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Biochemistry lec
Three dimensional structure of proteins
NOTE:
 Loss of structure results in loss of biological function
 In reading/identifying peptide chains, start from the amino side
 All organic structures are in 3D
 There is no way to predict the secondary structure with the peptide chain alone.
 R groups with a pK value for similar charges still interact for repulsion is still an interaction.
 Gly is smaller than an R group so it is not part of a tertiary structure.
 Changing the shape/composition will change the function
 Proteins are designed to interact with others, hence able to resist different temperatures.

Protein - Most abundant biomolecule in the cell

Three Dimensional conformation - ^ adopt in this specific formation.
Conformation - Spatial arrangement of atoms in a protein
Native Conformation - The three dimensional structure of a protein. Essential for the biological function of a protein.
Native Proteins - Proteins in any of their functional, folded conformation.
Types of Protein
Structural - For support
Collagen, elastin -^ example
Catalytic - For hastening biochemical reactions
Amylase, Enzymes -^ example
Storage - For storage of amino acids
Casein, Ovalbumin - ^ example
Transport - For transport of other substances
Hemoglobin, protein channels - ^examples
Regulation - For regulation/coordination of bodily activities
Insulin, Glucagon -^ example
Receptor - For response of cell to external stimuli
Neuron receptors in nerve cell - ^ example
Contractile - For movement
Myosin, Actin -^ example
Defensive - For protection against disease
Antibodies -^ example

LEVELS OF STRUCTURAL ORGANIZATION OF PROTEINS

Primary Structure - Refers to the sequence of amino acids in a polypeptide chain
Native conformation -^ determines this. The most basic 3D structure a protein has.
Oligopeptides - Are proteins with 2-10 peptide bonds.
Polypeptides - Are proteins with more than 10 peptide bonds
Dipeptide - Has two peptide bonds, the smallest
Tripeptide - Has three peptide bonds
Secondary Structure - Refers to the ordered 3D arrangements in localized regions of a polypeptide chain
(regular folding).
Spatial Arrangement - The arrangement of atoms in the polypeptide chain.
Hydrogen Bond -^ is formed and stabilized by the amide proton and carbonyl oxygen.
Gylcine and Proline - Amino acids that prevent α-Helix formation.
Kinds of Secondary Structure
α-Helix - A spiral structure
Intramolecular H bonds - ^ is stabilized by this. All secondary structures are stabilized by this.
Every fourth amino acid - C=O of each peptide bond is hydrogen bonded to the N-H of the ______ away. Needs
to
be this far due to the bond length.
3.6 aa/turn - ^ ‘s turn
5.4A - α-Helix’s pitch
Helical axis - H-bonds are parallel to this.
Outward - Position of the R groups from the helix, this allows more interaction
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Right/Left- handed - Two versions of the coil of the helix. This depends on the enantiomer present.
Clockwise - The right-handed version the usual spin of amino acid.
Counter-clockwise- The left-handed version.
Constraints to Helix Stability
Proline - This is a big constraint that forms with H3N, preventing the H3N to form H bonds. It is
also due to the ring and N has no H to participate in H bonds.
Glycine - Since the R group is flexible, it allows more room for interaction hence not prioritizing
the α-Helix and the possibility for forming a coil or bend.
Electrostatic Repulsion - This plays a part with charged particles, this constraints helix stability if this is found
between successive charged aa residues. (+ will repulse + and vice versa)
Bulkiness/steric strain - Found in adjacent R-groups, can cause constraints in helix stability.
Ala, Leu - Are small hydrophobic residues which are strong helix formers.
β- Pleated sheet - It is formed when two or more polypeptides line up side by side.
Hydrogen bonds - ^ is stabilized by these bonds (interchange/ intrachain) of adjacent polypeptide chain.
Zigzag - Each β-strand (polypeptide chain in β-sheet) is extended to this formation.
H-bonds - These bonds are formed adjacent between β-strands
Above/below ,alternate - The R groups are arranged in this way in the β-sheet
Parallel/Anti-parallel - Adjacent β-strands can run in this.
Anti-parallel β-sheet - This is stronger. Has directly parallel and linear H bonds. All β strands run in opposite direction.
Parallel β-sheet - Hydrogen bonds are bent. All β strands run in the same direction.
β Bends - It permits the change in direction (usually about 180 degrees) of the peptide chain. Has
4 amino acid residues, has excess glycine. Connects helices and β strands,
allows the polypeptide chain to fold back on itself, producing a compact 3D
conformation.
H bond - This stabilizes the β-bend
4 aa residues - A β-bend is accomplished over this.
Gly and Pro - Are frequently part of the β bend
Random Coil - Are nonrepetitive structures, irregular/unique conformation, are still stable. Usually
links the alpha helix and beta sheets.
Supersecondary Structures - Combinations of alpha and beta strands. Are general patterns seen in larger proteins.
Has motifs or themes. Are limited by the H bonds of the primary structure.
Motifs - Are repetitive supersecondary structures
βαβ - Consist of α bonds in between β sheets
βββ - This is common in β strands
β Mender - ^ is also called this
αα - Interact in a perpendicular-like angle, interacts in the middle and link between β sheets
βαβ βαβ - This is a βαβ within a βαβ
Greek Key -^ is also known as this
Tertiary Structure - Refers to the three-dimensional conformation of the entire polypeptide.
Amino Acid side chains - Stabilized by numerous interactions between these chains.
Covalent Bonds - The first interaction, usually between sulfides (Cys)
H Bonds - Where all H bonds interact (Leu, Ile, Ala, Val, etc) Nonpolar interaction, no dipole moments.
Salt Bridges/ Electrostatic - Ionic bonds, bond is based on charge, interaction of basic and acidic groups. (K,R,H,E,D)
Hydrophobic Interaction - Non polar groups interact, between amino acid residues.
N,Q,K,R,H,S,C - Can have ^
Fibrous Proteins - Polypeptide chain arranged in long strands or sheets
β Sheets - ^ consists largely of this. Only one type of secondary structure.
Structural (strength/support)- ^’s function
Collagen and Keratin - ^ example
Water Insoluble -Most ^ are this. Meaning they are non-polar.
Globular Proteins - Polypeptide chain folded into a compact spherical structure. Contains many types of
secondary structures.
Metabolic (Catalytic/Transport) - ^’s function. Can also be for storage, can regulate movement and reactivity of proteins.
Enzymes, Hemoglobin -^ example
Water Soluble -^ are this, meaning It is polar but still has nonpolar components.
Quaternary Structure - Refers to spatial arrangement of polypeptide subunits. Over all 3D structure of proteins.
Polypeptides (subunit/monomer) -^ is formed by the assembly of this into a larger functional cluster.
Noncovalent Interaction -Subunits are stabilized by this interactions, making it easy to break and maintains the
integrity for reactivity.
Dimer - Two subunits
Trimer - Three subunits
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Tetramer - Four subunits
Hemoglobin -^ example.
Denaturation - Technique used to study proteins, changes the natural conformation of a protein and
describing a change from their natural shape. Change in the native conformation
that disrupts their function.
°1 - Interaction of peptide bonds
°2 - Interaction of H bonds of the backbone
°3 - Interaction of multiple R groups
Cys -^ except this amino acid
°4 - Weaker interaction of R groups
High Temperature - The molecules will move faster to maintain equilibrium, interactions are broken hence
breaking noncovalent bonds and h bonds.
°2 -^ will denature this structure.
Hydrophobic/H bonds -^ affected interaction
Change in pH - This is the losing or gaining of H atoms
°2 -^ will denature this.
H bonds/ Ionic Interactions- ^ affected interaction
Change in Ionic Strength - Measure of the concentration of ions in that solution
°3 -^ will denature this
Ionic Interactions -^ Affected interaction
Organic Solvents - This affects the hydrophobic interactions, low polarity
°3 - ^ will denature this
Hydrophobic -^ affected interaction
Urea, Alcohol -^ example
Reducing Agents - Redox reactions, can donate or accept protons, loosing of H is losing protons and
gaining electrons.
°3 - ^ will denature this
Disulfide bridges - ^ affected interactions
Performic acid/mercaptoethanol - ^ example
Detergents - Having hydrophobic interaction, the lipid portion binds with oil and the salt portion
binds with water (reason why it dissolves in water)
°3 -^ will denature this
Ionic/Hydrophobic -^ affected interactions
Soap -^ example
Salts of Heavy Metals - Has electrostatic interaction
°3 -^ will denature this
Ionic -^ affected interactions

Protein structure and function

Collagen - Most abundant protein in mammals. Has great tensile strength. Stress-bearing
component of connective tissues.
Water-insoluble fibers - ^ is this, meaning it repels water. *Though it can still absorb water.
Skin, Hair, Nails, Teeth -^ is found here.
Tropocollagen -^ is made up of this aligned in a staggered fashion and cross-linked for strength.
Ontogenesis imperfecta - Characterized by very loose skin, caused by mutant alleles of collagen.
Ehlers-Danlos Syndrome - Another disease due to collagen defects.
Cys/Ser -^ these diseases are due to these amino acids replacing Gly in mutant collagen.
Ascorbic Acid (Vitamin C) - This is needed in the synthesis of collagen.
Pro/Lys - These enzymes are needed for the hydroxylation of these amino acids in collagen.
Scurvy - Lack of Vit C leads to this disease wherein there is collagen instability and connective
tissue problems.
Primary Structure
X-Y-Gly - Each collagen tripeptide is a sequence of this. The backbone
X - Any amino acid
Y - Often Pro or Hydroxyproline
Secondary Structure
Lys, 5-Hydroxylysine, His - These residues are present at some of the X and Y in the triplet repeat.
1000 amino acid residues - Number of amino acid residues in each polypeptide chain.
Left-handed helix - The secondary structure of collagen.
Gly - This residue is found in every turn, resulting to sharp twists in the helix.
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Tertiary Structure
Triple Helical Structure (tropocollagen) - The tertiary structure of collagen.
H bonds -^ is held together by these bonds.
Hydroxyproline and Hydroxylysine- ^’s formation involves the presence of these.
Elastin - Connective tissue protein with elastic properties. Found in lungs, large blood vessels,
etc. Can be stretched multiple times and return to normal length.
Nonpolar Residues -^ is made up of these residues.
Random Coil Conformation - Conformation of elastin.
3 modified lys + 1 lys - ^ is associated by desmosine crosslinks made by this.
Heme - Has ability to bind to Oxygen. Contributes to the red color of blood.
Prosthetic Group -^ is classified as this, means it is a non-amino acid component required in protein function
Hemoglobin -^ is present here, makes it bind to Oxygen.
Fe2+ - ^ has this at the center of the protoporphyrin ring, makes it able to bind to Oxygen.
Myoglobin (Mb) - Made up of a polypeptide chain. Has a single heme group and high O2 affinity.
Globular Protein -^’s protein formation
O2 storage -^’s primary function
Skeletal Muscle -^ is abundant here
Hemoglobin (Hb) - Tetrameric protein. Function is to transport oxygen. Compared to myoglobin, this has
lower affinity to O2 making it more efficient to carry O2.
1 Heme: 4 O2 molecules -^ Ratio to oxygen.
Positive Cooperativity - ^ binds O2 reversible and exhibits this, meaning the more O2 binding to heme, the more
susceptible it is to binding to O2.
pH, Presence of O2, Bisophosphoglycerate - Factors affecting Hb affinity to O2
Low pH - This decreases Hb affinity to O2, seen in actively metabolizing tissues.
Lung - High pH is found here, making Hb release both CO2 and H and binds to O2
Sickle Cell Anemia - Characteristic crescent shape RBC. Less efficient in delivering O2.
Val - ^ is characterized by the substitution of polar Glu to this amino acid which is nonpolar.
Hydrophobic patch -^ produces this on the surface of Hb, this interacts with others causing Hb to aggregate
into strands that align into insoluble fibers.
Insulin - Promotes glucose intake from blood into fat, liver and skeletal muscle cells. To lower
blood sugar.
Glycogen or fat - The glucose in the cell is converted to this.
Glycogenesis - Glucose to glycogen
Lipogenesis - Glucose to fat
β –Cells - ^ is produced from these cells located in the Islets of Langerhans in the pancreas.
Hypoglycemic Hormone - Hormones that works against the action of insulin. Intake of glucose.
Glucagon - Elevates blood glucose level by promoting synthesis of glucose and breakdown of
glycogen into glucose. Glucose synthesis. Raises blood sugar.
Hyperglycemic Hormone -^ classification of hormone.
Gluconeogenesis - Synthesis of glucose
Glycogenolysis - Breakdown of glycogen into glucose.
α-cells - ^ are produced from these found in the Islets of Langerhans in the pancreas.
Type 1 Diabetes Mellitus - Failure of the pancreas to produce enough insulin.
Type 2 Diabetes Mellitus - A condition in which cells fail to respond to insulin (insulin resistance)
Antibody (Ab) - Detects foreign materials. Y-shaped molecule wherein each chain contains constant and
variable regions that serve as binding sites to the epitope of the antigen.
Immunoglobulins -^ AKA
B Lymphocytes (Plasma Cell) -^ Is secreted by this.
Disulfide bonds -^ is held together by these bonds
Paratope - The binding sites in the variable regions.
Autoimmune Diseases - A disease characterized by the presence of self-reactive immune response.
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Enzymes
NOTE:
 Chemical reactions in the cell show little tendency to happen in vitro.
 Enzymes do not change the equilibrium reaction
 Enzymes function at milder reaction conditions
 Enzymes are efficient in catalyzing high reaction rate than a chemical catalyst.
 Greater Reaction Specificity: Some catalyze the reaction of only one stereoisomer, others catalyze a family of similar
reactions
 Enzymes can have one or two specific actions
 Enzymes are subject to regulation
 Without enzymes/catalyst we would have slow processes eventually leading to death
 Catalysts don’t get used up.
 Most enzyme interactions are reversible
 Sometimes enzymes and substrates can be covalently linked
o Happens when there is a nucleophilic group.
 Enzymes can participate in proton transfer with the substrate
o Donates or accepts a proton to make it more reactive
o Example is the reaction from an acid and base (residue in active site is acidic)

Enzymes - Biological catalysts that accelerate rate of biochemical reactions.

Free Energy Activation -^ accelerates the rate of a reaction by reducing this.
1020 - A factor of this over an uncatalyzed reaction
Regeneration - Happens after the reaction.
-ase - Suffix that indicate that something is an enzyme.
Proteins - Majority of enzymes are this.
RNA (ribozymes) - Some enzymes can be in this form.
Catalase - Best example to describe enzyme efficiency
Substrate - Biomolecule acted upon by the enzyme. The “reagent” that binds to active site of an
enzyme.
Active Site - Specific region of the enzyme that creates a 3D surface complementary to the substrate.
Transition State - The stat wherein the enzyme/substrate complex turns into an enzyme/product complex
His, Cys, Asp, Arg, Glu (CHEDR) - The five amino acids that participate in the active site in more than 65% of the enzymes.

MECHANISM: Enzyme + Substrate  Enzyme/Substrate Complex Enzyme/Product complex Enzyme + Product

E+S  [E/S]  [E/P]  E+P

Inactive Enzymes - Some enzymes are this, used for regulation.

Holoenzyme - Catalytically active enzyme-cofactor complex
Whole Enzyme -^ aka
Apoenzyme - Protein component of holoenzyme that is catalytically inactive. “empty hell”
Protein Portion -^ aka
Cofactor - Nonprotein component required in the activity of an enzyme.
Nonprotein Enzyme -^ aka
Vitamins and Minerals -^ most common example.
Cofactor - Heavy metals
Coenzymes - Organic molecules such at vitamins.

Binding Models
Lock-and-key model - Substrate binds to that potion of the enzyme with a complementary shape. 1 substrate:1
portion of enzyme. Very specific/ perfect fit
Catalytic Activity -^ Example
Induced Fit Model - binding of the substrate induces a change in the conformation of the enzyme that results
in a complementary fit.
Enzyme - This will adjust in the induced fit model.
Build Up & Synthesis -^ example

CLASSIFICATION ON ENZYME
Oxidoreductases - Enzyme that catalyze a redox reaction. Most biochemical redox reaction involve NADH
NAD or FAD  FADH
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Oxidation-reduction -^’s reaction
Transferases - Catalyzes the transfer of a functional group from one molecule to another.
Group Transfer -^ reaction
Hydrolases - Enzyme that catalyzes the hydrolysis of a molecule
Hydrolysis reaction -^’s reaction
Water - This is used to break bonds
Acids and Base - ^ usually happens between this.
Lyases - Enzyme that catalyzes the addition or elimination of functional group to form double
bonds. No ATP needed. Cleaves covalent bonds.
Isomerases - Enzymes that catalyzes the isomerization of a molecule. Forms isomers.
Isomers - Same composition, different function group
Carboxylic acid  Ketone - ^ example
Ligases - Enzyme that catalyzes the fusion of two molecules at the expense of ATP, ligation of 2
substrates at the expense of ATP.
CLASSIFICATION ON ENZYME MINADALI
Hydrolase - Catalyzes hydrolysis.
Lyases - Cleaves covalent bonds, no use of ATP
Ligase - Combines two molecules, use of ATP.
Transferase - Transfers one functional group from one molecule to another
Isomerase - Catalyzes the special rearrangement of the substrate
Oxidoreductase - Transfers electrons from one molecule from another.

FACTORS AFFECTING ENZYME ACTIVITY

pH - This alters the charge of acidic and basic amino acid residues found in active site.
Optimal ph - ph at which an enzyme exhibits maximum activity
Vmax - ^ this is achieved. The maximum reaction range.
Extreme ph - This can denature enzyme irreversibly, the loss of catalytic activity.
Temperature - The higher the more KE due to molecular collision hence the higher the reaction rate.
Optimal Temperature - Temperature at which an enzyme exhibits maximum activity.
Enzyme Concentration [E] - Is directly proportional with the reaction rate. Comparable lower than [S]
1st Order -^ is in this order of relationship.
Substrate Concentration [S] - The concentration of substrates.
1st Order Kinetics - Reaction rate dependent on an increase [S]
Zero Order Kinetics - Reaction rate independent on increase in [S]; reach of saturation point. All enzymes are
bound to substrates.
Saturation Point - S are bound to all available active sites of [E]. Increase in [S] will not affect rxn rate.
Inhibitor - Substances that reduce an enzyme’s activity
Irreversible Enzyme Inhibitor - Binds tightly, permanently blocks alterations in E. Enzyme does not function after
binding.
Covalent Bonds -^ binds via these bonds.
Suicide Substrate - Kills itself when it links to an irreversible inhibitor. Inhibitory substrate analog that
generates reactive group (through normal E action) and covalently links
to active site on E.
Trojan Horse Substrate- ^ AKA
Reversible Enzyme Inhibitor - Binds with E through non covalent interaction. Enzymes can be preserved.
Secondary and Tertiary - ^ can bind with these structures.
Competitive Inhibitor - Still reach maximal velocity but will take more time (since inhibitors are reversible)
Competes for the same site as substrate.
Km - This is raised
Vmax - This stays the same
Noncompetitive Inhibitor - Binding site is not the same as S. Binding will make the enzyme inactive.
Km - This remains the same
Vmax - This is lowered
Cofactor - Non Protein component required in the enzyme activity.
Essential Ions - Mostly metal ions.
Active Ions - Reversibly bound and often participate in the binding of the substrates.
Tightly-bound metal ions - Participate in catalytic reactions, found in metalloenzymes.
Coenzymes - Organic compounds and act as group transfer reagents; supply reactive groups not
found on the R-groups of amino acids in E.
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Summative quiz
Histidine - What amino acid contains an imidazole functional group.
DANCEGPSYQ - Which following amino acids are non-essential
Basic Amino Acids (KHR) - Which amino acids will react with an acid.
LIMAPWVF - Which amino acids are polar uncharged?
0 - What is the dominant ionization form of GAIL at pH=4
-1 - What is the dominant ionization form of GAIL at pH=10
6 - What is the approximated pH of MANILA
7.2 - What is the IpH of CHIKEN
+3 - What is the dominant ionization form of CHIKEN at pH=1
Low pH - What is the approximate pH of F?
High pH - What is the approximate pH of R?
Ones with most non-polar amino acids - Which polypeptides is the most hydrophobic?
Secondary/Tertiary/Quaternary - What level of organization refers to the 3D arrangement in localized regions of a
polypeptide chain?
Ones with Gly and Pro - Which polypeptides will not show a helical structure?
pH Change - Which will cause denaturation through ionic bond disruption?
Competitive - What kind of inhibitor binds directly to the active site?
Noncompetitive - What kind of inhibitor binds to an enzyme other than the active site?
Glucagon - Which protein increases blood sugar by stimulating gylcogen breakdown?
400 - What is the maximum number of molecules of O2 that can bind to 100 molecules of hemoglobin.
Same Vmax -Relationship the interaction of the competitive inhibitor in terms of Vmax