BIOC 3021 Exam 1, Biochem 3021 - Exam 1

What are the major elements in living organisms?

C, H, O, N

What are the minor elements in living organisms?

P, Na, K, Ca, Mg, S, Cl

What are trace elements in living organisms?

Fe, Zn, Cu

What are the 4 types of chemical bonds?

1. Covalent

2. Ionic

3. Hydrogen Bonds

4. Weak Non-Polar Interactions

- van der Waals

- hydrophobic interactions

What are the 5 unique properties of water?

1. Cohesiveness/adhesiveness

2. High heat capacity

3. High heat of vaporization

4. Expansion upon freezing

5. Versatility as a solvent

What is a Bronsted Acid?

What is an Bronsted Base?

Acid = proton donor

Base = proton acceptor

How do you calculate pH?

-log[H3O+]

What is the Henderson-Hasselbalch Equation?

pH = pKa + log[A-]/[HA]

How do you calculate the buffer range of a solution?

pKa +/- 1

What is the carbonic acid/bicarbonate buffer system? What are its benefits?

CO2 + H2O <-> H2CO3 <-> HCO3- + H+

pKa = 6.1, but CO2 can be removed or retained by respiration which can shift equilibrium.

Oxidation Levels of Carbon

Reduced -> Oxidized

Alkane, Alcohol, Aldehyde, Ketone, Carboxylic Acid, Carbon Dioxide

Catabolism

releases energy by oxidizing carbon atoms by moving them to a higher oxidation state

Anabolism

uses energy to reduce carbon atoms by moving them to a lower oxidation state

Reduced carbon

contains energy that the cell can use. because it is fully reduced, it can be oxidized by using oxygen as the oxidizing agent and thus release the energy

Oxidized carbon

has no energy that the cell can capture, only plants can extract energy and convert it to food source (photosynthesis)

Stereoisomers

D (R in organic chemistry) and L (S in organic chemistry)

L is the preferred form in nature

Non-Polar Amino Acids

Alanine (Ala)

Valine (Val)

Leucine (Leu)

IsoLuecine (Ile)

Methionine (Met)

Proline (Pro)

Phenylalanine (Phe)

Tryptophan (Trp)

What is the pKa of Cysteine?

8.3

What is the pKa of Aspartic Acid?

4.1

What is the pKa of Glutamic Acid?

4.1

What is the pKa of Tyrosine?

10.9

What is the pKa of Histidine?

6.0

What is the pKa of Lysine?

10.8

What is the pKa of Arginine?

12.5

What amino acid can form Disulfide bonds?

Cysteine

What is the charge of an amino acid at...

1. pH 7

2. pH 1

3. pH 11

1. 0 (Zwitter ion)

2. +1

3. -1

What is an essential amino acid?

It is an amino acid that cannot by synthesized by the organism and therefore is needed to be obtained through the diet.

How does a peptide bond form?

Through a condensation reaction which requires energy, enzymes, activated precursors + catalysis

Planar Peptide Bonds

Because of double bond character between C and O and C and N in a peptide, the alpha carbon (one with R group) can swivel.

(Nth)peptide

20^n unique sequences

Protein structure levels.

Primary, Secondary, Tertiary, Quaternary

Primary structure

Core of primary structure is 3 atom repeating unit (amino nitrogen, carbonyl carbon, alpha carbon)

Secondary structure

alpha and beta sheet formation

Tertiary structure

3 dimensional form of a single polypeptide chain

Quaternary structure

deals with interaction of two or more polypeptide chains to form an aggregate protein

How to cleave (by reduce) a disulfide?

Use Beta mercaptoethanol or dithiothreitol.

Stabilize with iodoacetate

How to cleave (by oxidize) a disulfide?

Use HCOOOH

What is Edman Degradatin?

Sequential subtractive sequencing:

1. Use Phenylisothiocyanate in alkai

2. Trifluoracetic acid to selectively remove PTH-derivative

3. Identify PTH-amino aicds by HPLC

Automation - peptide attached to carboxyl terminal to insoluble bead.

Cleavage Reagents

1. Trypsin

2. Chymotrypsin

3. Staphylococcal protease

4. Cyanogen bromide

1. Lys or Arg

2. Phe, Tyr or Trp

3. Glu or Asp

4. Met

Cuts at C terminal

Secondary/Tertiary/Quaternary Protein Structures

are consequences of primary structure and its interactions with aqueous environment.

most native protein structure is achieved by spontaneous folding into thermodynamically low energy form that does not require enzyme catalysis or external energy.

sometimes aided by molecular chaperones which require ATP

Forces that maintain secondary structure

1. hydrogen bonds between carbonyl and amino group.

2. amino acid r-groups

3. planar peptide bonds

4. steric exclusion

Beta sheets can be

antiparallel or parallel

Determinants of 3o structure.

H bonds between polar amino acid and water,

H bonds between two polar AA

H bonds between carbonyl oxygen and peptide amino hydrogen

Stacking of aromatic acids

Hydrophobic interactions

Ionic interactions

Disulfide bridges

Proline disruption

True or False: Tertiary is a spontaneous event?

True

Salting out procedure

1. Add salt to aqueous solution of proteins.

2. Because salt and protein compete for water, protein molecules aggregate and precipitate.

3. Protein redissolves if salt is removed.

Salt of choice: ammonium sulfate (pure, soluble, gentle)

Gel filtration chromotography

Separates proteins by size.

Smaller molecules enter beads and are slowed down.

Large molecules flow around beads and exit faster.

Ion Exchange Chromatography

Based on attraction between charged groups in protein and column medium.

Selective absorption and elution accomplished by changing pH or salt concentration.

Affinity Chromatography

Based on selective binding of ligand by binding protein.

1. Ligand linked to insoluble column medium.

2. Pass proteins through column

3. Only binding protein is absorbed

4. Elute with high concentration of unbound ligand

PAGE

1. Form gel by polymerizing acrylamide with bis-acrylamide in buffer solution.

2. Load protein sample

3. Apply electrical voltage to separate proteins based on charge and size

4. Detect with stain or x-ray

X-ray crystallography

Determines 3 dimensional character of proteins

NMR

nuclear magnetic resonance spectroscopy, proton and carbon

What are enzyme reaction rates affected by?

1. pH

2. Temperature

3. Substrate concentration

4. Presence of cofactors/ions

Lock and Key vs Induced Fit

Theories on Enzyme-substrate mechanism

Units of Activity of Enzyme

1U = 1umole product/min

Specific activity of an enzyme

is ratio of enzyme activity to amount of protein (units/mg) which is (umole product/min/mg)

increases as enzyme is purified

What is turnover number?

It is the maximum number of molecules of substrate that an enzyme can convert to product per catalytic site per unit of time.

kcat = Vmax/[E]

What is a coenzyme?

It is a low molecular weight organic compound which cooperates with an enzyme to facilitate reaction catalysis.

can be a substrate or product

What are the two types of linkages in ATP?

Phosphoanhydride linkages (2) and phosphoester linkage (1)

Vitamin vs Coenzyme

Many coenzymes have structures that are derived from vitamins which are nutritional requirements because organism is unable to synthesize it itself. (Niacin)

NAD+ is involved in what type of reactions? NADP+?

Catabolic, anabolic

3 parts of Flavin Adenine Dinucleotide

Isoalloxazine, ribitol, riboflavin

Enzyme Catalyzed Reaction Scheme

E + S <-> ES <-> P + 3

What does a enzyme do?

Lower activation energy.

What don't enzymes do?

Do not change equilibria, products, or reactants, change in free energy

Gibbs free energy equation

http://o.quizlet.com/Zf3Qj5p.1F5WbkfjJa5FHA_m.jpg

Determinants of 4o structure

non covalent, sometimes disulfide bridges

What is the pH of a 0.01 M solution of HCl?

0.01 M HCl = 10^-2 M HCl = pH 2

( dont use H-H equation)

A buffer solution is prepared by mixing 10 mL 1M HA with 1 ml of 1 M NaA and diluting to a final volume of 100ml. What will be the pH of this buffer solution? The pK for HA is 4.

(Use H-H equation)

10 ml 1M HA = 0.01 equivalents of HA

When you have .01 equivalents (moles) of acid in a volume of 100ml it is the same as 0.1 equivalent/liter or .1M or 10^-1 M.

1ml of 1 M NaA = .001 equivalents of NaA

When you have .001 moles of base in a volume of 100ml it is the same as .01 equivalents/liter or .01M or 10^-2

pH = pK + log(base/acid)

= 4 + log (.01 M/.1M)

= 4 + log 1/10

= 4-1

= 3

** at this point you have 90% acid and 10% base and you are 1 pH unit below the pK.

A buffer soltuion is prepared by mixing 10 ml 1M HA with 10 ml of 1M NaA and diluting to a final volume of 100ml. What will be the pH of this buffer solution? the pK for HA is 4.

10 ml 1M HA = 0.01 equivalents of HA

When you have .01 equivalents (moles) of acid in a volume of 100ml it is the same as 0.1 equivalent/liter or .1M or 10^-1 M.

10 ml of 1M NaA = .01 equivalents of NaA

When you have .01 moles of base in a volume of 100 ml it is the same as 0.1 equivalent/liter or .1M or 10^-1 M

pH = pK + log (base/acid)

= 4 + log (.1M/.1)

= 4 + log 1/1

= 4-0

= 4

** at this point you have 50% acid and 50% base and the pH equals the pK.

A buffer solution is prepared by mixing 1 ml 1M HA with 10 ml of 1M NaA and diluting to a final volume of 100ml. What will be the pH of this buffer solution? the pK for HA is 4.

1 ml 1M HA = .001 equivalents of HA

when you have .001 equivalents of acid in a volume of 100 ml it is the same as 0.01 equivalent/liter or 0.01M or 10^-2 M

10 ml of 1 M NaA = 0.01 equivalents of NaA

when you have 0.01 equivalents of base in a volume of 100 ml it is the same as .1 equivalent/liter or .1M or 10^-1 M.

pH = pK + log (base/acid)

pH = 4 + log 0.1M / .01M

= 4 + log (10/1)

= 4 + 1

= 5

** at this point you have 90% base and 10% acid and the pH is one unit above the pK.

When there is a 1/10 ratio of base to acid the pH is

one unit below the pK

When there is a 1/1 ratio of base to acid the pH is

at the pK

When there is a 10/1 ratio of base to acid the pH is

one unit above the pK

A weak acid has a pK of 5. what is the ratio of acid to base at pH 4?

pH = 4, pK = 5.

pH = pK + log (base/acid)

4 = 5 + log (base/acid)

-1 = log (base/acid)

1/10 = base/acid

a weak acid has a pK of 5. what is the ratio of acid to base at pH 5?

pH = pK + log (base/acid)

5 = 5 + log (base/acid)

0 = log (base/acid)

1/1 = (base/acid)

a weak acid has a pK of 5. what is the ratio of acid to base at pH 6?

pH = pK + log (base/acid)

6 = 5 + log (base/acid)

1 = log (base/acid)

10/1 = (base/acid)

??? A buffer solution is made from a weak acid, HA (pKa = 6) and its conjugate base A-. what is the ratio of the base A- to the acid HA at pH = 5?

pH = pK + log (base/acid)

5 = 6 + log (base/acid)

-1 = log (base/acid)

1/10 = base/acid

??? which of the following elements is the LEAST common in organic compounds within living cells?

Carbon

Hydrogen

Nitrogen

Sulfur

Fluoride

Fluoride

??? If the Hydrogen ion [ ] of blood increases 10-fold, how much does the pH change?

For each whole number change in the pH scale, the actual H+ ion concentration changes ten-fold. For example, a pH change from 7 to 8 represents a drop in hydrogen ion concentration from 1 in 10 million to 1 in 100 million.

** it is lower by one pH unit

??? If the pH changes from 7 to 6 which amino acid R group is the most affected? (the most affected R group is the one with pKa the closest to pH = 7)

Histidine

??? which type of bond involves shared electrons and serves as the basic linkage in organic compounds?

Covalent

??? Which aa is essentially incompatible with alpha helix and beta sheet formation?

Proline

??? Which type of interaction is NOT stabilized by H-bonds?

between water and a non-polar R-group

In proteins the R-groups of the polar but uncharged aa, serine and glutamine generally can form ___ bonds with each other.

Hydrogen

the side chains of valine and isoleucine can form ____ bonds with each other.

Hydrophobic

which aa changes the charge on its R-group as a function of pH?

Lysine

Primary protein structure refers to:

A series of amino acids linked by peptide bonds

organic carboxyl groups generally function as

Weak acids

which of the following does not contain a type of amide bond?

a. the R-group of glutamine

b. The R-group of asparagine

c. The peptide bond

d. The R-group of alanine Correct

e. The reaction product of an amine and a carboxylic acid.

The R-group of alanine

a purification method which depend on highly selective interactions b/t a protein's binding site and a specific ligand

affinity chromatography

NMR analysis is used to determine

interactions between hydrogen atoms within a molecule

What type of protein would stick very tightly to a (+) charged DEAE cellulose ion exchange column?

a protein that was highly negatively charged

the migration of protein subunits in a SDS polyacrylamide gel electrophoresis system depends mostly on

the size of the native protein subunits

a technique that is used to determine the 3D form of a protein is

X-ray Diffraction

what is not true about a peptide bond?

it has a planar structure because of partial double bonding

it can pick up a proton to carry a net positive charge

it has a type of amide bond

it has a carbonyl group linked to a N atom

It resonates between single and double bonds (exists as a hybrid)

It can pick up a proton to carry a net positive charge

Enzymes can:

change the rate of a reaction

What is the primary reagent used to sequence proteins during the Edman degradation?

phenylisothiocyanate

what reagent is used to prevent reoxidation of sulfhydryl groups during the reduction of protein disulfides?

iodoacetate

the phi and psi bonds that flank peptide bonds in proteins

are able to rotate but generally assume certain combinations of bond angles.

the overall free energy change for a chemical reaction is positive if the reaction

does not favor product formation