Chem 2770 Midterm 2

Alanine, Methionine, Glutamic Acid

Proline adds bend

Lysine/Arginine and Glutamic Acid/Asparagine are not helical because of helical charge

Glycine adds flexibility and destabilizes helix

Oxygen storage in t muscle. Gene bonds the oxygen and is buried inside

Hydrophobic side chains point into the interior.

Hydrophilic side chains are on the outside and are in contact with the water.

Common in globular proteins

Cytochrome c, needs heme to function.

39% alpha helices, 0% beta strands

Immunoglobulin fold

47% beta stands, 5% alpha helices

Breaks down(hydrolyses) RNA

26% alpha helix, 35% beta strands

Disulphide bonds stabilizes this structure.

1. Hydrophobic effect

2. H-bonding

3. Electrostatic Interactions

4. van der Waals Interactions

5. desulphide bonds (covalent bonds)

6. binding of metals and other ligands

False, proteins function via changes in conformation. They are dynamic and their atoms are constantly in motion

1. heat breaks the weak interactions

2. cold, the water entropy difference at low temperature is smaller and this causes the protein to unfold

3. pH, charge repulsion at pH extremes

4. mechanical, beating egg whites

5. urea disrupts h bonding and hydrophobic interactions

6. detergents, interferes with hydrophobic effect and exposes them

7. organic solvents

molecular chaperones

Quaternary

fibrous proteins

Found in hair, feathers, and nails. It is insoluble

True

collagen

glycine

Collagen helix, which is more extended. psi =-60 and phi is 160 degrees

3 left handed polypeptides form a right handed triple helix

glycine is found where the 3 polypeptides meet, therefore no steric clashes

stacked antiparallel beta sheets

glycine and alanine, allows for close packing of the sheets

apoenzyme is a protein (no coenzyme)

holoenzyme is a protein and a coenzyme

a substance that speeds up the rate of a chemical reaction but is not itself consumed

1. oxidoreductases, transfers electrons as H or H+

2. Transferases, group transfer from one molecule to another

3. Hydrolases, bond breakage through addition of a water

4. Lyases, addition to a double bond or helps formation of a double bond

5. Isomerases, takes a group from one molecule and put it somewhere else which creates an isomer

6. Ligases, uses ATP to form covalent bonds between carbons, sulfur, oxygen, nitogen

False: no enzymes are specific and there are no side reactions

True: enzymes can be regulated

the transfer of a phosphate group.

Break (hydrolyze) peptide bonds in proteins

Trypsin, chymotrypsin, and elastase, bind different classes of amino acids according to the size, shape and charge properties of their binding site.

chymotrypisn: recognizes the large aromatice amino acids, Tyr, Trp, and Phe

trypsin: recognizes Lys and Arg positive charges

elastase: recognize small side chains

true

energy is required to break the water so it can attach, and for the double bond to oxygen is stretched(breaking) into a single bond.

is the point at which there is an equal probability of the O-H and C=O bonds reforming and new HCO3- bonds forming

by lowering the activation energy so the activation energy of the catalyst is lower then the activation energy of the uncatalyzed

binding energy lowers the transition state

substrate induces a conformational change in the enzyme that will bind the transition state more tightly

substrate binding will reduce entropy and thus lower free energy of the transition state

Histidine, Aspartic acid, Serine

acids donate H+ and accept electron pairs

bases accept H+ and donate electron pairs

stabilized by h-bonding to groups in the enzyme

true

Big Ks or Km means weak binding

Small Ks or Km means strong binding

Y= 1/Vo

m= Km/Vmax

X= 1/[S]

b= 1/Vmax

the pH might change the ionization states

the pH might change the ionization state of the substrate

might denature enzymes

inhibitor has a similar structure as the substrate and binds competitively to the same site on the enzyme as the substrate would

Inhibitor bides a a different site from the substrate site, usually an allosteric site. Alters the conformation and prevents product from forming.

Inhibitor can bind to the free enzyme or the enzyme-substrate complex.

There is no effect on Km if they are the same

The last product will be an inhibitor to an earlier reaction in a metabolic pathway. This will regulate the entire pathway.

heterotropic: enzyme is regulated by molecules that are not substrate or product of the enzyme being regulated

homotropic: if the substrate or product of the activity of their own enzyme regulation

Vo vs [S] is sigmoidal

MM plots are hyperbolic (straight line)

the t-state is low affinity

the r-state is high affinity

the state will favours the T-state.

Small amounts of substrate do not bind because the affinity is low.

As more substrate is added, the R-state begins to stabilize because its binding

Allosteric inhibitors, enzyme is less sensitive to substrate

Allosteric activators, enzyme is more sensitive to substrate

hemoglobin binds O2 cooperatively

myoglobin binds O2 non-cooperatively

False, they bind at different sites and change the conformation of the protein

Kinase adds (or phosphorylates) a phosphate

Phosphatase removes a phasphate

reversible reaction by adding or removing phosphates

they usually form a covalent bond with an active site amino acid

An inactive enzyme, that needs another enzyme for activation.

ex. in the pancreas, production of inactive trypsinogen is produced. In the gut, an activating enzyme will activate this and make it into trypsin.