Proteins, DNA, ATP, Oxidation - Reduction and

Enzymes

Proteins

• Composed of long chains of amino acids each amino acid containing one of 20 R-groups

Amphiprotic

• Amino acids are amphiprotic meaning they possess both (carboxyl) acid and (amino) base groups

• both the amino and carboxyl groups are ionized

• in water the carboxyl group donates an H+

to the amino group, COOH becomes negatively charged, amino group becomes H+

Sequence of Amino Acids

• The 3D shape of a protein is determined by the sequence of amino acids it contains

• essential amino acids - 8 amino acids that the body cannot synthesize

• genetic information in DNA - directs RNA, ribosomes and enzymes to join amino acids to one another in a particular sequence

Peptide Bond

• Peptide bond holds amino acids together• See figure 30 page 43

Peptide Chain

• Each polypeptide chain will always have an amino terminus (A terminus) with an amino group

• and an carboxyl terminus (C terminus) with a carboxyl group

• peptide chains range in length from a few amino acids to more than a thousand

• Amino acids are joined together through a dehydration synthesis creating peptide bonds between the molecules

Primary protein structure

Four Levels of Structure

1. Primary structure: unique sequence of amino acids in the polypeptide chain

Sequence is very important, changing one amino acid alters 3D shape and protein may lose its functions. i.e. sickle cell anemia

Shape

• Many structural proteins are roughly linear in shape and form strands or sheets (secondary)

• some are rounded or spherical and are called globular proteins (tertiary)

• examples of globular proteins are enzymes

2. Secondary Structure

Secondary structure: coils and folds at various locations along polypeptide

Caused by H bonds between H and O atoms near the peptide bonds

H bonds, repeated, shape portions of polypeptide into a coil called an alpha helix separated by non-helical regions called beta pleated sheets.

I.e. Lysozyme - natural disinfectant in tears

Secondary Protein Structure• Proteins form secondary structures

through hydrogen bonds• α-Helix β – pleated sheet

3. Tertiary Structure

• Supercoiling stabilized by a number of different R group interactions

• sometimes a disulfide bridge is formed between the S-R groups of two cysteineresidues (see figure 33 page 46.

Tertiary Structure of Proteins

• Caused by the interacting (bonding and repelling) between the R groups

4. Quaternary Structure

• Two or more polypepetide subunitscome together to form a functional protein

• I.e. collagen - tendons, keratin - hair, haemoglobin - RBC

Quaternary structure • They are proteins formed from two or

more peptides (1 or more polypeptides) form a structure together

Protein Denaturation• Changes in PH, Temperature, and Ionic

concentration cause Proteins to unfold and lose their shape

Consequences of Denaturation• A denatured protein cannot carry out its

biological function• If the denaturing agent breaks the peptide

bonds that hold the amino acids together the protein will be destroyed

• Small proteins are able to refold into tertiary structures once the denaturing agent is removed

• Large globular proteins fail to refold spontaneously because many intricate folds are necessary to re-establish tertiary structure

Review

• 1. What does it mean to say that an amino acid is amphiprotic?

• It has both carboxyl acid groups and amino base groups.

• 2. What type of bond holds amino acids together?

• The peptide bond.•

Review Cont’d

• 3. What determines primary protein structure?

• The sequence of amino acids.• 4. What type of bonds cause secondary

structure of proteins?• Hydrogen bonds

Review Cont’d

• 6. How is tertiary structure stabilized?• By a number of different R group

interactions• 7. What happens when a protein

denatures?• It unfolds and loses its shape.

Nucleic acids

• Polymers composed of monomers called nucleotides

DNA (Deoxyribonucleic acid)• Composed of Long chains of nucleic

acid• Adenosine bases bond with Thymine

bases• Cytosine bases bond with Guanine

Linkage of Nucleotides

• Nucleotides are linked by a phosphodiester linkage: phosphate group of one nucleotide linked to the hydroxyl group attached to C#3 on the adjacent nucletoide

• DNA is a double stranded helix, RNA is a single stranded helix

• Each strand of DNA has a PO4 at one end and a free sugar at the other end

• DNA forms a double helix structure in which the two helixes run anti-parallel to each other

Review• 1. What are the components of a

nucleotide?• A base, a sugar and a phosphate.• 2. What is the name of the bond that

holds nucleotides together?• A phosphodiester bond.

ATP (adenosine tri phosphate)• A chemical that is formed when the

body breaks glucose down• The molecules are formed because they

are a much more efficient way of using the bodies energy, the energy from one glucose molecule can be sent 36 different places instead of just one

C6H12O6 + O2 + CO2 + H2O + 36ATP

Nucleotide Co-enzymes

• Co-enzymes NAD+, NADP+, FAD+ are involved in transport of H+ and electrons from reaction to another

• See summaries page 54 and 55

Bond Energy

• A measure of the stability of a covalent bond

• It is assumed that the energy needed to break a bond is equal to the relative stability of that bond

• In a chemical reaction bonds must be broken = energy absorbed and new bonds formed = energy released

• see potential energy diagram page 60

Activation energy• Reactions need energy to be input into

them so the reactants can break their existing bonds and create new ones

Endergonic reactions• In an Endergonic reaction the energy of

the reactants is lower then that of the products and therefore energy must be put into the reaction for it to be possible

• These reactions are not spontaneous

Exergonic reactions• In an Exergonic the energy of the

products is less then the reactant, and therefore energy is released

Redox Reactions• Chemical reactions involve the transfer

of electrons from one reactant to another

• oxidation - process of losing e-

• reduction - process of gaining e-

• reducing agent - substance that provides the electrons

• oxidizing agent - substance that takes the electrons

• i.e. Figure 11 page 66

Oxidization/Reduction Reactions

• Reduction is the gain of an electron• Oxidization is the loss of an electron

Coupled Redox Reactions

• Series of redox reactions in which the product of one redox reaction becomes the reactant of the next (see figure 12 page 67)

• Electron moves to successively stronger electron acceptors, free energy is released in each step of the process

• Basis of electron transport chains in respiration and photosynthesis

• Electrons can be passed in a chain from product A to product B through an intermediary energy transferring compound

• When an electron is passed on energy is released

Review• 1. What is ATP?• A molecule formed when glucose is broken

down.• 2. What is activation energy?• Energy needed to break the bonds of reactants.• 3. What is an endergonic reaction?• A reaction which requires energy to be put in for

it to happen.• 4. What is characteristic of an exergonic

reaction?• It is a reaction that releases energy.

Review Cont’d• 5. What is oxidation? Reduction?• Oxidation is the loss of electrons, reduction is

the gaining of electrons.• 6. What is a coupled oxidation/reduction

reaction called?• A redox reaction• 7. Where do you find coupled redox reactions in

nature?• In respiration and photosynthesis.

Enzymes

• Protein catalysts (substances that speed up a chemical reaction without being consumed)

• reactant molecules require (in order to react)

• 1. Collide with enough force• 2. Correct geometric orientation

Enzymes are used to help reduce the activation energy. They stretch and weaken bonds so it takes less energy to break them (they act as a catalyst)

Model of Enzyme Activity

• Substrate binds to a very small portion of the enzyme

• Active site: the location where the substrate binds

• Substrate and active site must possess compatible shapes

• (enzyme) protein changes shape to accommodate the substrate - this is called induced fit model

Enzymes• A catalyst that helps to speed up a reaction• Molecules bind into a site on the enzyme, the

enzyme then helps separate that molecule into smaller fragments

Ie. Maltose ----- 2Glucose

Enzyme - Substrate Complex

• An enzyme with its substrate attached is called an enzyme-substrate complex

• See figure 3 page 70• Do try this activity page 71.

Co Factors/Co Enzymes

• Co Factors are Non-Protein components such as dissolved ions, that are needed for enzymes to function

• Co Enzymes are organic non protein compounds that are needed for some enzymes to function

Allosteric regulation• Some enzymes have a receptor sites called allosteric

sites, the body produces chemicals that attach to them which will cause the enzyme to either stabilize in it’s active or non-active form, the body uses this to regulate enzyme activity

Allosteric Regulation

• A receptor site called an allostericsite is some distance from the active site, substances bind here that activate or inhibit enzyme action

• activator - binds to allosteric site and stabilizes the protein conformation keeping all active sites available

• inhibitor - stabilizes inactive form of enzyme

Allosteric regulation

Competitive inhibition• Competitive Inhibition works by the competition of

the regulatory compound and substrate for the binding site. If enough regulatory compound molecules bind to enough enzymes, the pathway is shut down or at least slowed down.

• PABA, a chemical essential to a bacteria that infects animals, resembles a drug, sulfanilamide, that competes with PABA, shutting down an essential bacterial (but not animal) pathway.

• Where do you think a non-competitive inhibitorbinds on an enzyme?

Enzyme Regulation

sulfanylamide

PABA

Feedback Inhibition• Control of metabolic pathways where

the product of a series of reactions acts as an inhibitor of an enzyme earlier in the series.

• As levels of the final product drop, inhibition of the pathway decreases and more product is produced

• See Figure 8 page 74

Feedback Inhibition

Review

• What is the function of enzymes in a chemical reaction?

• They reduce the activation energy.• Where does the substrate bind to the enzyme?• At the active site.• What is an induced fit model?• When the protein (enzyme) changes shape to

accommodate the substrate.

Review Cont’d

• What are co-factors?• Non-protein components that are needs

for enzymes to function.• How do co-enzymes differ from co-

factors?• Co-enzymes are organic non-protein

compounds needs for some enzymes to function.

Review• Compare competitive and non-

competitive inhibitors• Competitive inhibitors bind directly to

the active site while non-competitive inhibitors bind elsewhere on the enzyme causing a shape change

• Summarize types of enzyme control• enzyme inhibition, allosteric regulation,

feedback inhibition