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Biochemistry > Exam 1 > Flashcards

Exam 1 Flashcards

AA/Water Chem/

1
Q

name two reasons nature chose phosphates

why dont ochemists use p-fate

A
  1. negative charge at physio pH so that is sequesters within the membrane. it can link two nucleotides and still ionize
  2. stable bonding (ester formation) which are resistant to hydrolysis

ochemists dont use p-fate b/c it is not reactive enough as an intermediary

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2
Q

name 8 unique prop. of water

A
  1. h-bond
  2. high heat capacity (thermal Buffer)
  3. high dialectric const.
  4. universal solvent (almost)
  5. hydrophobic effect
  6. surface tension
  7. expands when freezes
  8. participates in reactions
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3
Q

state ECF/ICF concentration as high or low for each:

Na+

K+

Cl-

HCO3-

inorganic phosphate**
why is each high or low?

A

All in mmol/L and ECF = extra cellular fluid (outside the cell)
ICF = intracellular fluid

Na+: ECF = high (145) ICF=low(12)

K+: ECF = low(4), ICF = high(150)

Cl-: ECF = high(105), ICF = low(5)

HCO3-: ECF = high(25), ICF = low(12)

inorganic p-fate: ECF = low(2), ICF = high(100)
ECF = low b/c of higher Ca2+ concentration outside the cell, and calcium p-fate ppts out.

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4
Q

primary noncoalent driving force holding biomacromolecules together?

A

hydrophobic effect

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5
Q

normal AA with NH3 to the left side, what is the chiral config?

which ones can we use?

A

left = L

Right = D

humans use L AA

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6
Q

what AA can be phosphorlyzed and how?

A

Ser/Thr/Tyr = phosphoester bond formation

His/Lys/Arg = Phosphoramidate bonds

Asp/Glu = mixed anhydride linkages

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7
Q

What is the assumed (for class) pka of alpha Carboxyl group

and for alpha amino group

A

pka = 3 COOH

pka = 10 NH3

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8
Q

formula of hendersonhassel eq and its use?

A

pH = pKa + log([A-]/[HA]) ; where A- = conj. base and HA = acid

it is the eq for buffer calc. shows where HA = A- and where pH = pKa

applies to all ionizable groups no matter the charge state

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9
Q

if pH = 6 and pKa = 4, what does this tell you about A- and HA

A

each pH unit = factor of 10.

therefore since the pH is 6 which is greater than 4, A- is 100x greater concentration than HA.

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10
Q

the lower the pKa

A

the sttronger the acid

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11
Q

defn of a buffer

A

weak acid + its conjugate base that cause solution to resist changes in pH despite acid/base being added.

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12
Q

when do buffers work best (what is effectiveness of buffer casued by?)

A

effectivness is determined by the

  1. pH of soln, they work best within 1 pH unit of their pKa
  2. concentration of buffer, works best with more buffer present, greater amnt of buffer = bigger buffer capacity
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13
Q

when looking at a buffer titration curve, pay very close attention to what?

A

the axis, some have eq. of OH- on the x-axis while some have it on Y which changes the slope of the titration curve buffer zone

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14
Q

describe the blood buffer system and a common disease

give overall formula

A

CO2 = acid, HCO3 = base

they buffer the pH to maintain at 7.4 = normal

pulmonary obstruction = increase in CO2 = incrrease acid = decrease pH = respiratory acidosis

H+ + HCO3- –> H2CO3 –> Water byprod. –> CO2

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15
Q

drug charge and membrane crossing trend

explain why aspirin readily crosses into bloodstream in stomach

A

uncharged drugs (more nonpolar) cross more readily than charged drugs.

aspirin = lots of COOH residue AA, therefore at pH = 1.5 in stomach, and the lowest pKa of AA residues on aspirin around 3, the aspirin are protonated and thus uncharged and readily move across membranes

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16
Q

define:

acidemia

acidosis

aciduria**
what is the special note to remember with aciduria (hint:think pH/pKa of urine)

A

demia = acidic blood

acidosis = proces that tends to acidify blood

aciduria = urinary extretion of abnormal amnts/types of ochem acids
**aciduria ochem acids exist as conjugate bases despite being called aciduria b/c the pH of urine is well above the pKa of organic acids

17
Q

define alkalemia

alkalosis

A

alkiline blood (>7.4)

process that alkalinize blood

18
Q

str?

carbonic acid

carbonate

bicarbonate

A

carbonic = H2CO3

carbonate = CO32-

bi = HCO3-

19
Q

what is the key feature of each?

  1. metabolic acidosis
  2. metabolic alkalosis
  3. respiratory acidosis
  4. respiratory alkalosis

**how to remember which is which species?

A
  1. decrease in blood bicarbonate
  2. increase blood bicarbonate (HCO3)
  3. increase in CO2
  4. Decrease in CO2

**think about where the pathology is ocuring. Respiratory indidcates at the lungs, which is the local site of the CO2 portion of the eq. = resp.

20
Q

name the atoms:nomenclature

A
21
Q

whats makes a carbon an alpha on AA?

A

it is the carbon attached to both COOH and NH3 at the same time = chiral carbon. This is true both in an AA chain and a lone AA.

In a chain, only one AA on the primary upper str (not R groups) will be attached to both COOH and NH3

22
Q

which two AA have two chiral center?

A

Ile and Thr

23
Q

describe what is occuring to the str in black.

give biochem function reference

A

oligosaccharides bound to proteins by N or O linkages.

N link = cell surface to protect cell from proteolysis or immune attack.

O-linl = common way to attach oligosach to Thr or Ser OH group in secrted proteins.

24
Q

what is occruing to both?

A

fatty acylation of both AA

25
Q

describe what occured to str in black

A

reversible post translation modifications of AA = regualtion of metabolic pathways

the phophorlation leads to huge str confirm changes b/c it is a very large and VERY polar moleciule.

26
Q

list 4 functions of post translate mod. of AA

A
  1. str confirm changes
  2. regualtion (altering enzyme/str)

3 . carrying molecules

  1. membrane/chemical interactions
27
Q

what is the str and whats occruing

which is reduced/oxid.

A

2 cys are being redoxed into a disulfide bridge

the left is reduced and right is oxidized

28
Q

Four Levels of Protein Strct

A

Primary (AA Seqs)

Secondary (B-pleated sheets and alpha helix)

Tertiary (3D Protein)

Quaternary (Multiple subunits)

29
Q

How to compare a query to a subject seqs of AA in two different specimens

A
  1. Look at how similar the two are to each other
  2. Look for gaps, proper alignment, number of AAs
  3. Look at AA seqs
  4. Is the seqs conserved or similar to the origional seqs?
30
Q

Geometry of Peptide Bonds and its effect on Protein Strct

A

Peptide bonds bet AA are planar and have double bond characteristics due to resonance

therefore peptide bond may not rotate (fixed)

31
Q

2ndary Strct of Alpha Helix

A

Parallel H bonding of the carbonyl + amide of the backbone of the helix holds its shape + strct

Tight packing, helical shape, + H bonding allow movement of alpha helix through memb

R Groups tend to protrude from helix and 3-4 AA per turn

32
Q

2ndary Strct B pleated sheets

A

exhibit a parallel or anti-parallel geometry w/ perpendicular protruding side chains to sheet

B sheets are not flat they always have a twist to some degree

33
Q

Nonrepetitive regions (B loops)

A

four AA form a loop (hairpin turn) and H bond bet AA1 and AA2 to stabilize the loop

helps reverse the sheets direction

makes up 50% of globular protein strct

34
Q

5 Major Protein Types

A
  1. Globular
  2. Membrane (Lipid soluble)
  3. Strct (fibrous)
  4. unstrct proteins
    1. interact w/ other substances to fold into active strct
  5. Protein fibrils
    1. abnormal aggregates forming thin fibrils through beta sheet stacking
    2. not covalently attached
35
Q

Motifs vs Fold vs Domain

A

Motif is a common strct feature that show patterns involving 2+ 2ndary strct

Fold is a large motif repeat

Domain are independently folded units that when removed maintain their function + strct

36
Q

C2 + C3 Cyclic symmetry

A

Two fold is C2 (180 degrees)

Three fold is C3 (120 degrees)

Related by rotational symmetry

37
Q

D2 + D4 Dihedral Symmetry

A

D2 has multiple twofold planes

D4 has a fourfold and three twofold planes of symmetry

38
Q

Two Effects of Mutations

A

Loss of Function

  1. decrease amt of protein
    1. less stable, not transported, nonsense mutation
  2. decrease activity
  3. decrease regulation of activity
  4. disruption to protein strct
    1. fold incorrectly or lack of cofactor

Gain of Function

  1. Increase amt of protein
  2. Increase activity
  3. Increase regulation activity
  4. new function gained
39
Q

What drives protein folding?

What counters protein folding?

A

Hydrophobic effect + dipole forces (smaller impact) drives protein to fold

Law of Thermodynamics (Entropy) wants disorder so it tries to counter the forces of the hydrophobic effect

Biochemistry (5 decks)

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