L4 - Proteins PDF - Biochemistry Exam Notes

ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO OUTLINE CLASSIFICATION OF PROTEINS 1. Chemical structure I....

ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO OUTLINE CLASSIFICATION OF PROTEINS 1. Chemical structure I. Classification based on composition, physical, 2. Classification and chemical properties 3. Physical and chemical properties II. Classification based on the shape and certain 4. Functions physical characteristics CLASSIFICATION BASED ON COMPOSITION, PROTEINS PHYSICAL, AND CHEMICAL PROPERTIES organic nitrogenous substances A. SIMPLE PROTEINS ○ contains CHON 1. Albumin - soluble in water and dilute ○ when we say protein, it has lots of nitrogen aqueous salt solution; heat coagulable high molecular weight i. Important because albumin is a ○ it is a big macromolecule plasma protein that acts as a found in all plant and animal cells transporter. It transports a lot of ○ the cells are comprised by proteins things in our blood. consist of alpha-amino acids 2. Globulin - insoluble in water; soluble in ○ proteins in nature are primarily composed aqueous salt soln; heat coagulable of amino acids 3. Glutelin – soluble in dilute acids and linked by peptide bonds alkalies; heat coagulable ○ In carbohydrates, it is linked with i. e.g., plant proteins – glutenin glycosidic bonds. In proteins, it is linked (wheat), oryzenin (rice) with peptide bonds. 4. Prolamine – alcohol-soluble protein e.g., seed proteins – zein (corn), gliadin FUNCTIONS OF PROTEINS (wheat) 1. Catalyst of chemical reactions - enzymes 5. Albuminoid – least soluble e.g., animal 2. Transport and storage - hemoglobin proteins – keratin, collagen ○ Albumin is another example of transport 6. Histone – basic protein; soluble in water, protein. dilute acid and alkali; found in ○ Example of a substance stored by our combination with DNA proteins is iron. 7. Protamine – simplest; basic; soluble in 3. Coordinated motion - actin and myosin water, dilute ammonia, acid and alkali; 4. Mechanical support - collagen and keratin found in spermatozoa ○ These are structural proteins. 5. Immune protection - gamma globulins B. CONJUGATED PROTEINS (proteins that ○ Immunoglobulins contain other functional groups or other 6. Transmission of nerve impulses - macromolecules) neurotransmitters 1. Nucleoproteins – contain nucleic acid ○ These serve as a communication, along (DNA, RNA) as the prosthetic group with hormones. i. Ex. histones ○ There are neurotransmitters that are 2. Glycoproteins and proteoglycans – proteins and that are derived from amino contain carbohydrates acids. i. Proteoglycans have more carb ○ Proteins are also found in membrane content than proteins. receptors like G Protein Coupled ii. Glycoproteins have more protein Receptors content than carbs. 7. Cell signaling - membrane receptors 3. Chromoproteins – contain prosthetic 8. Hormones – insulin, thyrotropin, somatotropin groups that give color e.g., hemoglobin i. Iron is the prosthetic group 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 1 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO ii. “Prosthetic group”: have groups components of certain proteins. The following other than our macromolecules are its examples.) 4. Lipoproteins – associated with lipids e.g., a. Hydroxyproline & hydroxylysine – VLDL chylomicron, LDL, HDL collagen i. Transporters of lipids in the body b. Gamma-carboxyglutamic acid - 5. Metalloproteins – contain minerals e.g., prothrombin iron in cytochromes c. Desmosine (derivative of lysine) – elastin i. Somewhat similar to 5. Phosphorylation and dephosphorylation of chromoproteins except that in amino acids with rings such as serine. Ser, play chromoproteins, their prosthetic a major role in activation and inactivation (or group would give them color. inhibition) of enzymes. ii. Metalloproteins would contain a. In cell signaling, there are other amino metal as their prosthetic group acid residues found on receptors that are like iron, copper, or magnesium. important in communication such as serine, threonine, and tyrosine. CLASSIFICATION BASED ON THE SHAPE AND 6. Some amino acids or their derivatives act as CERTAIN PHYSICAL CHARACTERISTICS chemical messengers e.g. GABA, serotonin A. FIBROUS PROTEINS 7. Several amino acids act as metabolic tough intermediates involved in structural functions a. e.g. Arg, citrulline, ornithine – urea cycle e.g., collagen, keratin b. There are also amino acids that are B. GLOBULAR PROTEINS (has more functions as converted to the intermediates of the transport proteins or enzymes) krebs cycle that is why amino acids are involved in mobile and dynamic functions metabolically important. e.g., enzymes, plasma proteins, hemoglobin BASIC STRUCTURE OF AMINO ACIDS Each amino acid has a central carbon, called the alpha FUNCTIONS OF AMINO ACIDS carbon, to which four different groups are attached 1. Building blocks of proteins (chiral carbon): 2. Precursor of various substances 1. a basic amino group (-NH2) a. Glycine – heme, purine, creatine 2. an acidic carboxyl group (-COOH) b. Glutamic acid – GABA 3. a hydrogen atom (-H) c. Phe and Tyrosine – thyroxine, 4. a distinctive side chain (-R) epinephrine a. this side chain would denote the different d. Tryptophan – niacin, serotonin, chemical property of each amino acids. melatonin *Except glycine because its distinct side chain is a 3. Source of energy hydrogen atom hence it is not chiral anymore. If our glucose and fat storage is already depleted, the next thing that is used for DIFFERENT FORMS OF AN AMINO ACID energy would be amino acids. Under There are different forms of acid. It can be ionized or normal conditions, we do not want that unionized, depending on the pH. because we will lose substrate for the 1. Unionized form building blocks of our proteins. Usually this condition is reserved for prolonged cases of low blood glucose or starvation 4. Special amino acids as components of certain types of proteins (Specialized amino acids are modified amino acids that have plant 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 2 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO COMMON AMINO ACIDS III. Amino acids with positively charged R groups a. Basic amino acids 1. Lysine 2. Arginine 3. Histidine IV. Amino acids with negatively charged R groups a. Acidic amino acids 1. Glutamic acid 2. Aspartic Acid I. AMINO ACIDS WITH NONPOLAR OR HYDROPHOBIC R GROUPS Neutral amino acids R groups do not bear (+) or (-) charges Interact poorly with water Play an important role in maintaining the conformation or 3-dimensional structure of Most of the time, the three-letter abbreviation is proteins used. Within nonpolar groups, there could be interactions (bonding / Van der Waals CLASSIFICATION OF AMINO ACID force on non-polar). Due to this force, BASED ON R-GROUP (OVERVIEW ONLY) they could play a role in maintaining the stability of the protein conformation. I. Amino acids with nonpolar or hydrophobic R groups *Distinct R chains are enclosed by the white box in the figures. a. Amino acids with aliphatic side chains A. Amino acids with aliphatic (straight 1. Glycine hydrocarbon) side chains 2. Alanine 1. Glycine 2. Alanine Branched-chain amino acids 3. Valine 4. Leucine 5. Isoleucine 6. Methionine 7. Proline Glycine is the simplest amino acid. b. Amino acid with aromatic side chains Glycine R group: Hydrogen only; 1. Phenylalanine the only amino acid that is not 2. Tryptophan chiral. Alanine R group: Methyl group II. Amino acids with uncharged polar R groups (CH3). a. Hydroxyl-containing amino acids 1. Serine 2. Tyrosine 3. Threonine b. Amide derivatives of Glu and Asp 1. Glutamine 2. Asparagine 3. Cysteine (Thiol Group) 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 3 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO Branched-chain amino acids B. Amino acid with aromatic side chains 1. Valine 2. Leucine 3. Isoleucine Aromatic - contain unsaturations or double bonds 1. Phenylalanine 2. Tryptophan (benzene ring) (indole ring) Branched because there is tree-like branching in their R group. Differs in hydrocarbon length Mnemonic: LIV, because these amino acids are the ones affected by metabolic errors for Phenylalanine has CH2 in its R group which branched chain amino acid metabolism. would contain the phenyl group (“piattos”). ○ Alanine R group is CH3, while here, instead *Other examples of branched-chain amino acids, but belongs to of additional hydrogen, phenyl group is another group. attached. 4. Proline 5. Methionine Tryptophan; indole - has phenyl group and attached to that phenyl ring is a 5-membered ring. II. AMINO ACID W/ UNCHARGED POLAR R GROUP have functional groups capable of hydrogen bonding -OH groups serve other functions in proteins ○ Formation of the phosphate ester of Proline Tyrosine is a common regulatory mechanism R group is a distinct closed ring ○ Formation of hydrogen bonds with other Secondary amino acid or an imino acid, macromolecules that would contain covalent because amino group is NH2 instead of NH3. bonds Nitrogen is bonded to the α-carbon and the ○ -OH groups of Serine and Tyrosine are side-chain group points for attaching carbohydrates also known as “helix-breaker” - NH is unable to bond because it is part of the R group A. Hydroxyl (-OH) -containing amino acids Methionine 1. Serine 2. Threonine 3. Tyrosine Sulfur-containing, non-polar amino acid Converted to S-adenosylmethionine (SAM), an important methyl group donor in methylation reactions, since it is able to donate the CH3 in its R group. Important in cell-to-cell communication, because these are sites of phosphorylation reaction; -OH can be used as attachment for phosphate groups, which in turn can either activate or inhibit 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 4 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO the enzymes - important in regulation of enzyme Selenocysteine – the 21st L-α-Amino Acid activity Found in peroxidases and reductases site of glycosylation reaction - important in Selenium (Se) atom replaces the sulfur of its formation of mucin structural analog cysteine There is no codon for selenocysteine Serine Inserted into the polypeptide during translation Simplest amino acid that contains the -OH group Note: Selenocysteine is not inherently introduced by your Threonine sense from your DNA, RNA what happens is that during the Has branching but still contain -OH synthesis of your cysteine, it is modified, hence Tyrosine posttranslational modification forms selenocysteine. Closely related to Phenylalanine; difference: additional -OH group in Tyrosine III. AMINO ACID W/ POSITIVELY CHARGED R GROUP Basic amino acids - have a net positive charge B. Amide derivatives of Glutamine and Asparagine 1. Lysine Contains -NH2 instead of -OH 2. Arginine- contains the guanido group Derived from Glutamic acid (Glutamine) and 3. Histidine- contains the imidazole group Aspartic acid (Asparagine) - responsible for the buffering capacity of hemoglobin Important in detoxification of ammonia ○ Able to get extra ammonia from the body system. Ammonia will be taken up by Glutamate and Aspartate to form Glutamine and Asparagine. ○ These lower down our ammonia level, such that Glutamine is the primary source of urinary ammonia. 1. Asparagine 2. Glutamine Lysine Arginine Histidine Note: When you look at the charges of the Lysine: COO-, H3N+, and NH3+, when you total it there is still remaining positive charge. III. AMINO ACID W/ NEGATIVELY CHARGED R GROUP Acidic amino acids 1. Glutamic acid - or glutamate 2. Aspartic acid - or aspartate - interactions between acidic and basic amino acids results in the formation of ionic bond (aka salt bond, Cysteine electrostatic bond) Instead of -OH, it contains a - Important in maintaining protein structure sulfhydryl (-SH) group (a.k.a. thiol group) Two cysteine residues combine and form a strong disulfide bond, and cystine is the resulting product. Important in maintenance of protein structure (e.g. insulin, immunoglobulins) Speaker’s note: Principle behind hair rebonding is that the chemicals used break the disulfide linkages between Aspartic acid Glutamic acid cysteine residues, and by doing so, protein structure is lost. Note: under a normal pH you have a net negative charge 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 5 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO Types of interactions entered into by the different R 7. Acid-base properties groups of amino acids The amino (NH3) and carboxylic acid (COOH) groups 1.Hydrogen bonding- Hydrogen is attracted to other readily ionize. electron rich areas Note: Amino will give off its H and will be positively charged a. -O-H …….. O=C (NH3 -> NH2+) , Carboxylic acid will donate H and will be b. -O-H …….. O negatively charged (COOH -> COO-). c. -S-H ……... O 2. Ionic interaction- usually involved in the carboxyl pK (&-COOH) = around pH 2.2 grp and amino grp of another amino acid pK (&-NH2) = around pH 9.4 -COO- ……..NH3+ *pK is a constant that determines that R grp is able to 3. Hydrophobic interactions of nonpolar R grps.(Van give off or receive protons. der waals interaction) 4. Disulfide bond Hence COOH will be COO- at pH 2.2 but at pH 1 which is below ph 2.2 it will not give off H and will remain as COOH PHYSICAL PROPERTIES OF AMINO ACID Amino grp will not donate proton at lower pH (less 1. Solubility than pH 9.4) like pH 7 (neutral) it will remain as 2. Melting points NH3 but at higher pH beyond pH 9.4 the amino grp 3. Taste will become NH2+ 4. Appearance An amino acid can act as a base or proton 5. Optical property recipient and an acid or proton donor For all the standard amino acids, except glycine, (amphoteric). the & carbon is asymmetric , bonded to four different substituent groups. In this case the Different Forms of an Amino Acid &-carbon is a chiral center. All molecules with a chiral center are optically active 1. Unionized form – i.e., they can rotate the plane-polarized light either to the right (dextrorotatory) or to the left (levorotatory). Stereoisomerism – D and L amino acids - due also to the presence of chiral center - D isomer if NH2 group is oriented to the right - L isomer if NH2 group is oriented to the left - amino acids that occur in protein (body or in nature) are all L form 2. Dipolar ion or zwitterion form Zwitterion - electrically neutral; zero charge - number of positive charge equal to number of negative charge - remain stationary in an electrical field 6. Ultraviolet absorption spectrum of aromatic amino acids Ultraviolet absorption properties of proteins are determined solely by Phe, Tyr and Trp (Aromatic AA) 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 6 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO 3. Fully protonated form (pH 1) DISSOCIATION OF MONOAMINO, MONOCARBOXYLIC ACID ) NEUTRAL AMINO ACID) 4. Fully ionized form (pH 11) This is an example of a titration of a neutral amino acid. The R group does not bear a charge so you only have to take into account the amino group and the carboxyl group. At lower pH, if the PKa is 2.34 for the COOH, lower than that example ph+1, there will be no donation of hydrogen. So the overall net charge of the whole amino structure will have some left over, positive which is why at lower pH like ph +1 , it’s plus one. TITRATIONS OF AMINO ACIDS ( PROTONIC EQUILIBRIA) Titration of Amino Acids (Protonic equilibria) Protonic equilibria is the step-by-step dissociation of the amino acid starting from the fully protonated or positive form up to the fully ionized or negative form. Beyond the pKA for example, Ph 7.4, the ph has Uses: already exceeded the pKa of the carboxyl group, the 1. can predict the charge of the amino acid in a carboxyl group can now readily donate the proton such given solution with known pH that at pH 7.4 if you look at the carboxyl group, it has 2. can devise a procedure of separating amino already donated a proton.When you look a the net acids based on their charge charge of this Alanine,it’s zero because the negative charge cancels out the positive charge in the amino ISOELECTRIC POINT ( pHI, pI, IpH) group. Isoelectric Point (pHI, pI, IpH) - That pH at which an amino acid bears no net charge and hence does not move in an electrical field. - That pH exactly at the midpoint between the pK values on either side of the zwitterion species. - General rule regarding pI: At higher pH, let’s say at ph 10, this one exceed the The pI of neutral amino acids are in the neighborhood pkA of the Amino group.So the amino group can now of 6.0; that of acidic amino acids – very much below readily donate the proton. So when it donates the 6.0; and that of basic amino acids – very much above proton, the positive charge disappears and what is left 6.0. behind is the negative charge. So if we calculate the net charge, it will be -1. 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 7 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO PEPTIDES Peptides – amino acid polymers with low molecular weights, typically consisting of less than 50 amino acids. Proteins – more than 50 amino acids. Oligopeptides – consisting of 2 to 10 amino acids Polypeptides – have more than 10 amino acid residues PEPTIDES WITH SIGNIFICANT BIOLOGIC ACTIVITIES 1.Glutathione (gamma-glutamyl-L-cysteinylglycine) - reducing agent; due to –SH group It is the cysteine group esp. the Sulfhydryl group that is important in its activity. It has to be in an -SH form to be This is used to compute for the isoelectric point by a good reducing agent/ antioxidant. ( reduced form) getting the average of the pKa of the different groups. - protects the cell from the destructive effects of oxidation by peroxides 6.02 is the isoelectric point where the amino acid is - works hand in hand with glutathione peroxidase electrically neutral. Composed of 3 amino acids: Glutamate, Cysteine, If the R group is able to donate or receive H+. The Glycine basic and acidic amino acids have an additional 2. Oxytocin and vasopressin - contain nine amino dissociation constant so there will be an additional pKa acid residues that will help you determine the isoelectric point of that oxytocin stimulates contraction of uterine muscle amino acid. during childbirth TWO vasopressin is an antidiuretic hormone; stimulates TITRATION CURVE OF MONOAMINO, CARBOXYLIC water reabsorption in the kidney AMINO ACID ( NEUTRAL AMINO ACID) 3. Met-enkephalin and Leu-enkephalin - FORMS OF BETA-PLEATED SHEET pentapeptide; opioid peptides - relieve pain; bind to receptors in the brain and induce analgesia 4. Atrial natriuretic factor - has 28 amino acid residues - stimulates the production of a dilute urine. The effect is opposite of that Vasopressin. 5. Substance P and bradykinin - stimulate the perception of pain 6. Glucagon - has 29 amino acid residues - opposes the action of insulin 7. Corticotropin – with 39 amino acid residues; stimulates adrenal cortex 8. Aspartame (L-aspartylphenylalanine methyl ester; artificial sweetener 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 8 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO FORMATION OF PEPTIDE BOND ◈ The 3-dimensional shape of a folded polypeptide is result of the interactions among the R groups SECONDARY STRUCTURE Due to the formation of hydrogen bonds between peptide bonds ◈ Two types: 1. Coils or helices - intrachain hydrogen bonding 2. Sheets or pleats - interchain hydrogen bonding Speaker’s notes: The formation of your peptide bond is ALPHA-HELIX very similar to Glycosidic bond, it is a condensation reaction or a dehydration reaction but the interaction is 1. Alpha-helix: discovered by Linus Pauling in 1951 between the carboxyl group of Amino Acid 1 and the Important features: Amino group of Amino Acid 2. - Stabilized by inter-residue hydrogen bonds formed bet. the H atom attached to a peptide N and the If you look at the dipeptide, it has an amino end and a carbonyl O of the residue 4th in line behind in the carboxyl end. If you add more amino acids, it will primary structure always have an amino end. ( N- terminus and - Each peptide bond participates in hydrogen bonding. C-terminus). - An alpha-helix forms spontaneously as it is the lowest PARTS OF PEPTIDE CHAIN energy, most stable conformation for a polypeptide chain. - There are 3.6 amino acid residues per turn with a pitch (distance bet. corresponding points per turn) of.54 nm (5.4 A); spacing per residue is.15 nm (1.5 A) - Amino acid R groups extend outward from the helix. In between the Amino acids are peptide linkages LEVELS OF STRUCTURAL ORGANIZATION OF PROTEINS a. Primary Structure b. Secondary Structure c. Tertiary Structure d. Quaternary Structure PRIMARY STRUCTURE Refers to: - quantitative amino acid composition - sequence of amino acids - number of peptide chains ◈ Most abundant amino acid in proteins: - Leu, Ala, Gly, Ser, Val and Glu ◈ Rarest in proteins are: - Trp, Cys, Met and His ◈ The backbone of a protein refers to the atoms that participate in the formation of peptide bonds 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 9 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO Speaker’s Notes: Take note that the hydrogen bonds are INTERchain, not intrachain. TWO FORMS OF BETA-PLEATED SHEETS BETA-SHEETS OCCUR IN TWO DIFFERENT ARRANGEMENTS: 1. ANTIPARALLEL BETA-SHEET - neighboring H bonded polypeptide chains run in opposite directions - more stable FACTORS THAT DESTABILIZE THE ALPHA HELIX 1. Presence of adjacent similarly charged amino acids. 2. Presence of adjacent bulky R groups. 3. Presence of proline - contains rigid ring that prevents the N-C bond from rotating - no N-H group available to form intrachain hydrogen bonds Speaker’s Notes: destabilize = destroy like charges repel, so if there are similar charges (e.g, 2 basic amino acids), they tend to repel 2. PARALLEL BETA-SHEETS bulky R groups = groups with aromatic ring - hydrogen bonded chains extend in the Proline = helix breaker; incapable of forming same direction. hydrogen bonding 2. BETA-PLEATED SHEET BETA-PLEATED SHEET – second most commonly occurring protein 2o structure IMPORTANT FEATURES: 1. Formed when 2 or more almost fully extended polypeptide chains lie side by side such that hydrogen bonding occurs between adjacent peptide chains. 2. Hydrogen bonds are interchain. 3. R grps lie above or below the zigzagging planes of the pleated sheet and are nearly perpendicular to them. 4. Amino acids with less bulky R groups are present. 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 10 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO Speaker’s Notes: Between the antiparallel and parallel beta-sheets, the antiparallel is more stable because the H bond in between is somewhat perpendicular to the plane. FACTORS THAT DESTABILIZE THE BETA-PLEATED SHEETS 1. Bulky R groups. 2. R groups with like charges. SUPERSECONDARY STRUCTURES OR MOTIFS Combinations of 2o structure Occur as part of a larger functional unit Have a particular function C. TERTIARY STRUCTURE Have different functions in different proteins Have roughly 10 to 40 amino acid residues each 3-dimensional structure Protein conformation COMMON SUPERSECONDARY STRUCTURES Results from further folding of a poly-peptide with regions of α-helix and/or beta-sheet, into a 1. Helix-loop-helix closely packed, nearly spherical shape. 2. Coiled-coil motif Indicates how 2o structural features – helices, 3. Beta-alpha-beta unit sheets, bends, turns and loops assemble to 4. Hairpin form domains. 5. Zinc finger 6. Leucine zipper IMPORTANT FEATURES OF TERTIARY STRUCTURE 7. Greek key 1. Amino acid residues that are distant from each other in the 1o structure come into close proximity when the polypeptide folds. 2. When polypeptide folds, proteins become more compact; most water molecules are excluded from the proteins’ interior making interactions bet. polar and nonpolar AA possible. 3. Large globular proteins (> 200 AA) often contain several compact units called domains. Domains are structurally independent segments that have specific functions (e.g. binding an ion) TYPES OF INTERACTIONS THAT STABILIZE TERTIARY STRUCTURE Hydrophobic interactions Electrostatic interactions (salt bridges) Hydrogen bonds Covalent bonds (disulfide bridges) 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 11 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO task such as binding of a substrate or other ligand. they consist of combinations of several units of supersecondary structures. Size of domains varies from 25-30 to about 300 amino acid residues, with an average of about 100 amino acids. D. QUATERNARY STRUCTURE Exhibited only by proteins containing more than one polypeptide chain. Most proteins with molecular masses above 100 kD, consist of more than one polypeptide chain. *Each polypeptide component is called a subunit. Oligomeric proteins are those with more than one subunit. * Subunits maybe identical or different. * Protomers are identical subunits. Quaternary structure describes the characteristic manner in which the individual , folded polypeptide chains fit each other or interact with one another so that they can act as one single molecule. PROTEIN FOLDING IS ASSISTED BY MOLECULAR CHAPERONES AND ENZYMES Molecular chaperones – proteins that have the net effect of increasing the rate of correct folding by binding newly synthesized polypeptides before they are completely folded. - assist in the translocation of polypeptide chains across membranes e.g., heat-shock proteins, chaperonins Enzymes involved in protein folding Speaker’s Notes: 1. Peptidyl prolyl cis-trans isomerase When you have more than 1 tertiary structure, 2. Protein-disulfide isomerase you have a quaternary structure. Hemoglobin, a classic example of a quaternary DOMAINS OR LOBES structure, has 4 subunits. Each subunit has a tertiary structure. When you combine them they are discrete, independent folding units together, you have the quaternary structure of within the 30 structure that perform a particular the hemoglobin. 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 12 ITM 101 | BIOCHEMISTRY LESSON # 4 - PROTEIN AND AMINO ACID CHEMISTRY 1st YEAR | A.Y. 2023-2024 | AUGUST 25, 2023 DR. RALPH CYLON JACINTO CHEMICAL ALTERATIONS INTERACTIONS THAT HOLD SUBUNITS TOGETHER 1. Decrease in solubility – most visible effect in globular proteins Hydrophobic interactions 2. Many chemical groups which were inactive Electrostatic interactions become exposed and more readily detectable Hydrogen bonds Interpolypeptide disulfide bonds Speaker’s Notes: Whenever there is decrease in solubility, it can ❖ Hydrophobic interactions are the principal also signify a loss of function. forces that hold the subunits together. ❖ Electrostatic forces contribute to the proper alignment of the subunits. PHYSICAL ALTERATIONS DENATURATION OF PROTEINS increased viscosity decreased rate of diffusion increased levorotation occurs when a protein loses its native cannot be crystallized secondary, tertiary and/or quaternary structure; there is cleavage of noncovalent bonds. Speaker’s Notes: always correlated with the loss of a protein’s function. All of these would result in the loss of function of the proteins. DENATURING AGENTS BIOLOGICAL ALTERATIONS A. PHYSICAL AGENTS increased digestibility extremes of pH and temperature enzymatic or hormonal activity is destroyed high pressure antibody functions are altered ultraviolet light ultrasound -END- B. CHEMICAL AGENTS organic solvents – acids, alkali, urea, guanidine Detergents Speaker’s Notes: Denaturation = process where in the natural configuration of protein is destroyed Example 1 - extreme pH: Milk (which contains a lot of proteins), when you add vinegar (acetic acid) to it, it will lower down the pH, causing the proteins to denature or coagulate. Example 2 - extreme temperature: Boiling an egg denatures its proteins. Detergents = substances that would disrupt ionic bridges (electrostatic bonds) in between proteins (e.g. soap, lysol) 101 INTRODUCTION TO MEDICINE | BIOCHEMISTRY AYURA 2027 13