BIOCHEM Mod1A Amino Acids and Peptides PDF

BIOCHEMISTRY MODULE AMINO ACIDS AND PEPTIDES...

BIOCHEMISTRY MODULE AMINO ACIDS AND PEPTIDES 1A Dr. Jan David Monzon, DPAAB 08/21/24 Section B LEGEND ▪ 🗨 signalling - hormones and neurotransmitters → Must-know ⚠ 🗨 Lecturer 📖 Book 📄 Previous Trans ▪ 🗨 how cells would communicate with each other These many different roles and functions can be OUTLINE ▪ 📖 traced to how varied their structures can be. Certain microorganisms secrete free D-amino acids, or peptides that may contain both D- and 🗨 “In progress” L-α-amino acids. ○ gives rise to harmony of the many LEARNING OBJECTIVES processes in the body to keep us alive → At the end of the lecture, the student should be able to: Have a basic understanding of amino acids structure and ○ 📖organ systems Amino reabsorbed acids in are almost totally the proximal tubule, nomenclature conserving them for protein synthesis and Understand the different ways amino acids are classified other vital functions. ○ e.g. structural and chemical properties (polar vs. non-polar, charged, acidic vs. basic, etc); nutritional and metabolic characteristics Cite specific characteristics and properties of amino acids and correlate with their physiologic significance Understand notable clinical correlations Understand the different levels or tiers of peptide structures Differentiate the different peptide-containing complex molecules Understand how amino acids respond to perturbances in homeostasis (change in pH, temperature) ○ protonation and deprotonation FIGURE 1. Formation of proteins from amino acids 🗨 OVERVIEW OF AMINO ACIDS Amino acids are the building blocks of protein ○ 🗨 Protein is life processes that define life are rooted in cellular activities where much of the work is performed by ○ The bond that keeps the amino acids together to form the peptide is called the peptide bond. ○ 📖 proteins L-α-Amino acids provide the monomer units of the long polypeptide chains of proteins. In addition, these amino acids and their derivatives participate in such diverse cellular functions as nerve transmission and the biosynthesis of porphyrins, purines, pyrimidines, and ○ 🗨 urea. gene expression, the blueprint of life, is the process ○ 📖 of protein production Humans and other higher animals cannot synthesize 10 of the L-α-amino acids present in proteins in amounts adequate to support infant growth or to maintain adult health. FIGURE 2. General structure of amino acids ○ structural: architecture of cells and tissues, which are the building blocks of the organs that make up the All amino acids are composed of an amino group, carboxyl organ systems and ultimately, the organism 📖 group, and a unique side chain attached to a central ○ functional: enzymes, receptors, carrier proteins, etc. carbon. ▪ The neuroendocrine system employs short polymers of amino acids called peptides as ○ Central Carbon (Cα) hormones, hormone-releasing factors, ▪ Also called the alpha - carbon 🗨 neuromodulators, and neurotransmitters. ○ Amino Group (-NH2) (-NH3+ if not attached) ▪ enzymes catalyze the majority of cellular ▪ Consists of nitrogen with hydrogen molecules 🗨 attached to it. processes and reactions for growth and survival ▪ enzymes are the most focused or studied type of protein in this course Page 1 of 21  AMINO ACIDS & PEPTIDES N-terminus of the next amino acid, a.ka. Peptide Bond → Side chain → C-terminus (Carboxyl Group) In this example, peptide bonds are joining Glycine, Serine, and Valine together. The carboxyl group is connected to the amino group. Peptide bonds connect two amino acids together. ○ These are COVALENT BONDS between the carboxyl group of one amino acid, and the amino group of 📖 another. Once bonded, these groups are no longer available for chemical reaction except for hydrogen bond or ionic bond formation (e.g., stabilizing protein structure) FIGURE 3. General structure of amino acids ⚠ Peptide bonds define the SEQUENCE of amino acids in a peptide or protein and thus, its primary structure Carboxyl Group (-COOH) ⚠ Proteolysis - breakdown of peptide bonds. When ○ Carboxyl group that is bound to the alpha-carbon → proteolytic cleavage occurs, the primary structure is Carboxylic acid altered and subsequently alters the protein’s higher R Group (Side Chain) order structures (secondary, tertiary, and quaternary) as ○ Also known as the functional group well. ○ 🗨 ○ What makes each amino acid unique; Variable Can be virtually non-existent in GLYCINE. Glycine is the tiniest amino acid and has no side chain. It only contains the basic structure of the amino acids which are the Amino group and the Carboxyl group). FIGURE 6. Nomenclature of standard 🗨 HOW CAN WE CLASSIFY AMINO ACIDS Our ultimate goal is to understand the amino acids’ roles so far as homeostasis is concerned. ○ to relay the structures and characteristics of amino acids, and appreciate the bigger FIGURE 4. Zwitterionic form of amino acids picture– how these parameters ultimately 📖 At physiologic pH (∼7.4), an amino acid typically exists in a zwitterionic form, where the molecule has both a positive fulfill certain roles that come together in maintaining homeostasis. charge on the amino group and a negative charge on the carboxyl group, thus is electrically neutral. Here, the carboxyl STRUCTURAL AND CHEMICAL PROPERTIES group of an amino acid is dissociated, forming the negatively General Structure charged carboxylate ion (−COO−), and the amino group is ○ Aliphatic - linear structure protonated (−NH3+) ○ Aromatic - cyclical, big, bulky, closed chain, usually hexagon (benzene ring). FIGURE 5. Peptide bonds in between glycine, serine, and FIGURE 7. Structural classification of Amino Acids valine 🗨 Structural sequence in FIGURE X: ○ N-terminus (Amino Group) → Side Chain → C-terminus (Carboxyl Group) covalently bonded to the Page 2 of 21  AMINO ACIDS & PEPTIDES PRACTICAL OR OPERATIONAL GROUPINGS Polarity ○ Polar - possesses side chains that are able 🗨 ( Termed as practical because they are loose and are not bound to any nomenclature. They are also practical because to react with solids in water. they are associated with their functions) side chain that has an OH, Small and compact sulfhydryl, amino group, carboxyl ○ AAs that are very simple, very compact group made it polar. They are able ○ Characteristics of these AAs can form to react in water “kinks”, or “bends” in a polypeptide chain. ○ Nonpolar - opposite of polar, some are ○ Examples are Glycine (Gly) and Proline outright hydrophobic and repels water, found (Pro) in inner surfaces or folds of a protein for ▪ Glycine (Gly) is the tiniest amino they are repelled by water. acid, providing variation in the Solubility in Water uniformity of chain. ○ Hydrophilic - dissolves well in water ▪ Gly is also the very important building block in forming Collagen ○ Hydrophobic - insoluble in water, relatively Sulfur-containing less soluble in blood, but lipid-soluble (mixes ○ AAs that contains sulfidal group with compounds that are fat in nature). ○ Examples are Cysteine (Cys) and Nonpolar and hydrophobic amino acids tend to be Methionine (Met) found in the inner surfaces or inner folds of a protein ▪ Cysteine sulfidal group has clinical away from the surrounding plasma or blood. significance, while Methionine ○ They are repelled by water. provides the sulfur atom for Cys. Polar and Hydrophilic amino acids are further divided Branched-chain Amino Acids (BCAAs) into: ○ ⚠ Polar: Either charged or uncharged ○ 🗨 e.g. Valine, Leucine, Isoleucine Plays a vital role in neuronal 🗨 ⚠ Charged: Either acidic or basic metabolism. They are the major amino acid They can either have negative charge or a positive charge in ▪ 🗨 food for the brain. Neurons – makes use of either glucose or ketone bodies to physiologic pH and that makes generate energy. But sometimes them either acidic or basic. glucose runs out of glucose that is immediately available. So, our body instead breaks down BCAAs into 🗨 glucose and ketone bodies. ○ All 3 of them acts as energy reserves for 🗨 the brain. ○ Forms a big chunk of lean muscle mass. This is why there are BCAA supplements available for gaining muscle mass. Large, aromatic ○ “Chunky” amino acids ○ Tryptophan, Tyrosine, and Histidine ○ Cyclic groups POLARITY AND HYDROPHOBICITY 🗨 Hydrophobic amino acids tend to be found in the interior of typical plasma protein FIGURE 8. Amino acids classification 🗨These are must-knows but we should not memorize 🗨 As the blood flows through the body, the protein travels along with it and the protein is exposed to the surrounding them. Rather, approach them through characterizing them because they stick to us knowing what is special about elements: other cells, different molecules, compounds, acids 🗨 them. and other proteins By focusing on what is unique on a certain group, it will be easier to remember Page 3 of 21  AMINO ACIDS & PEPTIDES environment. By occupying the interior of the folded protein, these nonpolar R groups help give proteins their three-dimensional shape. ▪ For proteins located in a hydrophobic environment, such as within the hydrophobic core of a phospholipid membrane, nonpolar R groups are found on the outside surface of the protein, interacting with the lipid environment. ⚠ Clusters of isoleucine, leucine, and valine side chains (nonpolar AA) define cores of stability in high-energy 🩺 states of globular proteins. Sickle cell anemia, a disease that causes red blood cells to become sickle shaped rather than disc shaped, results FIGURE 9. Hydrophilic and hydrophobic amino acids from the replacement of polar glutamate with nonpolar 🗨 Interior Compact 🩺 valine at the sixth position in the β subunit of hemoglobin A. In cystic fibrosis, secretions from organs contain significantly less water because the transporter protein is Hydrophobic amino acids can be found in this area, misfolded. The most common mutation is a 3-bp deletion which help stabilize the structure while avoiding being that results in the loss of phenylalanine at position 508, in contact with the environment which weakens hydrophobic interactions in the Imagine it is a sphere with folds and inside the folds transporter leading to some degree of misfolding. are the hydrophobic amino acids ⚠ LDL and HDL are lipoproteins responsible for transporting ○ Such as Gly, Phe, Val, Leu various lipids and cholesterol from the liver to tissues and 🗨 Exterior More exposed to the surrounding environment back. The protein component of this molecule is called apoprotein and is responsible for interacting with tissue receptors. These apoprotein most likely possess polar Contains polar amino acids amino acids in its interactive sites. The polar ends of every ○ Have reactive side chains phospholipid molecule in a lipoprotein face outward to ○ Such as Glu, Asp, Tyr, Ser interact with water, which can then be transported through 📖 Nonpolar AA: has an “oily” or lipid like property that promotes hydrophobic interactions. the blood. Polar amino acids are usually active in enzyme catalysis and are key components of receptors. FIGURE 11. Polar amino acids NUTRITIONAL CLASSIFICATION FIGURE 10. Location of nonpolar amino acids in soluble and Non-essential membrane proteins ○ Made within the body. ○ i.e. Collagen is made up of Lysine, Glycine, and 📖 ▪ Location in proteins: For proteins found in polar environments such as proline. ○ Glycine and proline are made in the body, therefore aqueous solutions, the side chains of nonpolar amino they are non-essential amino acids. acids tend to cluster together in the interior of the Essential: protein. This phenomenon is known as the ○ Must be taken up through one’s diet. hydrophobic effect and is the result of the ○ The body does not have the enzymatic machinery to hydrophobicity of the nonpolar R groups, which act produce these amino acids. much like droplets of oil that coalesce in an aqueous Page 4 of 21  AMINO ACIDS & PEPTIDES The distinction between nutritionally essential amino acids o composed of multiple polypeptides: sub-units (AA) and those which are considered non essential ▪ Singular proteins - singular/one entire unit ○ There is actually a middle ground, the so called ▪ Several (2 or more) units/sub-units conditional essential but that's something we'll take up Primary later this year o basic linear sequence of amino acids Essential AA - AA that the body cannot synthesize from o how they are arranged in a line scratch; must be taken up through one’s diet o from the first amino acid → one end: N-terminus ○ the body does not have the enzymatic machinery to (amino terminus) all the way to the other end: produce these AA, thus for us to acquire them, they C-terminus (carboxyl terminus), or vice versa have to be part of what we eat o Example: 10 amino acids arranged in a line ○ Tried and tested mnemonic for essential AAs (Private o When asked what structure, amino acids are aligned in Tim Hall): a sequence like: Each letter stands for an essential AA ▪ Alanine-Valine-Tryptophan-Tyrosine-Tyrosine-Alanin P.V.T. - phenylalanine, valine, threonine e T.I.M. - tryptophan, isoleucine, methionine Secondary H.A.L.L. - histidine, arginine, leucine, lysine o Alpha-helices ○ Arginine can be produced in the body but to a very limited ▪ Spiral or helix structure capacity o Beta-pleated sheets ○ Reason why arginine is conditionally essential ▪ Flat layer like a sheet ○ Much better to ensure that we get enough arginine from o In reality, Primary structures forms these secondary what we eat because the body won't survive if you force it structures as spiral or sheets to synthesize arginine from scratch all the time. ▪ Flat layer like a sheet Tertiary METABOLIC CLASSIFICATION o 3D conformation o Not just a helix or a sheet, they can fold over each *NO AUDIO* other. which type of fuel source can the amino acid be converted o There are different bonds or ways that an amino acid to? can ultimately fold into its 3D formation. ○ both glucogenic and ketogenic o Involves more complex structures ▪ isoleucine, phenylalanine, tyrosine, tryptophan, ▪ Such as: several helices joined together and there threonine (“IPTTT”) will be a kink in between. ○ exclusively ketogenic Quaternary ▪ leucine, lysine (“LL”) Applicable to proteins with multiple ○ exclusively glucogenic subunits/chains/polypeptides. ▪ all the rest o First three levels are applicable to all proteins. 🗨 LEVELS OF PEPTIDE STRUCTURES Dr. Jan David C. Monzon Amino acids → Peptides/Polypeptides → Proteins o Tells how these different subunits interact with each other to arrive at the final ultimate conformation that is the quaternary structure. o Amino acids: ▪ building blocks of peptides; joined by peptide bonds o Polypeptides: ▪ from small peptides, you can have longer peptides: polypeptides o Proteins: ▪ polypeptides form functional proteins SUMMARY OF THE DIFFERENT STRUCTURAL FIGURE 12. Example of a Primary Structure LEVELS / TIERS Primary Each amino acid is connected by a peptide bond. o Basic linear sequence of amino acids Basically, the primary structure shows you the linear Secondary sequence of amino acids o Alpha-helices, beta pleated sheets o ⚠ In reality, it is not this way (in space). A Tertiary sequence of amino acids can bend and form 🗨 o 3D conformation (folds, domains) Dr. Jan David C. Monzon Polypeptide various structures, including folds and loops. interchangeable w/ the term protein, because most proteins are polypeptides long sequence of amino acids joined together Proteins Page 5 of 21  AMINO ACIDS & PEPTIDES ⚠ Take note of how the alpha-helices and beta-pleated sheets appear. Alpha-helices o Look like they are twisted into a coil when imagined in a 3D conformation Beta-pleated sheets o See how individual amino acids with each of their side chains are arranged side by side With each of the side chains are arranged side by side and they are stabilized in between by these bonds Bonds that stabilize the primary structure o Peptide bonds FIGURE 13. Overview of Protein Structures Bonds that stabilize the secondary structure o Hydrogen bonds The image above shows how the primary structure differs from the other structural levels Secondary o The primary structure can be arranged in a spiral or beta pleated sheets ▪ In the beta pleated sheets, there is a linear arrangement of amino acids that are antiparallel to each other (opposite direction) Tertiary o 3D linear sequence o Like a ball in space o Many of the plasma proteins, like those dissolved in the blood, have this shape Quaternary Structure o Combination of tertiary structures o In the image, it is seen that the tertiary structure and its done four times over FIGURE 15. Secondary structure showing the hydrogen bonds o Other proteins, can have less or more subunits Another diagram showing those hydrogen bonds that ▪ Receptors or transporters found on stabilize the alpha helices and the beta pleated sheets. the cell membrane can have 5 or 🗨 SUPERSECONDARY STRUCTURES more subunits o The subunits can be taken apart Additional Information (good to know) o While the subunits are individually o A level in between secondary and tertiary levels, is considered polypeptides, in reality they super secondary structures, it's like 2.5. It is an would form one whole arrangement expanded form of the alpha helices where there is ▪ There are several interactions that more complex arrangements of the alpha helices and exist between the subunits and it beta pleated sheets. helps with stability. SECONDARY STRUCTURE FIGURE 14. Secondary Structure FIGURE 16. Supersecondary structures Page 6 of 21  AMINO ACIDS & PEPTIDES ALPHA HELIX MOTIFS TERTIARY STRUCTURE 🗨 Helix-turn-helix: the turn may be caused by the presence of a proline residue (in the non-helix region of Tertiary structure defines the 3D or three-dimensional conformation of the protein. the motif) because of the amino acid’s unique structure. o Tertiary for thre. o Proline is the only amino acid that has its side chain The various interactions stabilize the 3D conformation continued to its amino group which causes kink/bend (hydrogen bonds, ionic bonds, disulfide bonds, to the polypeptide structure. hydrophobic interactions, Van Der Waals Forces) Amino acids can form hydrogen bonds, just like in secondary structures. o THE DIFFERENCE: In the tertiary structure, the hydrogen bonds form between the side chains of the amino acids, instead of between the amino groups in the carboxylic acid groups. o Therefore, in this case, one amino acid located in the area of the fold is bonded through a hydrogen bond FIGURE 17. Structure of proline with a distant amino acid located on the other side of the fold. Helix-loop-helix Ionic bonds occur between two amino acids with Coiled-coil opposite charges. BETA MOTIFS o For example, an acidic amino acid like aspartate or glutamate, which is negatively charged, can form 📖 β hairpin Greek key: Formed when a polypeptide chain doubles back on itself. an ionic bond with a basic, positively charged amino acid like histidine, lysine, or arginine. o This ionic bond is also called a salt bridge because, similar to how salt is made from two oppositely charged compounds that form a neutral compound, the bond between these amino acids creates a stable o 🗨connection. Or.. so when they form this bond, it is synonymous to a salt bridge. Similarly, disulfide bonds are formed between two sulfhydryl groups, which are part of cysteine amino acids. o When a disulfide bond forms, it can link two cysteine residues that may be located far apart in the actual sequence of a protein. o This bond brings together different parts of the protein, effectively stabilizing its three-dimensional structure by holding these distant regions close to FIGURE 18. Beta barrel each other. β-barrel:📖 created when β-sheets are extensive enough to fold back on themselves. Hydrophobic Interaction, a special type of interaction, may occur between two hydrophobic amino acids o This is applicable for nonpolar amino acids. ALPHA + BETA MOTIFS 📖 o For example, when valine comes into contact with βαβ: two parallel strands of β-sheets are another nonpolar amino acid. 🗨 connected by a stretch of α-helix. Zinc Finger: important structure that interacts with the DNA, and it is what makes the process transcription o In this case, no true bond or covalent bond formed. o However, because the hydrophobic residues tend to cluster together and repel water, they create a optimal. The transript (RNA) is then translated into a stabilizing force that helps the protein fold in a specific protein. o Transcription: DNA to RNA area, contributing to its overall stability. 🗨 o Translation: RNA to protein Finally, the Van Der Waals Forces, which are relatively IMAGINE: Deficiency of Zinc (a mineral) = less than weaker forces or interactions that also contribute to the optimal expression of genes, protein synthesis or stability of the proteins. everything becomes lower. Hydrogen bonds both contribute to the secondary and the o Reason: Protein is life tertiary structures. Page 7 of 21  AMINO ACIDS & PEPTIDES Because of those 3D folding, 3D confirmation that is In Figure 20, we have collagen representing the fibrous formed we get (2) two prototypical structures from the protein and we have hemoglobin representing the globin interaction of the different amino acids. or the globular protein. You can have a collection of helices. In this case (see left What makes these two proteins unique is they are made part of the picture above) there are 3 of them, they are up of several (more than one) polypeptides. You have (3) wound together and they form Fibrous Proteins. three individual linear proteins for collagen and they’re just o You can imagine that once they are tightly wound coiled together forming this single collagen fiber but it’s together they form like a fiber structure that’s why it’s actually (3) three peptide chains. fibrous. Collagen Globular proteins (globins) ○ Composed of 3 individual linear proteins or peptide o You can also have a protein where the different chains. helices from the secondary structure are folded (right ○ Chains are wound together or cross-linked to form a part of the picture above) or kinked at a certain triple helix and achieve its optimal tensile strength. location ultimately causing them to form a compact ○ Found in bones, cartilage, and much of the circular or round structure. connective tissues that lend support and structural 📖 integrity to other tissues. ○ Initially synthesized as a larger precursor polypeptide (procollagen) ○ Important Components of Collagen: 1. Glycine Smallest of all the amino acids and has a compact structure Fills in multiple gaps Creates folds to allow the triple helix structure to be formed. 2. Lysine Relatively long and has a linear structure Forms the cross-links (acts like ‘scaffolding’) which strengthen the 3 chains of collagen. Hemoglobin FIGURE 19. Fibrous and globular proteins ○ Composed of 4 globular subunits, namely 2 α-chains and 2 β-chains, which are responsible for the QUATERNARY STRUCTURE transport of O2 and CO2. Defines how multiple peptide subunits organize to form a single functional protein and achieve a stable 3D OVERVIEW OF PROTEIN STRUCTURES Primary Protein Structure conformation. 📖 ○ Linear sequence of a chain of amino acids Present in proteins made up of 2 or more polypeptide ○ Stabilized by covalent peptide bonds, whereas chains. higher orders of structure are stabilized by weak forces—multiple hydrogen bonds, salt (electrostatic) bonds, and association of hydrophobic R groups. Secondary Protein Structure ○ Local folding of the polypeptide chain into helices or 📖 sheets (i.e. α-helix or β-pleated sheet) ○ The folding of short (3-30 residue) contiguous segments of polypeptide into geometrically ordered units Tertiary Protein Structure ○ 3D conformation or folding pattern of a protein due to 📖 side chain interactions ○ The assembly of secondary structural units into 📖 larger functional units FIGURE 20. Quaternary structure ○ Concerns the relationships between secondary and other small structural units to form functional protein domains and polypeptide monomers Page 8 of 21  AMINO ACIDS & PEPTIDES ○ NOTE: Do not forget the different types of Example: In most cases of Duchenne Muscular interactions that stabilize tertiary protein structures Dystrophy, the protein Dystrophin cannot be Quaternary Protein Structure encoded at all or encoded, but the resulting ○ Protein consisting of more than one amino acid ○ 📖 chain/subunit The number and types of polypeptide units of 📖 protein is abnormally short. Altered forms of dystrophin to support the formation of functionally competent oligomeric proteins and their spatial arrangement synaptic junctions ○ Trinucleotide repeat Repeated addition of a sequence of 3 nucleotides encoding for a single amino acid to the tail of the growing polypeptide chain Example: In Huntington’s disease, the protein Huntingtin is elongated with senseless repeats of 3 nucleotides (trinucleotide) ○ Silent mutation FIGURE 21. Protein structure overview A change in the primary structure, but does not 🗨 REMEMBER: All proteins have a primary, secondary, and affect the function of the protein significantly (either no changes at all or no significant decline tertiary structure, but only those with multiple subunits have in function) a quaternary structure. The patient is asymptomatic and has an ALTERATIONS IN PEPTIDE STRUCTURE underlying mutation, but the patient did not show Many diseases can be traced to genetic mutations which clinical manifestations. first alter the DNA. This subsequently leads to an altered ○ A mutation can also occur if peptide bonds, which RNA transcript, ultimately changing or altering the protein connect amino acids and define the primary structure or peptide product after translation. of a protein, are broken or destroyed, leading to a loss These abnormalities can be traced to problems affecting of the protein's primary structure. the primary structure of proteins. Mutations or problems in DNA or genetic code (even just SECONDARY STRUCTURE ALTERATION changing one amino acid in the sequence) can lead to Proteins are made up of a combination of alpha helices changes in protein function. and beta-pleated sheets. Certain arrangements of these sheets determine the structure and function of the PRIMARY STRUCTURE ALTERATION proteins. Makes the protein dysfunctional. Components of secondary structures: Examples: Example: ○ Point mutations Exchange or swapping of an amino acid Example: Sickle Cell Anemia, Glutamate is 📖 ○ Prion Diseases Recognized as protein conformation diseases; transmitted by altering the conformation of proteins 📖 replaced by Valine A 6-sequence codon of the beta chain A condition wherein normal alpha-helices in proteins are replaced by abnormal beta-pleated changed from GAG in the normal gene to sheets. GTC in the sickle cell gene that results to the These sheets pile up and fit snugly together, substitution of glutamate by valine forming aggregates in neurons (in brain tissue). ○ Deletion/insertion mutations Since the neurons can't remove them, it leads to Creates shorter or longer proteins Example: In Cystic Fibrosis, Phenylalanine is 📖 rapid neurological decline. Can be infectious, genetic, or sporadic with 📖 deleted. Cystic Fibrosis (CF) is a recessive no viral or bacterial gene found in the pathological prion protein genetic disorder common in America and 📖 Europe Mutation in the gene encoding for cystic 📖 ○ Creutzfeldt-Jakob Disease A variant form of the same disease affects younger patients which causes psychiatric and fibrosis transmembrane protein (CFTR) behavioral disorders ○ Truncations Massive deletion or shortening of a normally long or large protein Page 9 of 21  AMINO ACIDS & PEPTIDES ○ Bovine Spongiform Encephalopathy (Mad Cow Disease) 📖 Prions are recognized as protein conformational diseases ○ Kuru Happens in weeks to months, then the Acquired from the consumption of brain tissue as patient dies part of ritual ceremonies in Papua New Guinea Alzheimer’s disease and other dementias, the pathophysiology/course of these conditions can TERTIARY STRUCTURE ALTERATION Disruption of the interactions that define tertiary 📖 take up to a decade Prominent feature is the refolding or 📖 structures leads to the misfolding of proteins misfolding of B-amyloid proteins ○ Alters or disrupts normal function or structural integrity Levels of B-amyloid are elevated, and of proteins undergo a conformational transformation ○ Different from denaturation that results from the from a soluble alpha-helix to a Beta-sheet, 🗨 📖 destruction or dissolution of peptide bonds making it prone to self-aggregation When you have the tertiary level, you have the 3D Apolipoprotein E is implicated as a structure/conformation potential mediator ○ There are several interactions that define this 3D structure of the protein QUATERNARY STRUCTURE ALTERATION ○ Tertiary structure can be altered if the interactions Disrupted interactions that stabilize quaternary structure 🗨 that define the structure are altered: can lead to a loss of function of that protein. Change or destroy the disulfide bonds PUT A PIN ON THIS CONCEPT FOR NOW Create new salt bridges, or ○ Disruption of the tertiary structure of proteins can lead Disrupt the hydrogen bonds, 📖 to decline of complete loss of function Disrupt hydrophobic interactions, and so on. 📖 Best known defect in collagen synthesis is Scurvy REMEMBER: We are talking about the Due to the dietary deficiency of vitamin C, which interactions that happen at the tertiary level, 📖 is required by prolyl and lysyl hydrolases this is different from the Decreased number of hydroxyproline and denaturation/dissolution of peptide bonds hydroxylysine undermines the conformational stability (which happens at the primary structure) 📖 of the collagen fibers NORMALLY, misfolded proteins are tagged for Bleeding gums, swelling joints, poor wound 🗨 degradation When you have abnormally/misfolded protein arising 📖 healing, and even death 📖 Menkes syndrome from disruptions of interactions, the cells are able to get rid Kinky hair and growth retardation of them Deficiency of copper, which is required by lysyl 📖 ○ Example: the neurons can attempt to get rid of those oxidase abnormally folded proteins Catalyzes the formation of cross-links that 📖 It is possible for cells to get rid of any abnormally strengthen the collagen fibers folded protein Genetic disorders of collagen biosynthesis There are mechanisms for disposing of those include osteogenesis imperfecta, characterized 📖 potentially harmful, injurious, not functional by fragile bones 📖 misfolded proteins. Ehlers-Danlos Syndrome ○ However, they pile up too rapidly which results in Group of connective tissue disorders that involve 📖 neurologic decline, as neurons are overwhelmed by impaired integrity of supporting structures how fast these abnormal β-pleated sheets containing Results in mobile joints and skin abnormalities proteins stack up 🗨 They may accumulate within cells and surrounding tissues PROTEINS FUNCTION AS pH BUFFERS forming insoluble aggregates that cause cell injury and Homeostasis eventually, cell death. ○ Cells try to keep everything normal ○ Forms a really big aggregate, and then cell death can ○ How the body, different tissues, organs, and organ ensue. systems interact to keep everything normal to sustain Same outcome with prion disease in which you get neurodegenerative diseases Presented in a more gradual or protracted 🗨 life. One of the very important parameters that is critical to survival is the blood pH. course like brain diseases Page 10 of 21  AMINO ACIDS & PEPTIDES ○ Keeping this variable within the normal limit is crucial no for us to survive TABLE 2. Characteristics of amino acids across pH levels REMEMBER: proteins act as pH buffers ○ Owing to their structure, amino acids through their pH Level Characteristics COOH/COO- (carboxyl) and NH3+/NH2 (amino) 🗨 groups can aid in acid-base balance. low pH environment ○ acidic environment has ○ REMEMBER: They possess the carboxyl groups (pH < 2.09) many hydrogen ions. and the amino groups Fully Protonated ○ Side groups that are bound Aid in acid-base balance, by single bonds have a Accomplished through the process of proton on it. protonation and deprotonation ○ Ex. Gastric Mucosa ○ Some functional groups (R-Groups) role in buffering ▪ OH and NH3 have a process: positive charge, they Acidic - Aspartate and Glutamate have proton bound to them (They are all Basic - Histidine, Arginine, Lysine protonated) COOH/COO- and NH3+/ NH2 groups ○ Carboxyl and Amino group respectively. ○ These are all present in amino acids. ○ acidic environment has ○ aid in Acid-Base Balance less low pH less hydrogen ions. environment ○ Zwitterion TABLE 1. pH of amino acids (pH = 2.98) ▪ Ionized yet net neutral Not Fully Protonated Amino Acid Charge/pH molecules due to equal numbers of + and - Aspartate & Glutamate Acidic charged groups. ○ Ex. Vaginal Mucosa Histidine, Arginine, & Basic ○ From low to a higher pH Glutamate level, one hydrogen ion was released making it O- ○ Those that are charged whether Acidic or Basic possess a side chains which: slightly basic pH ○ alkaline environment, - play a big role in the buffering process. environment lacking in hydrogen ions. - is charged, whether neutral, positive, or negative. (pH < 9.82) ○ donated protons Deprotonated ○ pH < 9.82 (can mirror PROTONATION AND DEPROTONATION physiological pH [7.35 - 7.45]) R-group of amino acids can: ○ Donate or release (deprotonation) protons very basic pH ○ alkaline environment, ○ Bind or accept (protonation) protons (hydrogen ions) environment almost no free hydrogen ▪ depending on the ambient pH or the environment. (pH > 9.82) ions. Environment Fully Deprotonated ○ gave everything ○ Acidic environment = amino acids bind the excess H+ ○ H3N+ -> H2N ions (protonation). ▪ Further deprotonation ○ Alkaline environment = amino acids release H+ ions is expected to happen to neutralize the OH- groups forming water. as the environment is ○ getting more Alkaline (Less hydrogen ions in the environment) As the environment gets more alkaline = less and less H+ ions. FIGURE 22. Amino acid across different pH levels Buffering Function ○ The released H+ ions will now go to the blood or its surrounding environment. Page 11 of 21  AMINO ACIDS & PEPTIDES ○ In a very basic or alkaline environment, the amino acids IMAGINE: Think of this figure as an acidic blood or a patient in will fulfill its buffering function by releasing H+ ions. acidosis. To buffer the excess hydrogen ions around, the Basic → Acidic environment = the different groups will amino acids in the protein will become protonated. become protonated because they accept H+ ions. ○ The hydrogen ions will be taken up or Because they can accept or donate protons, bound to the different amino acids. amino acids can serve as a buffer in aqueous ○ The amino acids are all contributing to the solution. pH buffering. In contrast, if the medium/environment is alkaline, PROTONATION & DEPROTONATION OF AMINO the proteins will be deprotonated. ○ The hydrogen ions bound to the many GROUPS different amino acids found in a singular Protonation protein will be released to the environment. ○ Happens in Relatively or Highly Acidic Environments / ○ This results in a change in the protein's Mediums structure and function. ▪ Where H+ ions are abundant ○ The protein may become more or less ○ The Amino group (NH2) will then bind another soluble, depending on the specific amino Hydrogen ion to form NH3+ acids involved. ▪ Then it becomes positively charged..in contrast.. Two important proteins that contribute a lot to the buffering process: Deprotonation Hemoglobin ○ Happens in Relatively Alkaline Mediums ○ Possesses Histidine residues which are the ○ The amino group will release the extra proton primary buffers of blood pH. Histidine is able ▪ From NH3+ to NH2 to get either protonated or deprotonated easily. PROTONATION & DEPROTONATION OF ○ Found in red blood cells and can respond CARBOXYL GROUP almost instantly whenever there are Protonation perturbances to the plasma pH or the blood ○ From COO- it turns into COOH pH. ○ COOH is already present in the Gastric Mucosa ▪ a highly acidic medium..in contrast.. Deprotonation ○ Happens in Relatively Alkaline Mediums ○ The Carboxyl group will release the extra proton / H+ ▪ This process buffers or covers the relative lack of hydrogen ions in the alkaline environment. From a larger scale, the protonation and deprotonation mechanisms function as a whole pH buffer. they are either binding the hydrogen ion or releasing the hydrogen ion. FIGURE 24. Protonated and Deprotonated Histidine Histidine is unique because the pKa of its side chain is near 7. At pH 7 a significant fraction of histidines have a positive charge: ○ 9% of side chains are protonated (+charge) ○ 91% of side chains are not protonated (no charge) Histidine residues are the primary or first-line buffer because it can go from either protonated to FIGURE 23. Plasma Protein floating in a Milieu surrounded by deprotonated state and vice versa. Protons pKa = 6.00 Page 12 of 21  AMINO ACIDS & PEPTIDES ○ The pH value wherein it can stay in the ○ Progressive protein dysfunction in various middle state (protonation and deprotonation) tissues ultimately lead to multiple organ failure Albumin ○ Example: Severe sepsis/septic shock lead to ○ Found in blood plasma metabolic acidosis → protonation of amino ○ Albumin and other plasma proteins also acids → disruption of existing hydrogen buffer blood pH owing to their numerous bonds → various proteins become amino acid residues which can bind or dysfunctional release H+ / protons depending on the In patients who are suffering from heart attack or when ambient pH. there is loss of too much blood, their tissues are ○ They can also respond readily to changes in generating plenty of lactic acid due to lack of oxygen to the blood pH due to its high molecular weight be used. which signifies its abundant amino acid While the patient is in acidosis, the different proteins residues that can all participate in the become protonated which disrupts their structure and thus protonation and deprotonation processes. it can lead to loss of contractility in particular to proteins in the heart and that is why the heart further weakens in such 📖 CHANGE OF pH IN PROTEINS situations. ○ e.g. proteins in the heart lose their contractility, Compounds that contain O or N can serve as numerous enzymes are no longer able to function, hydrogen bond donors and/or acceptors, which misfolded receptors are no longer able to bind ligands makes protein (composed of C, H, O, N) a candidate → cell-to-cell communication becomes impaired → AGAIN, it is not just one organ that is affected. 🗨 for such a role. ○ Proteins found in the white blood cells, which respond Changes in the ambient pH ultimately alter to infections, can also be damaged or sub-optimal. hydrogen bonding between amino acids (building (IMAGINE: What will happen to the response if the blocks of protein) → structural then functional patient who is critically ill happens to be in septic changes The process of protonation and deprotonation alter hydrogen ions present in the functional group of 🗨 shock?) All these scenarios that can alter the pH among many amino acids in the carboxylic group and the amino others, it’s not just pH, you can have temperature, group (whichever participating relative to the pH) other parameters that can change – all of this has the If protein is releasing or binding with H ions, hydrogen potential to ultimately affect the molecular structure of bonds can be disrupted thus forming new bonds and what makes up life (i.e., tissues, organs, organ disrupting old ones. systems, etc.). This change may signify either a decline or loss of It is like a double edged sword. It is quite ironic as it 🗨 the protein’s function. goes both ways. ○ While our amino acids can respond to This reaction (change in pH) may be good for changes in the pH by providing a buffering proteins that act as buffers (e.g. albumin and effect, other proteins will suffer when such histidine) however, it may have a negative effect on changes in the pH become too much to the proteins that are not designed to become buffers point that their structure and function is (IMAGINE: proteins in tissues and supporting already affected. structures in cells losing their functions due to change This leads to in pH and release/bind of H ions) Ultimately leading to LOSS OF HOMEOSTASIS Changes in pH also alter the H bonds that stabilize ○ This is why we get multiple organ failure as a the amino acids in tertiary and secondary complication of: structures of proteins. Septic shock Severe shock DISRUPTION OF H-BONDS People critically ill for whatever reason When we disrupt the hydrogen bonds in response to Example: acidosis or alkalosis, it can lead to protein structural Trauma changes, affecting proteins everywhere in the body which Infection are exposed to those changes in the blood pH or Suffering from cancer malignancy (stage environment. 4) ○ In critically ill patients, this happens throughout the Somebody who has just undergone body (across different organ systems) major surgery Page 13 of 21  AMINO ACIDS & PEPTIDES Someone who has bled a lot in the operating table. The pH of that patient’s blood can fluctuate and unfortunately, this causes so many little changes that add AMINO ACID AS AN ANTIOXIDANT up; it is like dying from a thousand cuts. GLUTATHIONE This leads to eventual DEATH major antioxidant tripeptide SPECIFIC AMINO ACID FUNCTIONS, cysteine is the active component DERIVATIVES, AND SELECTED CLINICAL N-acetylcysteine (NAC) CORRELATIONS ○ given in paracetamol-induced liver injury to neutralize free radicals AMINO ACIDS IN METABOLIC PATHWAYS Alanine, Aspartate, and Glutamate are highly active energy ○ given to patients undergoing contrast 🗨 in metabolism. enhanced imaging procedures to prevent oxidative injury in the kidneys 🗨 Technically, they are non-essential. Prototypical amino acids that participate in different metabolic pathways such as transamination reactions. Alanine is the prototypical glucogenic amino acid → converted to glucose to maintain blood sugar levels during fasting (e.g. overnight). Aspartate and Glutamate participate in many reactions involving energy substrates AMINO ACIDS AS BUILDING BLOCKS Amino acids serve as building blocks for many key molecules in metabolism: 🗨 GLYCINE: forms part of the building blocks of DNA ( particularly of purine and pyrimidine molecules) and FIGURE 24. Structure of glutathione 🗨 is a precursor of heme (important component of hemoglobin); ( ASPARTATE may also contribute to pyrimidine formation) N-ACETYLCYSTEINE N-acetylcysteine (NAC) is the active component that does oxidant scavenging via disulfide reduction. 🗨 METHIONINE: is coded by the starting segment of every peptide (start codon) ( it is the starting segment of every protein code; you get methionine at the start of all o NAC-SH + RSSR --> RSH + NAC-SSR N-acetylcysteine (NAC) is also given as a mucolytic. o Mucolytics are drugs used to manage mucus proteins) hypersecretion, taken when one has thick and ARGININE: participates in ammonia detoxification through tenacious secretions or phlegm. o Disulfide bridges or bonds are what makes mucus 🗨 the urea cycle, provides the nitrogen molecule for nitric oxide (NO) ( which is a potent vasodilator), and (along with Glycine) forms high energy molecule creatine sticky and thick; NAC thins mucus by disrupting these bridges. ○ Creatine: molecule we find in muscles and it is high energy because when it is phosphorylated, as creatine phosphate, it provides greater energy than ATP for when the muscle needs burst of energy, e.g. for heavy lifting, crossfit, sprint BCAAs AS KEY SUBSTRATES FOR NEURONS Valine, leucine, and isoleucine are branched-chain amino acids (BCAAs) BCAAs provide energy reserve for neurons as these amino acids are broken down to produce glucose and ketones ⚠Valine is strictly glycogenic, leucine is strictly ketogenic, and isoleucine could be broken down into both glucose and ketone bodies BCAAs make up a significant bulk of lean muscle mass FIGURE 25. Mechanisms of NAC Page 14 of 21  AMINO ACIDS & PEPTIDES 🗨 In addition to vitamin C, copper (a micronutrient) is required by lysine oxidase which is responsible for AMINO ACIDS IN CELL-TO-CELL SIGNALING crosslinking. ○ 🗨 Both vitamin C and copper are needed to have very strong collagen. These are key components of receptors that facilitate cell Lysine is particularly critical for growth as it is essential, and signaling. Serine, Threonine, and Tyrosine are three amino acids 🗨 because of its role in collagen unlike proline and glycine. This is why lysine is always highlighted as a component of many nutritional supplements, that have a hydroxyl (-OH) group, making them very especially those marketed for children and young 🗨 🗨 effective in cell-to-cell signaling. adolescents. These cell receptors possess either a Serine, Threonine, or ○ Ex. Growee and Cherifer Tyrosine moiety. Having lysine deficiency means there is less Many Cytokines and Hormones bind to receptor Ser-Thr collagen in the bones, making the bones shorter and and Tyr-kinases. leading to short stature. These are important types of receptors that play a significant role in the signaling functions of many AMINO ACIDS AS DERIVATIVES hormones and cytokines. Among the most important functional proteins in the body ○ Cytokines are signaling molecules that cells use to are those that act as signaling molecules ○ Neurons make use of neurotransmitters to pass signals communicate with other cells, giving them orders to each other that allow the body to have a unified and harmonious ○ Hormones, in a similar fashion, pass signals from one response to a certain stressor. cell to another (either adjacent or distally located) Many hormones (or signaling molecules), neurotransmitters, among others, are also derived from amino acids ○ These many hormones are peptide in nature as opposed to steroid hormones which are derived from cholesterol TABLE 3. Amino Acid Derivatives Amino Acid Precursor Derivatives Thyroid hormone, Tyrosine Catecholamines: Dopamine, Norepinephrine, Epinephrine Tryptophan Serotonin, Melatonin Histidine Histamine Glutamate, GABA Glutamate (𝝲-Aminobutyric acid) Glycine Glycine Tyrosine derivatives ○ The smallest hormone, thyroid hormone, is a direct FIGURE 26. Serine, Threonine, and Tyrosine derivative of tyrosine ○ Catecholamines are the main signaling molecule used AMINO ACIDS IN COLLAGEN by the Sympathetic Nervous System which are released Collagen, the most abundant protein in the body (outside as an attempt to cope with stressful situations such as the blood/plasma), is made up of cross-linked fibers. having an infection, sustaining injuries, or for the body It is composed of semi-recurring units of proline, glycine, to optimally perform a strenuous task (e.g. lifting a 🗨 hydroxyproline and hydroxylysine. heavy object, running a 100-m dash) These hydroxylated amino acids provide them Tryptophan derivatives with hydroxyl groups (-OH) that form hydrogen bonds ○ Tryptophan is another aromatic amino acid which optimizes the interactions between the ○ Serotonin is the so-called mood or happy hormone individual fibers of the collagen molecule. ▪ Only 1-3% of the body’s serotonin is found in the Take note: Hydroxylation of proline and lysine requires brain or the Central Nervous System vitamin C (ascorbic acid). ▪ The vast majority of serotonin is found in the Glycine enables formation of a taut triple helix formation. intestines or gut where it regulates the movement of Lysine residues allow for maximal tensile strength via the intestinal muscles and this might be the reason crosslinking. why when one gets anxious, they feel their stomach/intestines cramping or when one is pissed off they get hungry Page 15 of 21  AMINO ACIDS & PEPTIDES ▪ There is a big connection between the gut and the brain ▪ 🗨 Selenoproteins - proteins or enzymes that have Selenium ▪ Platelets, also make use of serotonin (found in the ▪Two important proteins (enzymes): (1) Thyroid granules whose contents are released by platelets deiodinase and (2) Glutathione peroxidase when they form a clot) ○ Loss of thyroid deiodinase activity ▪ Also a vasoactive molecule (substance that ▪ Disruption of thyroid hormone activation and regulates blood vessel tone and function, how narrow or wide a blood vessel are at a particular ▪ 🗨 turnover Thyroid deiodinase - convert thyroxine (T4; ▪ 🗨 time) sero-tone-in initial thyroid hormone) to triiodothyronine (T3; more potent/active form) → removal of one of the iodine ○ Serotonin is the precursor of melatonin ▪ This makes melatonin a derivative of tryptophan as well ▪ 🗨 atoms It is also essential in making thyroid function optimal. ▪ Its most notable function is to regulate sleep ▪ ⚠ If you do not have Selenocysteine, you can have ○ 🗨 Histidine derivatives Histamine is a versatile molecule because of the ○ 🗨some form of hypothyroidism. Loss of antioxidant f