} = 115.6^\circ$ (or $116^\circ$), $\text{C-N-C}_\alpha = 121.9^\circ$ (or $122^\circ$), $\text{C-N-H} = 119.5^\circ$, $\text{H-N-C}_\alpha = 118.2^\circ$ (or $118.5^\circ$), $\text{N-C}_\alpha\text{-C} = 111^\circ$

• Medical Example of Primary Structure Mutation: Sickle Cell Anemia:

  • A single nucleotide substitution in DNA alters the primary amino acid sequence of the $\beta$-globin chain of hemoglobin.

  • Normal DNA: CAA GTA AAC ATA GGA CTT CTT $\rightarrow$ mRNA: GUU CAU UUG UAU CCU GAA GAA $\rightarrow$ Protein Sequence: val-his-leu-thr-pro-glu-glu

  • Sickle Cell DNA: CAA GTA AAC ATA GGA CAT CTT $\rightarrow$ mRNA: GUU CAU UUG UAU CCU GUA GAA $\rightarrow$ Protein Sequence: val-his-leu-thr-pro-val-glu

  • Pathophysiology: Replacing hydrophilic Glutamic acid at position 6 with hydrophobic Valine produces sticky hydrophobic patches on mutated hemoglobin ($\text{HbS}$). These form long fibrous aggregates under low oxygen conditions, distorting red blood cells into rigid sickle shapes that obstruct microvascular circulation.

Protein Size and Subunit Molecular Architecture

• Representative Molecular Mass and Subunit Table:

  • Bovine Insulin: Molecular Weight $M_r = 5,733\,\text{Da}$; $21$ residues (Chain A), $30$ residues (Chain B); Subunit organization: $\alpha\beta$ ($2$ subunits).

  • Equine Cytochrome c: Molecular Weight $M_r = 12,500\,\text{Da}$; $104$ residues; Subunit organization: $1$ monomeric subunit.

  • Bovine Pancreatic Ribonuclease A: Molecular Weight $M_r = 12,640\,\text{Da}$; $124$ residues; Subunit organization: $1$ monomeric subunit (stabilized by $4$ disulfide bridges).

  • Egg White Lysozyme: Molecular Weight $M_r = 13,930\,\text{Da}$; $129$ residues; Subunit organization: $1$ monomeric subunit.

  • Horse Myoglobin: Molecular Weight $M_r = 16,980\,\text{Da}$; $153$ residues; Subunit organization: $1$ monomeric subunit.

  • Bovine Pancreatic Chymotrypsin: Molecular Weight $M_r = 22,600\,\text{Da}$; Chains: $13$ residues ($\alpha$), $132$ residues ($\beta$), $97$ residues ($\gamma$); Subunit organization: $\alpha\beta\gamma$.

  • Human Hemoglobin: Molecular Weight $M_r = 64,500\,\text{Da}$; Chains: $141$ residues ($\alpha$), $146$ residues ($\beta$); Subunit organization: $\alpha_2\beta_2$ tetramer ($4$ subunits).

  • Human Serum Albumin: Molecular Weight $M_r = 68,500\,\text{Da}$; $550$ residues; Subunit organization: $1$ monomeric subunit.

  • Yeast Hexokinase: Molecular Weight $M_r = 96,000\,\text{Da}$; $200$ residues per chain; Subunit organization: $\alpha_2$ dimer ($2$ subunits).

  • Horse Globulin: Molecular Weight $M_r = 149,900\,\text{Da}$; Chains: $214$ residues ($\alpha$), $446$ residues ($\beta$); Subunit organization: $\alpha_2\beta_2$

  • Liver Glutamate Dehydrogenase: Molecular Weight $M_r = 332,694\,\text{Da}$; $500$ residues per chain; Subunit organization: $\alpha_6$ hexamer.

  • Rabbit Myosin: Molecular Weight $M_r = 470,000\,\text{Da}$; Chains: $1800$ residues (heavy chain), $190$ residues ($\alpha$), $149$ residues ($\alpha'$), $160$ residues ($\beta$); Subunit organization: $\text{heavy}_2\alpha_2\alpha'_2\beta_2$

  • Spinach Ribulose Bisphosphate Carboxylase: Molecular Weight $M_r = 560,000\,\text{Da}$; Chains: $475$ residues ($\alpha$), $123$ residues ($\beta$); Subunit organization: $\alpha_8\beta_8$

  • E. coli Glutamine Synthetase: Molecular Weight $M_r = 600,000\,\text{Da}$; $468$ residues per chain; Subunit organization: $\alpha_{12}$

Secondary Structure of Proteins

• Definition:

  • Secondary structure refers to local thermodynamically favorable conformations assumed by the polypeptide backbone, stabilized by hydrogen bonds between peptide carbonyl oxygens and amide nitrogens.

• The $\alpha$\text{-Helix}}:

  • A right-handed helical coil arrangement of the polypeptide backbone ($\text{N-C}_\alpha\text{-C}$).

  • Helix Parameters:

    • Residues per turn: $3.6$ amino acid residues.

    • Pitch (advance per turn): $0.54\,\text{nm}$ ($5.4\,\text{\AA}$).

    • Rise (advance per residue): $0.15\,\text{nm}$ ($1.5\,\text{\AA}$).

  • Hydrogen bonding occurs between the carbonyl oxygen of residue $i$ and the amide nitrogen hydrogen of residue $i+4$

• The $\beta$\text{-Sheet / }\beta\text{-Strand}}:

  • Extended polypeptide backbone conformations aligned side-by-side, forming pleated sheet structures with amide planes oriented perpendicular to the sheet plane.

  • Parallel $\beta$\text{-Sheet}: Adjacent polypeptide strands run in the same N-terminal to C-terminal direction ($\text{N}\rightarrow\text{C}$ and $\text{N}\rightarrow\text{C}$).

  • Antiparallel $\beta$\text{-Sheet}: Adjacent polypeptide strands run in opposite directions ($\text{N}\rightarrow\text{C}$ and $\text{C}\rightarrow\text{N}$), resulting in linear, stronger inter-strand hydrogen bonds.

Super-Secondary, Tertiary, and Quaternary Structures

• Super-Secondary Structure (Motifs):

  • Recurring combinations of interconnected $\alpha$-helices and $\beta$-sheets that form distinct structural motifs within folding pathways.

• Tertiary Structure:

  • The complete three-dimensional folding of a single polypeptide chain driven by long-range interactions between proximal and distal amino acid side-chain $\text{R}$-groups.

  • Stabilizing Forces:

    • Hydrophobic Interactions: Clustering of nonpolar aliphatic and aromatic side chains into the internal core to exclude water molecules, reinforced by van der Waals forces.

    • Hydrogen Bonds: Electrostatic attractions between polar uncharged side-chain groups.

    • Ionic Bonds (Salt Bridges): Electrostatic interactions between oppositely charged acidic ($-\text{COO}^-$) and basic ($-\text{NH}_3^+$) side chains.

    • Disulfide Bridges: Strong covalent cross-links formed between the sulfhydryl ($-\text{SH}$) groups of two Cysteine residues ($-\text{CH}_2-\text{S}-\text{S}-\text{CH}_2-$).

  • Protein Domains:

    • Large globular proteins containing more than $200$ amino acid residues typically fold into semi-independent, compact functional units called domains.

    • Examples of Specialized Structural Motifs/Domains:

      • $\text{EF-Hand}$: A $\text{Ca}^{2+}$-binding motif composed of an E helix and an F helix.

      • $\text{C}_2\text{H}_2\text{ Zinc Finger}$: A nucleic acid-binding motif in which a central zinc ion ($\text{Zn}^{2+}$) is coordinated by $2$ Cysteine and $2$ Histidine residues.

      • $\text{Leucine Zipper}$: A dimerization motif formed by interacting $\alpha$-helices containing regularly spaced leucine residues.

• Quaternary Structure:

  • The spatial arrangement and non-covalent/covalent assembly of multiple polypeptide subunits into multimeric functional protein complexes.

  • Multimeric proteins composed of identical sub-units (protomers) are termed oligomers.

  • Most quaternary proteins exhibit allostery, where ligand binding at one subunit induces conformational changes in neighboring subunits.

  • Biological Advantages of Quaternary Structure:

    • Synthesizing smaller individual subunits is more efficient and less prone to translational errors than synthesizing exceptionally long single polypeptide chains.

    • In macromolecular structures like collagen fibers, defective or worn individual subunits can be replaced efficiently.

    • Inter-subunit contacts provide crucial regulatory mechanisms (e.g., cooperativity in substrate/ligand binding).

  • Prototypical Quaternary Assembly: Hemoglobin:

    • Composed of $4$ polypeptide subunits: $2\,\alpha\text{-chains}$ ($141$ residues each) and $2\,\beta\text{-chains}$ ($146$ residues each).

    • Each subunit contains an iron-binding organic cofactor called Heme ($\text{Fe}^{2+}$-protoporphyrin IX), which reversibly binds oxygen ($\text{O}_2$) molecules for transport through the cardiovascular system.

Protein Denaturation and Loss of Structure

• Definition:

  • Denaturation is the unwinding or structural disruption of a protein's innate native secondary, tertiary, or quaternary conformation, resulting in complete loss of biological function without altering the primary amino acid sequence.

• Eight Key Denaturing Agents and Factors:

  • Strong Acids and Bases: Alter the protonation states of ionizable side chains, destroying ionic salt bridges and hydrogen bonds.

  • Organic Solvents: Disrupt internal hydrophobic interactions by competing with nonpolar side chains.

  • Detergents: Amphipathic molecules that disrupt hydrophobic interaction networks within the protein core.

  • Reducing Agents: Cleave covalent disulfide bridges ($-\text{S-S}-$) reducing them back to free sulfhydryl ($-\text{SH}$) groups.

  • Salt Concentration (Ionic Strength): Alters electrostatic shielding and disrupts native ionic networks and protein solubility.

  • Heavy Metal Ions: Coordinate with thiol groups or carboxylates, disrupting disulfide bonds and ionic interactions.

  • Temperature: Elevated thermal energy overcomes weak non-covalent interactions (hydrogen bonds, van der Waals forces).

  • Mechanical Stress: Physical shearing forces (agitation, stirring) disrupt native backbone orientation and hydrophobic folding.

Prion Biology and Pathological Protein Misfolding

• Bovine Spongiform Encephalopathy (BSE / Mad Cow Disease):

  • A fatal epizoonotic neurodegenerative disease occurring in cattle, causing microscopic spongy vacuolation and degeneration of the brain and spinal cord.

  • Incubation Period: Ranges from $30\text{ months}$ to $8\text{ years}$.

  • Peak Onset: Occurs in adult cattle at $4$ to $5\text{ years}$ of age, with all cattle breeds being equally susceptible.

  • Etiology: Research demonstrates that BSE is not caused by a virus, bacterium, protozoan, or fungus.

• Prion Hypothesis and Conformational Conversion:

  • BSE and related transmissible spongiform encephalopathies are caused by infectious misfolded proteins termed Prions.

  • The primary amino acid sequence of the prion protein remains completely identical between normal and pathogenic forms.

  • Conformational Shift Parameters:

    • Normal Cellular Prion Protein ($\text{PrP}^\text{C}$): Soluble structure containing approximately $40\%$ to $43\%\,\alpha\text{-helix}$ content and minimal $3\%\,\beta\text{-sheet}$ content.

    • Pathogenic Infectious Prion ($\text{PrP}^\text{Sc}$ / Scrapie Form): Insoluble aggregate in which the structure undergoes a massive conformational transition to $43\%\,\beta\text{-sheet}$ content and reduced $30\%\,\alpha\text{-helix}$ content.

  • The rich $\beta$-sheet conformation forms insoluble, protease-resistant amyloid fibers that deposit in central nervous system tissue, leading to fatal neurological decay.

Additional Notes

Proteins formed by amide bonds are called peptide bonds

Peptide bonds link amino acids

Proteins 50% dry body weight

Proteins not stored, must be consumed

» Hence recommended daily intake for adults which is 0.8 grams of protein per kilogram of body weight.

— more suited for children because they are still developing so they need more protein for them to build more muscles

» Dietary proteins comes from eating milk and meat

— meat is best way to get daily dose of amino acid

» Complementary foods like rice and legumes combine amino acids

— rice is rich in either methionine or cysteine, which is sulfur containing which is good antioxidant but lacks lysine which is responsible for cognitive development— legumes, on the other hand, like nuts, monggo, and others, are high in lysine but low in methionine, thus by pairing these two food sources, individuals can obtain a more balanced intake of essential amino acids necessary for optimal health.

» Whatever you ate while reviewing, you will likely to remember what you were reviewing if you ate it again

» Nuts improve cognition but lack sulfur amino acids so it does not help precent cancer. So nuts and rice complement each other

» Amino acids contain two functional groups—an amino group and a carboxyl group

» You have to be careful in identifying the amino and carboxyl group because in some structures the amino group is represented by an NH3+ but sometimes its just NH3

» Carboxyl group in some references uses COO- —it loses its H

» The skeletal structure of your amino acid it always has an amino group,a hydrogen and a carboxyl group

» R group will be the one to determine the identity of an amino acid—especially when you are given eight peptide sequence

» Your protein is joined together by a peptide bond—it is a bond exclusively for joining two or more amino acids together

» In the formation of a peptide bond there is loss of water

— later in metabolism discussion you will realize why water is taken away and why would it be returned and where is the returned water came from to reverse the process

»Met and Ethanine is an is an example of peptide bond and it’s one of the eight—its an important neurotransmitter

» You read a peptide sequence from left to right

— you read from amino terminus going to your carboxyl terminus

— that is why you need to identify which is the amino and which is the carbocyte

— you always have to look for amino acid then thats your amino acid 1 and it always have to end with a carboxyl group

— you have your parallel and anti parallel beta sheets

» Eliminate the others so carbon will be left along with R group

» It is quite confusing and challenging if you try to read the ones above because it too is included. So practice to identify the R group as quick as posible

» Sulfur can vanish and brach out into leucine

» Oxytocin vs Vasopressin

— in terms of the three letter abbreviation their only difference is one has isotocine and one has brucene.

— this one has phenylalanine and the other one has arginine but the rest remains the same

» At tertiary level you will see a disulfite bond

— the way this amino acid gets represented in its primal sequence is already in terms of its tertiary structure.

» Tertiary structure is where your proximal residues come in close contact with one another in terms of four different kind of bonds.

— Either it's your van normals or your hydrophobic interaction. You have your hydrogen bonding, you have your ionic bonding or you have your disulfide bridge.

» And remember, your disulfide bridge only happens between only one.

— it only happens with cysteine, because sulfur is on the end of cysteine

— and usually it is next to hydrogen

— when disulfite bond is formed, hydrogen will be gone, it is liberated, the the sulfur atoms bond with each other

* read primary sequence in exam

» only two amino acids are the difference of oxytocin and vasopressin, which have roles in different physiological functions despite their similar structures.

— oxytocin is the love/bonding hormone because it has several functions in the body and brain

— one of the greatest manifstation of a mothers love towards her child

— oxytocin start in childbirth

» childbirth does not involve anesthesia

» osytocin still has function after chilbirth such as lactation

— once lactation phase is over then only oxytocin production witll stop

— once oxytocin production stop, mammary glands will return to original size

» Vasopressin has to survive an episode of diarrhea

— when undergoing diarrhea your body release a lot of water

— if you have diarrhea you cant pee because your vassopressin is in action

— it acts as antidiuretict to prevent severe dehydration—which could kill

» primary structures - you have to familiarized yourself in identification of hormones

— reading is from amino group to carboxilic

» secondary structure is the thermodynamically favorable structure stabilized with hydrogen bonding

— it either forms alpha helix or a beta sheath

» tertiary structure is the 3D sturcture wherein proximal residues come close contact with each other that we cant see in primary structure

» there are four types of bonds thta can interact with our proximal residues

— ionic if metal is involved

— van der waals if alopethic groups are invilved

— hydrogen bonding

— disulfide bridge in case of cysteine

» secondary is linear and tertiary is 3D shape stanilized by hydrogen bonding

— if alpha helix or beta sheets its just secondary if it dormed glocular or fibrous then it is tertiary

» All proteins exist up until tertiary structure but not all exist as quarternary

Assumptions if it is a quartrnary structure:

- protein is too big that it has subunits

- easier to repair the subunit rather than replace the whole protein

» if 2d bond to hydrogen bonding thn you have secondary
» if you have 3d sahpe stabilized by either one of the four electrostatic of attraction then you have tertuary

» if you have complex structure consist of subunits

» we have requirements for a protein to be a quarternary structure

sequence → hydrogen bonding → 3 dimensinal structures → subunits

» hemoglobin is the one respponsible for carrying oxygen throughout the body—carries maximum of eight oxygen

» iron as the central atom is important because it is where osygen attachs to form oxyhemoglobin, facilitating the transport of oxygen from the lungs to tissues.

— iron is also the reason why blood is red thats why iron defiency affects blood

» the same entity with this in plants is chlorophyll—the only difference is central atom

— hemoglobin has iron chlorophyll has magnesium and it is the reason why chlorophyll is color green

— one acts as a oxygen transporter while the other one captures light

» quarternary structure is important because it has subunit so if one gets damaged it can get fixed rather that get thrown away completely

» denaturation is where protei loses its internal structure and if you lose structure then it changes it function

— it is irreversible most of the time

» starting amino acid has diulfide bridges and loses it becoming fenuff but after some time itregenerate disulfide bridge andreturns back to original structure

» people with curly hair have many disulfide bridges

— rebonds purpose is to break disulfide bridge

— thats why rebonds arent permanent and overtime curls returnbecause disulfide bridge regenerates

— new rebonded people cant be wet beacuse hydrogen is missing in formation of disulfide bridge so in contact of hydrogen disulfide bridge will connect again

» there are foods with acids and bases

- kilawit is a dish that is not cooked and just soaked in vinegar for a long time wihich causes denaturation

— wihtout use of heat, just using the reaction of vingar acidity against fish protein

» sayote vs papaya in tinolo

— one has regeneration aged which makes the meat more tender and it is papaya

» food that utilize salt concetration is dainf and tinapa which is sunbathe and sprinkled with salt so it will draw water out

» heavy metal ions in cookinf is putting fork in rice or meat

— they believe putting fork will make the meat softer

» temperature any heat involved

» mechanical stress example is tenderizing meat through pounding or marinating, which helps to break down protein structures and improve texture.

— done by using mallet or poking meat with fork

» something clinical related to mechanical stress is domestic violence

— most victims of domestic violence dont immediately sekk out help because theres factors like fear

— but mechanical stress stay in the body for six month

— dosctors would ask where area were you beaten and they would check the tenderness of muscle—our muscle is made of protein

— not all violence victim have tangible evidence like bruises

» prions are protein that causes misfolding

» secondary level of structure the prions saken

» lambda to alpha

» in the presence of prions some of the alpha indices may be converted into beta sheet

» alpha leratin can be seen in the hairs

— you can be violent without trace of violence by plucking out hair one by one

— you should not grab hair by bundle if you are trying to pull someones hair if you want to inflict maximum damage then grab it one by one

» enzymes are proteins that serves as catalyst

— one of the seven functon of protein is catalyst—and catalys is one of the driving forces of why we have protein in our body

» enzyme is very specific— each enzyme catalyzes certIN reaction FOR A TYPE OF REACTION ONLY

» names of most enzymes end with suffix ase—peptidase: lipase, and amylase

» a cofactor is a metal ion or N ORGnic molecule for the enzyme catalyze reaction to occur

— your sNAD+ is a cofactor or coenzyme that oxidizes lactate to pyruvate with the aid of the enzyme lactate dehydrogen

— lactate formation is anaerobic process

— an example is cramping due to lack of oxygen

— your oxygen goes to krebb cycle

» an enzyme contains an active site that binds the substrate forming an enzyme substrate complex

— substrate is very specific—where active site it only attach there—it has specific area to attach

» once enzyme substrate complex is formed the reaction happen

— once the reaction ends and your products are formed it will be ejected by enzyme

»only when they let go the thing attached to them only then will they be ready to be attached by another

» we have two models for the enzyme substrate model

Lock and Key Model: This model suggests that the enzyme's active site is precisely shaped to fit a specific substrate, similar to a key fitting into a lock.

— in terms of clicnical pharmacology it is when your drugs comes in

— you can have more than one key to open a lock

— medicines mimics the natural substrate

Induced Fit Model: In this model, the enzyme undergoes a conformational change upon substrate binding, allowing for a more snug fit and enhanced catalytic activity.

» an inhibitor bonds the enzyme and alters or destroy the enzyme activity

— the inhibition can either be reversible or irreversible

» non competitive inhibitor binds to the enzyme but not the active sites

» competitive inhibitor looks like the substrate and will race the substrate to the bondig site

» proenzymes are inactive form of an enzyme that can be converted to the active form when needed

— we have many enzymes in body but majority are unactivated

— so when your body needs it, it just cut and becomes an active enzyme

» certain enzymes are present in higher amounts in particular cells

— if the cells structure die the enzyme are releaded into the bloodstream and can be detected

» if alphaline phospilase is elevated then its eithe precursor for liver or bone disease

» for the male population if acid phospatase it might be a trigger for prostate cancer

» drugs that inhibits wht enzymes one example is pinicilinThat inhibits the enzyme that forms the cell walls of bacteriadestroying the bacterium

» we also have ACE or aggravating blood breakig enzyme causing blood vessels to narrow increasing blood pressure

» ADE inhibitors that are given to those with high blodo pressure to preent ACE isynthesis from its typhogen

» HIV virus protease which is an essential enzyme that allows ths virus to make copies of itself

— HIV protease inhibitor interfere with this copy decreaing the virus population in the patient

— now we have modern ways to prevent the rampant progression of HIV

» Latest threat in HIV is nor patients can live a normal life with the right drug counceling and everything

— we have now what we call undettectable—they have HIV but they take care of themselves