OxPho & ETC along Inner Mitochondrial Membrane

Amino Acids & Proteins

Protein Structure/Dep on...1° Primary--DNA, 2° Secondary--H-bonds b/w amino acid backbone, 3° Tertiary--CHAPERONE PROTEINS non-cov folding

Alpha Helices & Beta Sheets are forms of 2° SECONDARY proteins structure because of H-bonding patterns

LIVER "deaminates" amino acids, converting them into ammonia (toxic), then combines them with CO2 to form UREA

Amino Acid TERMS

• The genetic code is composed of nucleotide triplets. In other words, three nucleotides in mRNA (a codon) specify one amino acid in a protein.
• The code is non-overlapping. This means that successive triplets are read in order. Each nucleotide is part of only one triplet codon.
• The genetic code is unambiguous. Each codon specifies a particular amino acid, and only one amino acid. In other words, the codon ACG codes for the amino acid threonine, and only threonine.
• The genetic code is degenerate (redundant!). In contrast, each amino acid can be specified by more than one codon.
• The code is nearly universal. Almost all organisms in nature (from bacteria to humans) use exactly the same genetic code. The rare exceptions include some changes in the code in mitochondria, and in a few protozoan species.

Hemoglobin and the Oxygen-Dissociation Curve (IB)

- "Partial Pressures" of O2 and CO2 are measurements of their concentrations

- As O2 binds, conformational change makes it easier for other O2's to join (4 in total, 4 heme groups per hemoglobin)

- As O2 leaves, makes it easier for other O2's to leave

- When CO2 is produced it diffuses into RBC, where it reacts with H2O and is converted into Carbonic Acid via carbonic anhydrase enzyme, ****the acid then dissociates into H+ and HCO3-

- The H+ ions made the blood more acidic which causes oxyhemoglobin to dissociate and release O2

- The HCO3- ions are pumped through the membrane of the RBC and into the plasma where they combine with Na+ to form NaHCO3

- To ensure that the RBCs remain uncharged, Cl- ions pass into them. This is known as the chloride shift!

- When the RBCs reach the lungs, the NaHCO3 combines with H+ to form H2O, CO2, and Na+

- The CO2 is then released from the body during exhalation

Partial Pressure of CO2

- As cells respire, the pO2 decreases, and the pCO2 increases

- An increase in the pCO2 causes Oxyhemoglobin to give up its O2 more readily

- This is because when the CO2 is converted to acid it produces H+ ions which lowers the pH of the blood

- The Oxyhemoglobin then dissociates, giving up its O2 so that the Hb can bind to the H+ ions to prevent a change in pH

- Therefore Hb acts as a buffer by taking up the H+ ions and forming "Hemoglobinic Acid"

BOHR EFFECT (shift in affinity graph)

- more oxygen released with increase in CO2 and lowering of pH levels

- as pCO2 increases, the dissociation curve shifts to the right & down

So Overall:

- When O2 diffuses into the lungs there is a high PP of O2, so it will load onto Hb forming Oxyhemoglobin

- The O2 is then carried in the blood to respiring cells that have a low pO2 and a high pCO2

- So the Oxyhemoglobin releases the O2 because of the low pO2 and ALSO because of the high pCO2 which causes a DROP in pH

- The O2 is used by cells for respiration and the Hb binds to the H+ ions to prevent changes in pH

The composition and O2 carrying capacity differs among organisms...

Leslie: http://www.interactive-biology.com/2643/061-the-bohr-effect/

Transport of Respiratory Gases: http://www.youtube.com/watch?v=Qrvrs6RXxwY

Biochem dude: http://www.youtube.com/watch?v=DgelvyH7iB8&feature=related

Transmembrane Domains

"...Because the interior of the bilayer and the interiors of most proteins of known structure are hydrophobic, it is presumed to be a requirement of the amino acids that span a membrane that they be hydrophobic as well..."

Blue, Pink, (some) Green FLASHCARDS!

Very Hydrophobic Amino Acids:

Enzymatic Monsters

Enzymes are your garden variety protein catalysts that perform a few very important functions, some of which they critically do or do not do. Let's call COOKIE MONSTER the enzyme, and his COOKIE the substrate.

DO:
1) Lower the Ea of the reaction
2) Increase the RATE of the reaction

DO NOT:
3) Do not affect the ΔG (free energy)
- energy from initial to final state
4) Are neither changed nor consumed during a reaction
5) Do not alter the equilibrium constant (K)!!!

Enzymes vary in their specificity to a substrate and are specific for a particular reaction or class of reactions. The most promising theory that accounts for ES complex formation is the "Induced Fit Hypothesis" in which the active site conforms to the contour of the substrate instead of maintaining a definitive shape ("Lock & Key Theory").
- Cookie monster eats chocolate chip cookies, not oreos

Enzymes may require co-enzymes (non-protein molecules) to be catalytically active. These may either help with substrate binding or induce the ACTIVE, as opposed to the alternate inactive, allosteric conformation.
- Cookie monster's allostery means he's either got on inhibitory Orthodontic headgear or is open-mouthed and cravin' some kooks

Enzyme affinity can be read from a chart that plots "reaction velocity (V)" and "substrate concentration (S)" against each other. Vmax is the tapering off of the reaction curve that says the enzymes are full and cannot increase the rate of reaction anymore. 1/2 Vmax is at the midway point of the vertical curve that says exactly half of the binding sites are open--the most ideal state for operating enzymes. Substrate concentration Km will correspond to 1/2 Vmax on the x-axis. A low Km means ES affinity is HIGH (if the reaction req. a short period of time, the affinity must be strong!). A high Km means the affinity is LOW (the ideal rate is taking a long time).
- Cookie monster has reached Vmax when his mouth is so full of cookies he can no longer fit anymore. He is at 1/2 Vmax when he's been offered a certain number of cookies (Km) at a comfortable pace such that he can swallow them in a generally useful fashion. A low Km (preferred) means he's been starvin' marvin'. A high Km means he had Applebee's curb-side to go before cookie time.

Also useful:

"Take Vmax first. A low value means that the enzyme does not convert much substrate to product per unit of time when the enzyme is saturated with substrate. Thus the maximal velocity of the enzyme is relatively small. A large Vmax means just the opposite. The Vmax is essentially a measure of how fast the enzyme can work when it is completely saturated with the substrate.

The Km is a little more confusing only because some people mix up a large value with a small value. For example, compare 1x10^-10 M to 1x10^-3 M. The 1x10^-3 M is much larger than 1x10^-10 M, and the larger the Km the lower the affinity of the substrate for the enzyme. Thus a high Km means it takes a greater concentration of substrate for the enzyme to be half saturated compared to a low Km which means it only takes a very little bit or a very low concentration of substrate for the enzyme to be half saturated (half maximal velocity)."

Enzymes are sensitive to pH and temperature conditions. Ideal pH is 7.4 (with stomach and pancreatic exceptions) and temperature is 40°C. Rates of reactions tend to double with 10°C increments.

Enzymes can also be inhibited by 1) Feedback inhibition--later product in cascade inhibits earlier enzyme in cascade, 2) Competitive Inhibition--compete with substrate's active site, or 3) Noncompetitive Inhibition--forms covalent bond with enzyme.

***2 & 3 are both forms of REVERSIBLE inhibition. IRREVERSIBLE inhibition involves permanent damage to the active site.

Holoenzyme

Cooperative Binding

Enzyme's affinity for its ligand changes with the amount of ligand already bound.

Cooperative binding is a special case of allostery. Cooperative binding requires that the macromolecule have more than one binding site, since cooperativity results from the interactions between binding sites. If the binding of ligand at one site increases the affinity for ligand at another site, the macromolecule exhibits positive cooperativity. Conversely, if the binding of ligand at one site lowers the affinity for ligand at another site, the protein exhibits negative cooperativity. If the ligand binds at each site independently, the binding is non-cooperative.

Allosteric Regulation (Allostery)

The regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site (that is, a site other than the protein's active site).

Allosteric Enzyme

enzymes that change their conformation upon binding of an effector. An allosteric enzyme is an oligomer whose biological activity is affected by altering the conformation(s) of its quaternary structure.

Allosteric enzymes

Enzymes with multiple subunits have quaternary structure. One consequence of multiple subunits is that individual catalytic subunits each have their own active site. This means that an enzyme with quaternary structure can bind more than one substrate molecule. Allostery means "different shape." Allosteric enzymes change shape between active and inactive shapes as a result of the binding of substrates at the active site, and of regulatory molecules at other sites. In the simple case of an allosteric enzyme with an active and inactive form, the change in reaction rate with increasing substrate concentration is typically an "S-shaped" curve. For more information on allosteric enzyme, see the tutorial for question 14.

Binding of effectors to regulatory subunits

Allosteric enzymes may also have regulatory subunits that bind either activators or inhibitors. Activators and inhibitors are termed "effectors." Inhibitors cause the allosteric enzyme to adopt the inactive shape. Activators promote the active shape.

An equilibrium exists between the active and inactive shapes. The amount of active and inactive enzyme is dependent on the relative concentrations of substrate and inhibitor, as suggested by the diagram:

The binding of an allosteric inhibitor causes the enzyme to adopt the inactive conformation, and promotes the cooperative binding of a second inhibitor.

An excess of substrate can overcome the inhibitor effect. Substrate binding causes the enzyme to assume the active conformation, and promotes the cooperative binding of additional substrate, leading to product formation."

The meaning of the S-shaped Curves with and without inhibitor

As the substrate concentration is increased, substrate binds to enzyme and triggers a conformation change to the active shape of the enzyme.

In the presence of inhibitor (plus inhibitor), higher concentration of substrate is required to shift the enzyme to the active conformation. However once a high enough concentration of substrate is reached to promote active shape, the substrate binds cooperatively (S-shaped curve), and the same maximum rate is achieved as without inhibitor.

Source:

http://www.biology.arizona.edu