1. All proteins in humans are polymers made up of ____ different __________.
1. 20 different amino acids.
What types of functions to structural proteins provide? Give 2 examples.
They provide structural components. Eg. Collagen in tendons and cartilage and Keratin in hair, skin, wool, and nails.
What types of functions to contractile proteins provide? Give 2 examples.
They provide movement of the muscles. Eg. Myosin and actin control muscle fibres.
What types of functions to transport proteins provide? Give 2 examples.
They carry essential substances throughout the body. Eg. Hemoglobin transports oxygen and lipoproteins transport lipids.
What types of functions to storage proteins provide? Give 2 examples.
They store nutrients. Eg. Casein stores protein in milk and Ferritin stores iron in the spleen and liver.
1. What types of functions to hormone proteins provide? Give 2 examples.
2. Hormones can be either protein based or _______ based.
1. The regulare body metabolism and nervous system. Eg. Insulin regulates blood glucose levels and growth hormone regulates the body's growth.
What types of functions to enzyme proteins provide? Give 2 examples.
They catalyze biochemical reactions in cells. Eg. Sucrose catalyses the hydrolysis of sucrose. Trypsin catalysez the hydrolysis of protein.
What types of functions to protection proteins provide? Give 2 examples.
They recognize and destroy foreign objects. Eg. Immunoglobulins stimulate immune responses.
1. What are the functional groups in amino acids (AAs)?
2. What three things are bonded to a central carbon atom in the 20 AAs found in proteins?
3. AAs with this structure are called _______.
4. The unique characteristics of these 20 AAs are due to the side chain (R-group) which occupies _______________.
1. an amino group (NH₂) and a carboxylic acid group (COOH)
2. an amino group (NH₂) and a carboxylic acid group (COOH) and a hydrogen
3. α amino acids
4. the 4th bond to the central carbon atom
What is a zwitterion and what is its charge?
A molecule with a positive and a negative charge on the same structure. It has a net charge of zero.
*** All amino acids are examples of zwitterions.
1. How are atoms combined in proteins?
2. What is important to remember about them?
3. What is the nature of the side chain in the AA? Why is this important?
1. The carboxyl and amino groups are combined in peptide linkage.
2. They are not available for chemical reaction, except for H-bonding
3. It dictates the AAs role in the protein and ∴ is useful to classify AA according to the properties of the chain.
1. With the exception of ___________, all AAs are (1°, 2°, or 3°) amines?
2. What are primary amines?
1. Proline. 1°.
2. Primary amines arise when one of three hydrogen atoms in ammonia is replaced by an alkyl.
1. The NP side chain (does/does not) bind, give off protons, or participate in H or ionic bonds.
2. What makes these AAs hydrophobic?
1. The NP side chain does NOT bind, give off protons, or participate in H or ionic bonds.
2. The HCs are NP and, therefore, not soluble in water. *** These AAs can be thought of as lipid-like. Therefore, they are soluble in lipids.
1. What happens with the side chains in proteins that are in aqueous solution and why?
2. What happens with the side chains in lipid cell membranes and why?
1. The side chains cluster together in the interior of the protein. This is due to the hydrophobicity of the non-polar R-groups.
2. When in a lipid cell membrane, the non-polar R groups are then found on the surface of the protein
1. Why are they hydrophilic?
3. Which 3 AAs contain a polar hydroxyl group that can participate in H-bonding?
4. Which 3 AAs exhibit some degree of polarity in the R groups.
1. B/c the EN atoms in the side chains form H-bonds with water.
3. The first 3: Serine, threonine, and tyrosine.
4. The last 3: Asparagine, cysteine, and glutamine.
What does the side chain of cysteine contain? Why is this important?
It contains a sulphydryl group (-SH). It is an important component of the active site of many enzymes. For example, in proteins, the -SH groups of two cysteines can become oxidized to form a covalent cross-link called a disulphide bond (S-S).
1. What do they contain?
2. They can ionize as a (strong/weak) acid).
3. Which two amino acids are proton donors?
1. a carboxylic acid group (COOH)
3. aspartic acid and glutamic acid. They become aspartate and glutamate.
1. What do these AAs contain?
2. ____________ is only weakly basic in comparison to the other two.
1. An amino group that can ionize as a weak base, by accepting proton(s).
1. The α-carbon of each AA is attached to _____________, except for glycine. This makes it a ________.
2. Why is glycine an exception?
1. 4 different chemical groups. Chiral carbon.
2. B/c its α-carbon has two hydrogen substituents.
1. AAs that have an asymmetric centre at the α-carbon can exist in two forms. What are they? This makes them ___________.
2. How are they drawn and identified?
3. Which is most dominant in biological systems?
1. D & L. Stereoisomers of each other.
2. Drawn using Fisher Projections. But for the L isomer, the amino group (NH₂) is on the left and for the D group, it's on the right
3. L-amino acids. D amino acids are in nature, but not in proteins.
1. What is the isoelectric point (pI)?
2. What happens when the pH is different from the pI?
3. In a solution that is more acidic than the pI, what happens with the -COO⁻ group?
4. What about in a solution more basic than the PI?
1. The point at which an AA exists as a zwitterion (+ and - charge).
2. The zwitterion accepts or donates H⁺.
3. It acts as a base and acceps an H⁺, giving an overall positive charge to the amino acid.
4. The HN₃⁺ group acts as an acid and loses an H⁺, giving the AA an overall negative charge.
When the conjugate base and acid are present in equal concentrations, their ratio is _____, the log is _____, and so the pH = ______.
2. A buffer has maximum buffering capacity at its _______, when the acidic and basic forms are present in ______ concentrations.
3. Each AA has 2 pKa's, referred to as ________ and ______.
4. An AA has minimal buffering capacity when the pH = _____ and it has maximal buffering capacity at each of its ______.
1. one, zero, pKa.
2. pKa, equal
3. pKa₁ and pKa₂
4. pI. pKa's (i.e. when [base]=[acid]
Of the 20 AAs, which are considered essential, meaning not produceable by the body?
mnemonic device: PVT TIM HALL
PVT: Phenylalanine (Phe), Valine, Threonine
TIM: Tryptophan, Isoleucine, Methionine
HALL: Histidine, Argine, Leucine, Lycine
1. How are the characteristics of a protein determined?
2. What is a peptide bond?
3. Two amino acids linked together by a peptide bond, form a ____________.
4. In a peptide, the AA on the left with the free NH₃⁺ group is called the _________, while the one on the right with the free COO⁻ group is called the ________.
1. By which AAs make up that protein.
2. An amide bond that forms when the COO⁻ group of one AA reacts with the NH₃⁺ group of the next AA. terminal
4. N-terminal AA , the C-terminal AA.
1. As a consequence of resonance contributors, the peptide bond has ~40% ________ character. What does this mean for it's structure and function?
1. double bond ∴ the peptide bond is shorter than a regular chemical bond, making it rigid and planar. This characteristic prevents free rotation about the bond.
1. The peptide bond is generally a _____ bond due to the steric hinderance of the R-groups when in the __________.
2. The C=O and the NH groups of the peptide bond are polar and are ∴ involved in _______ bonds.
1. trans, cis position
How do you name peptides?
2. What would be the name for a tripeptide consisting of alanine, glycine, and serine be named?
1. Each AA beginning from the N-terminal is named in order with its 3-letter abbreviated name.
1. When is a polypeptide (PP) chain called a protein?
2. What are the levels of protein structures?
1. When there are more than 50 AAs.
2. Primary (1°), secondary (2°), tertiary (3°), and quaternary.
1. How is a 1° protein structure determined?
1. Simply by the order of the amino acids held together by peptide bonds.
1. How is a 2° protein structure determined?
2. What are the most common secondary protein structures?
1. The secondary structure of a protein describes the way the AAs next to or near each other along the polypeptide are arranged in space.
2. Alpha-helix, beta-pleated sheet, and the triple helix. Each type looks at: (a) the H-bonding between the H atom of an amino group and the polypeptide chain and (b) the oxygen atom of the carbonyl group in another part of the chain.
1. Explain the α-helix structure of protein. (4 points)
2. What types of tissues have this structure?
1. Strong, spiral, tightly coiled like a telephone cord
2. Extensive H-bonding between each NH group and the O of a C=O group in the next turn of the helix, 4 AAs down the chain.
3. Individually bonds are weak, but together they are strong (like a zipper and its individual links)
4. All side chains (R-groups) are located on the outside of the helix.
2. skin and hair
1. Explain the β-Pleated Sheet structure of protein. (4 points)
2. What types of proteins have this structure?
1. PP chains are held together side by side by H-bonds between the peptide chains
2. Surfaces of the β-sheet appear pleated
3. β-sheet have 2 or more peptide strands that are almost fully extended and held together by H-bonds
4. H-bonds are perpendicular to the PP backbone
1. Explain the Triple Helix structure of protein. (1 point).
2. What is the most abundant protein and where is it found?
3. What does this protein have a high content of and how does it contribute to the strength of the helix?
1. * The result of three polypeptides woven together like a braid.
2. Collagen. Found in connective tissue, blood vessels, skin, tendons, ligaments, the eye and cartilage.
3. Glycine, proline, alanine, and hydroxylproline and hydroxylysisine. The -OH groups present in their hydroxyl forms in proline and lysine form H-bonds across the peptide chains giving strength to the helix.
What happens when a diet is deficient in Vitamin C? (4 points)
1. Collagen fibrils are weakened b/c the enzymes needed to form hydroxylproline and hydroxylysisine require Vitamin C.
2. Without the -OH groups to form hydroxylproline and hydroxylysisine, there is less H-bondng between collagen fibrils.
3. As a person ages, additional cross-links form making collagen less elastic.
4. Bones, cartilage, and tendons become more brittle and wrinkles are seen as skin loses elasticity.
1. How is a 3° protein structure determined?
2. What does tertiary refer to?
3. PP chains > 200 AAs generally consist of ___ or more domains.
4. What are the different stablizing interactions of 3° protein structures?
1. It involves attractions and repulsions between the side chain groups of the AAs in the PP chain. Segments twist and bend until the protein acquires a specific 3D shape.
2. Refers to both the folding of domains (the basic unit of structure and function) and the final arrangement of domains in the polypeptide.
4. Hydrophobic, Hydrophilic, H-Bonds, Disulphide bonds, and Ionic Interactions (Salt Bridges)
Describe hydrophobic interactions. (3 points)
1. NP side chains are located in the centre of the PP chain.
2. Hydrophilic portions of the PP chain are located on the surface
3. Proteins located in NP (lipid) environments have the reverse arrangement (i.e. Polar parts on surface and Hydrophilic parts in interior).
Describe hydrophobic interactions. (2 points)
1. Attractions between the external, aqueous envt and AAs that have polar or ionized side chains.
2. Polar side chains pull twd the outer surface of the protein and hydrogens bond with water.
Describe H-Bond interactions. (2 points)
1. H-bonds form between polar amino acids.
2. Eg. An H-bond can occur between the -OH group of serine adn the -NH₂ group of glutamine.
Describe Ionic (salt bridge) interactions. (2 points)
1. Ionic bonds between side groups of basic and acidic amino acids, which have + and - charges.
2. The attraction of the oppositely charges side chains forms a strong bond called a salt bridge.
Describe Disulphide Bond interactions. (2 points)
1. Covalent linkage between the -SH group of each two cysteine AAs.
2. The cysteines may be separated by many AAs or may be located in different PP chains altogether.
Secondary and tertiary structures are like the bricks and mortar of protein architecture.
1. Globular proteins have ______ shapes b/c of their secondary structures of the PP chain fold over on top of each other.
2. Globular proteins perform much of the work of the cells including these 3 functions?
3. Heme proteins are specialized globular proteins. What 2 are the most abundant in humans?
1. compact, sphirical
2. synthesis, transport and metabolism
3. myoglobin and hemoglobin. They serve to bind oxygen reversibly.
1. What is a porphyrin?
2. Explain the properties of Heme. (5 points)
1. Cyclic compounds that readily bind to metals, particularly Fe²⁺ and Fe³⁺.
2.a) It's a porphyrin ring with Fe²⁺ at centre.
b) Responsible for the red colour of blood.
c) Iron is held in centre of the heme molecule by bonds to the 4 nitrogens of the porphyrin ring
d) Fe²⁺ can form 2 additional bonds: One on either side of the ring
e) Each heme group can bond one molecule of O₂
1. What are fibrous proteins?
2. What are the two types? Describe them.
1. Long, thin, fibre-like shapes of proteins that are involved in the structure and cells of tissues.
2. α & β-keratins
1. Describe α-keratins. (2 points)
2. Describe β-keratins. (2 points)
1. Make up hair, wool, skin and nails.
2. Within the fibril, the α-helices are held together by disulphide (S-S) linkages btwn the R groups of the many cystein AAs in hair. Several fibrils bind together to form a strand of hair.
1. Found in feathers and scales.
2. The proteins consist of large amounts of β-pleated sheets.
1. What is the quaternary structure of protein?
2. How do they work? (3 points)
1. The spacial arrangement of the PP subunits (i.e. a single chain, or 2 or more chains that may/may not be related).
2.a) Held together by non-covalent interactions (ie. hydrophobic, ionic, etc.). b) ∴ interactions that stabilize the tertiary structure also stabilizes the quaternary. c) Subunits may work together or independently of one another.
1. How does protein denaturation occur? What happens?
2. What are some denaturing agents?
3. Is denaturation reversible? Explain.
1. The disruption of any of the bonds that stabilize the 2°, 3°, 4° of the protein. However, covalent bonds of the primary structure are unaffected. When denatured, proteins lose their shape and ability to be functional.
2.Heat, strong acids, bases, and heavy metals.
3. No. The protein is unable to retain its original structure.
1. What proteins sequester and deliver O₂ to the cells?
2. Where are they found and what are they responsible for?
1. Myoglobin (Mb) and Hemoglobin (Hb)
2. Mb found in skeletal and striated muscle.
Hb found in erythrocytes. Responsble for movement of O₂ between lungs and other tissue.
What is the maximum pO₂ (partial pressure of oxygen) in arterial blood? What about in air?
100mm Hg (mercury)
150 mm Hg
1. What is myoglobin?
2. How many AAs in a single PP chain of myoglobin with about 3/4 of the chain in the α-helix secondary structure?
1. a) A storage protein. A globular heme protein present in heart and skeletal muscle.
b) functions as a reservoir for oxygen & as an oxygen carrier that increases the rate of transport of oxygen within the muscle cell.
1. Hemoglobin is composed of ___ PP chains or subunits: ___ α chains and __ β chains, denoted as _____.
2. How are the chains held together?
3. Each subunit of Hb contains a heme group giving the molecule ___ heme groups in total (compared to 1 for Mb).
4. Te complete quaternary structure of Hb can bind and transport ___ molecules of oygen. It can transport CO₂ from tissues to lungs and carry O₂ from lungs to tissues.
1. 4. 2. 2. denoted as α₂β₂.
2. By non-covalent interactions.
1. Like O₂, CO₂ binds to heme groups. The affinity for CO is more than 10⁴ x that of O₂. What implications does this have if there was prolonged exposure of Hb to CO.
What would be the treatment of choice?
1. It would be irreversible and lead to highly toxic levels of arboxyhemoglobin.
2. Hyperbaric O₂
1. What unique role does Hb play in the body and why is
1. It gather incomming O₂ from lungs and releases it to tissues.
1. What is an enzyme?
2. How do enzymes affect the breakdown of proteins in our diet?
3. How are enzymes named? What is the exception?
1. A protein that is a catalyst. Large protein molecules that speed up the rates of chemical reactions without themselves undergoing any change. They lower the AE required. ∴ less energy is reqd to convert reactant molecules to products.
2. Enzymes speed up the breakdown of proteins. Without them they wouldn't break down quickly enough to meet the body's needs.
3. Replace the end of the name of the reaction/reacting compound with -ase. Exception: Early enzymes sometimes used the -in suffix, such as pepsin and trypsin which are used to break down proteins.
1. For the enzyme class oxidoreductases. What reaction is catalyzed?
2. For example, what do oxidases,
reductases, and dehydrogenases do?
1. Oxidation-reduction RXNs
2. Eg. Oxidases oxidize a substance. Reductases remove a substance. Dehydrogenases remove atoms, to form a double bond.
1. For the enzyme class transferases. What reaction is catalyzed?
2. For example, what do transaminases and kinases do?
1. Transfer a group between two compounds. 2. Eg. Transaminases transfer amino groups (NH₂). Kinases transfer phosphate groups (PO₄²⁻)
1. For the enzyme class Hydolases. What reaction is catalyzed?
2. For example, what do proteases, lipases, carbohydrases, phosphatases, and nucleases do?
1. Hydrolysis RXNs
2. Eg. Proteases hydrolyze peptide bonds. Lipases hydrolyze ester bonds in lipids.
Carbohydrases hydrolyse glycosidic bonds in carbohydrates. Phosphatases hydrolyze phosphate-ester bonds.
Nucleases hydrolyze nucleic acids.
1. For the enzyme class Lysases. What reaction is catalyzed?
2. For example, what do carboxylases and deaminases do?
1. Add or remove groups involving a double bond without hydrolysis.
2. Eg. Carboxylases add CO₂ and Deaminases add NH₃
1. For the enzyme class Isomerases. What reaction is catalyzed?
2. For example, what do Isomerases and Epimerases do?
1. Rearrange atoms in a molecule to form an isomer.
2. Eg. Isomerases converts cis to trans or vice versa and epimerases convert D to L isomers or vice versa
1. For the enzyme class Ligases. What reaction is catalyzed?
2. For example, what do synthetases do?
1. Form bonds between molecules using ATP.
2. Eg. Synthetases combine two molecules.
1. What are substrates?
2. What structure of an enzyme plays an important role in how the enzyme catalyzes RXNs?
3. How do enzymes work? What models do they use?
1. Reacting molecules.
2. The tertiary structure.
3. They bind to a substrat via its active site. They use a lock and key & Induced fit models.
1. What is the 2-step reaction of an enzyme catalyzed reaction?
2. What happens?
3. What factors affect enzyme activity?
1. E + S --> ES --> E + P
2. Leaves the exzyme and produces a product (i.e. sucrase + sucrose -->sucrase-sucrose complex --> sucrase + glucose + fructose
3. Temp., pH, substrate concentration, & competitive & non-competitive inhibition?
1. How does temperature affect enzyme activity?
2. How does pH affect enzyme activity?
3. Specifically, how does pepsin work in the stomach?
1. Low temp = little activity. Increase temp = increased activity until OPTIMUM temp is reached. For most enzymes this is body temp (37°C). At 50° and above, the protein can become denatured and lose its activity.
2. pH above or below the optimum causes a change in the 3D structure of the enzyme that disrupts the active site. Enzymes in most cells have an optimum pH at physiological pH (~7.4). But stomach enzymes have lower optimum pH.
3. Pepsin has optimum pH of 2. Btwn meals pH rises to btwn 4-5 and pepsin shows little activity. When we eat, it triggers the release of HCl to stomach, lowering the pH.
How does substrate concentration affect enzyme activity?
When enzyme [ ] is kept constant, increasing the substrate [ ] increases the rate of the catalyzed rxn as long as their are more enzyme molecules than substrate molucules. At some point, the substrate [ ] saturates the enzyme. All availble enzyme molecules are then bonded to the substrate, the rate of catalyzed reaction reaches its max 7 adding more substrate cannot increase the rate any further.
How does competitive inhibition affect enzyme activity?
Competitive inhibition: An inhibitor has a structutre so similar to the substrate that it competes for the same active site as the substrate. If the [ ] of the inhibitor is substantial, there is a loss of enzyme activity. Increasing the substrate [ ] displaces more of the inhibitor molecules. As more enzyme molecules bind to substrate (ES), enzyme activity is regained.
How does enzyme inhibition affect enzyme activity?
They prevent the active site from binding with a substrate.
How does non-competitive inhibition affect enzyme activity?
Non-competitive inhibition: The inhibitor acts on a site that is not the active site. It doesn't resemble the substrate and doesn't compete for the active site.
The binding causes the shape of the enzyme to be distorted, including the shape of the active site. Inhibition occurs b/c substrate cannot fit/does not properly fit the active site ∴ no catalysis can occur.
B/c a non-competitive inhibitor isn't competing for the active site, te addition of more substrate does not reverse this type of inhibition.
Examples include heavy metal ions that bond with AA R-groups.
Catalytic activity is restored when chemical reagents remove the inhibitors.
1. What are simple enzymes?
2. What are enzyme cofactors?
3. What is an apoenzyme?
4. What are coenzymes?
1. When their functional forms consist only of proteins with tertiary structures (eg. Trypsin and pepsin)
2. Non protein portions of enzymes required for carrying out a catalyzed reaction. They may be metallic ions or organic compounds.
3. The protein (polypeptide) portion of the the enzyme.
4. Organic cofactors. I.e B vitamins. If tan enzyme requires a cofactor, neither the protein structure or the cofactor aloe has catalytic activity.
1. What are proenzymes or zymogens? Give an example.
1. Enzymes that are manufactured by the body in inactive form. In order to make them active, a small part of their PP chain must be removed.
The body does this as a protective mechanism so that it will activate the enzyme where it wants it to work.
Eg. Trypsin is a protease (cleaves proteins). We want it to work in our stomachs on the proteins we eat. If it worked outside the stomach in its active form, it would destroy our body's own proteins.
1. What is allosterism?
2. What can happen if a substance binds non-covalently & reversible to a site other than the active site?
3. The substance that binds the allosteric enzyme is called ____________.
1. When enzyme regulation takes places by means of an event that occurs at a site other than the active site, but will effect the active site. The enzyme regulated by it is called an allosteric enzyme.
2. It may inhibit enzyme action (AKA negative modulation) or stimulate enzyme action (AKA positive modulation)
3. A regulator.
1. What are isoenzymes?
2. Different forms of the same enzyme are called ____ or ____.
1. Enzymes that perform the same function but have very different combinations of subunits in different tissues. (i.e. different quaternary structures)
2. isozyme or isoenzyme.
1. Heme has only up to a ___________ protein structure.