Biochem Test 1

Front 1

Four major biological Buffering systems

Back 1

1.) Bicarb-carbonic acid (ECF)
- most important
2.) Hgb (RBC)
3.) Phosphate (all cells)
4.) Protein (all cells & plasma)

Front 2

Henderson-Hasselbach

Back 2

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

Front 3

Factors determining effectiveness of buffer

Back 3

1.) pKa relative to pH of Soln
- Buffer works best w/in 1 pH unit of their pKa

2.) It's concentration
- higher the conc., greater the capacity to accept or donate H+

Front 4

Buffer

Back 4

CA & WB that resists changes in pH when acid or base is added

- Most effective w/in +/- 1 unit of their pKa

Front 5

treating metabolic acidosis

Back 5

(i.e.) decrease in blood pH

- Deep breathing, gives off CO2 and effectively lowers H+ which raises pH

Front 6

treating metabolic alkalosis

Back 6

(i.e) increase in blood pH

- Shallow breathing, takes in CO2 which raises H+, lowering pH

Front 7

Diabetic Keto acidosis

Back 7

-no insulin for glucose uptake
-FA converted to Ketone bodies by liver
- Causes metabolic acidosis (DKA)

Front 8

5 groups of AA

Back 8

1.)Nonpolar/aliphatic
2.)Aromatic
3.)Polar/uncharged
4.) Sulfur containing
5.)Charged

Front 9

Aromatic AA light absorbance

Back 9

Trp absorbs at 280 nm, which is the highest of all AA, explains why most proteins absorb light at 280nm

Front 10

Interactions between antigen & antibody are?

Back 10

Chemically complementary

Front 11

Chemical complementarirty

Back 11

Interactions between antigen and antibody

Conferred by:
1.) Shape of antigen binding pocket
2.) Charged positions
3.) Nonpolar H-bonds
4.) Polar H-bonds

Front 12

IgG

Back 12

-predominant antibody in serum
- Can traverse blood vessel walls and placenta
- Can activate complement system

Front 13

IgM

Back 13

- Largest
- Pentamer
- Size restricts it to blood stream
- Chains held together in pentameric form by a J-Chain

Front 14

IgA

Back 14

- Found in bodily secretions (saliva, sweat, tesrs, milk, ect.)
- Monomer or J-chain dimer
- binds to antigen and swept out of body

Front 15

IgD

Back 15

- found on surface of b-cells

Front 16

IgE

Back 16

- role in allergic response
- interacts with leukocytes in blood and histamine secreting cells
- Bind to mast cells causing release of histamine

-Recognizes pollen or other allergens as foreign, triggering immune response

Front 17

Fibrous Proteins

Back 17

1.) alpha-keratin (hair, feathers, nails)
2.)Collagen (Tendons, Bone matrix)
3.) Silk (silk fibroin)

- In each case the AA sequence and composition of these proteins favor a specific secondary structure that is important for their mechanical properties

Front 18

Alpha Keratin

Back 18

- IF
- role in cell structure
- alpha helical
- High [Ser, Glu, Gln, Cys]
- Pairs twin into left-handed coiled-coil
- Residues on interface interdigitate & are hydrophobic
(Ala, Val, Leu, Met, Phe)
- Lots of Disulfide bonds
- more disulfide = stronger

Front 19

Silk Fibroin

Back 19

- Individual polypeptide strands are in Beta conformation
- High [Gly, Ala]
- Form Beta sheets, which are stabilized by H-Bonds between peptide bonds
- Intersheet interactions are mainly Van der waals
- No stretch, but flexible
-

Front 20

Collagen

Back 20

- 2ndary structure -> Helix
1.) Left Handed
2.) 3 residues per turn
3.) Glu-X-Y
- Y often hyrdoxy proline or lysine

- 3 left handed collagen helixes (alpha chains) form a superhelical triple helix, stabilized by h-bonds
- Gly every 3rd
- Pro & hydroxy pro allows for sharp turns and twisting of collagen
-triple helical collagen = tropocollagen
- Collagen fibrils are staggered for strength

Front 21

Proline Hydroxylation

Back 21

- Post translational
- Vit. C dependent rxn
- Enzyme --> Proyl hydroxylase
*same for lysine, just lysyl hydroxylase

Front 22

Post Trans Mod of Collagen

Back 22

- Proline/Lysine Hydroxlation
- Lysine --> allysine
- Enz. Lysyl amino oxidase
- 2x allysine --> Aldol Cross-link
- Aldol condensation
- Allysine + Lys/Hydroxy lysine

in absence of covalent mods cross-linking between molecules of tropocollagen cannot occur and collagen is unstable

Front 23

Scurvy

Back 23

-Vit C defiency
-Impaired collagen synth
- no hydroxy proline, collagen becomes less stable at room temp.

Front 24

Kd and p50 for Hgb

Back 24

For a sigmoidal curve the Kd does not equal the [ligand] that yields half maximal binding P50

*However for Mgb the opposite of this is true

Front 25

H+ binding to Hgb

Back 25

- protons bind at His 146 in the bets subunit
- when protonated a salt bridge (disulfide bond) forms between his 146 & asp 94 that stabilizes the T-state
- therefore protonation of his 146 favors release of O2

Front 26

CO2 binding to Hgb

Back 26

- Does not bind to Heme
- forms a carbamate with the alpha-amino groups on each of the Hgb subunits
- Rxn produces a H+ contributing to the bohr effect

Front 27

2,3 - BPG

Back 27

- Produced by RBC from glycolysis
- Reduces affinity of Hgb for O2
- Favors release of O2
- Binds to central cavity favoring formation of T-state
- Central Cavity + & BPG -
- 1 BPG per Hgb Tetramer
- lowers aff for of HbA therefore HbA can cause O2 to HbF which does not bind BPG

Front 28

Factors favoring O2 release

Back 28

1.) H+
2.) 2,3-BPG
3.) CO2

Front 29

Factors affecting stability of secondary alpha helix

Back 29

1.) electrostatic repulsion of adacent AA
2.) R-groups 3-4 residues apart
3.) Bulkiness of R-groups (Asn, Cys, Ser, Thr)
4.) Pro or Gly

Front 30

Factors stabilizing secondary B-sheets

Back 30

H-bonds of adjacent strands

Front 31

Sickle Cell Mutation

Back 31

-Glu6Val on Beta subunit

Front 32

pH optimum

Back 32

pH range at which enzymes operate with maximum activity

*enzymes also have an optimal temperature

Front 33

standard conditions

Back 33

298K
1 atm
1 M
pH = 7.0

Front 34

Activation energy

Back 34

difference between the ground state & TS

* enzymes can lower activation energy, but cannot affect the equillibrium (Keq), but can increase rate of rxn

Front 35

Rate-limiting step

Back 35

The peak with the highest free energy change on an enzyme graph

Front 36

Transition State Theory

Back 36

"Enzymes catalyze reactions by stabilizing the TS"

- Most important that the TS state binds tightly to the Enzyme and not the substrate

- enzyme binding site is complementary and binds most effectively to the TS for the rxn

- binding of the substrate in the ES complex should be weaker than the interaction between the enzyme & the TS for the reaction

*if ES binds substrate too tightly the Ea will be higher when going from ES --> TS than when going from S --> TS, this is not favorable, actually slow rxn rate

Front 37

Induced Fit

Back 37

-upon substrate binding to an enzyme, the enzyme undergoes a conformational change converting the enzyme from the inactive to the active state
- sometimes this results in the exclusion of water
- Hexokinase is a good example of this

Front 38

Three drug targets for HIV

Back 38

1.) Reverse transcriptase
2.) Integrase
3.) Protease

Front 39

Examples of TS analagoues as HIV protease inhibitors

Back 39

"SNAIR"
1.) Saquinavir
2.) Nelfinavir
3.) Amprenavir
4.) Indinavir
5.) Ritonavir

Front 40

Factors that stabilize the TS and lead to rate enhancement

Back 40

1.) Decrease in Entropy
2.) Desolvation Effects
3.) Induced Fit
4.) General Acid-Base Catalysis
5.) Covalent Catalysis
6.) Metal Ion Catalysis
7.) Use of coenzymes

* Chymotrypsin used the first 5

Front 41

Decrease in Entropy

Back 41

* Also called rate enhancement by proximity

- proper orientation of S in E active site enhances rxn rate b/c it inc. prob. of "productive collisions"

-Bind of substrates to AS causes:
- Loss of rotational Energy
- Loss of translational Energy
- offset by favorable binding E of substrate

- ES complex now 1st order instead of 2nd called increase in "effective molarity"

Front 42

Desolvation Effects

Back 42

- When Enz binds S, desolvation of Substrate occurs

- H-bnds between S & H2O are replaced by interactions btwn Enz & S

- Contributes to rate enhancement b/c solvation shell of H-bonded H2O tend to stabilize biomolecules, making them less likely to react

Front 43

Induced Fit

Back 43

- binding of S to Enz causes a conformational change in Enz. causing interactions between R-groups on specific residues, so reaction can be catalyzed

Front 44

General Acid-Base Catalysis

Back 44

- side chains of certain AA can act as either proton donors or acceptors

Front 45

Covalent Catalysis

Back 45

- nucleophilic attack by an active site residue leads to the formation of a covalent intermediate

- Intermediate is more reactive than Substrate molecule

- A number of AA can can participate by acting as nucleophiles (e.g. Ser, Cys, His)

- Often used to activate a S for further Rxn

Front 46

Factors affecting BMR

Back 46

Body weight
Sex
Body Temp
ambient temp


BMR = (24kcal/day/kg) x (body wt. in kg)

Front 47

BMI

Back 47

(kg/m2)

18.5 --> 24.9 is desireable

Front 48

Essential components to diet

Back 48

- No essential carbs

FA essential
- Linoleic & alpha-linoleic are essential FA

Protein Essential
- Lys, Ile, Thr, Val, Trp, Phe, Met, & His
- PVT TIM HaLL

Front 49

Circumstances for neg nitrogen balance

Back 49

1.) Too little protein in diet
2.) Low quality protien (Lakcing essential AA) in diet

Front 50

anomeric carbon

Back 50

Attached to hydroxl group

rotation of hydroxyl group from beta -> alpha position is called mutorotation

Front 51

Glycosidic bond

Back 51

joins a carb(sugar) to another group, may or may not be another carb

Front 52

ECF (2parts)

Back 52

1.) Interstitial fluid
2.) Blood

* ECF is 40% of total body water ICF is 60%

Front 53

chymotryspin

Back 53

- Cleaves aromatics (Phe, Tyr, Trp)

Front 54

DCC

Back 54

- activate alpha-carboxylate of an amino acid in synthetic peptide formation

- goes C --> N