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Biochem 507 Exam 1 > Lecture 3 > Flashcards

Lecture 3 Flashcards

1
Q

Positively Charged AAs, and protonation at pH = 7

A

Lysine (Lys, K): R protonated at neutral pH; R’s pKa is high

Arginine (Arg, R): R protonated at neutral pH; R’s pKa is high

Histidine (His, H): R NOT protonated at neutral pH

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2
Q

Negatively Charged AAs, and protonation at neutral pH

A

Aspartate (Asp, D): R has low pKa; deprotonated at neutral pH

Glutamate (Glu, E): R has low pKa; deprotonated at neutral pH

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3
Q

Configuration vs conformation

A

configuration
-switch configs by breaking and reforming cov bond(s)

conformation

  • switch configs by without breaking cov bonds
  • esp: rotation about single bond
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4
Q

stereoisomers

A

differ only in spatial arrangement of atoms

  • cis/trans
  • enantiomers (nonsuperimposable mirror images)
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5
Q

proteins contain nearly all of which enantiomer (L or D?

A

L

-determination based on glyceraldehyde(–>alanine)

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6
Q

Trick to tell if L or D AA

A

alpha carbon in center. line up is R group. Line (wedge) out of page is H, carboxyl and amino groups are the left and right dashes. If spells Corn in clockwise arch, it’s an L- amino acid

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7
Q

Why must most AAs be same chirality (all L or all D)?

A

Can’t make uniform structures with mixture.

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8
Q

Peptide bond

A

creates amide
H
-C - N -
ll
O
This section is planar because of resonance.
Note C is carbonyl C, not alpha carbon (although it’s attached to an alpha C)

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9
Q

pI (notes say don’t need to know)

A

Looks like it’s pH at equiv point on titration curve

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10
Q

Merrifield Method for protein synthesis

A
  1. Attachment to resin (beads)
    - carboxyl terminal attached to resin
  2. Removal of protecting group
    - Fmoc protects amino group
    - remove by flushing with mild org base
  3. Activation of next amino acid
    - carbonyl activated with DCC (like opposite of protecting group)
  4. Peptide bond formation
    - amino of AA1 attacks activated carbonyl of AA2
  5. Removal of polypeptide from resin
    - HF cleaves ester between peptide and resin
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11
Q

Direction of protein synthesis

A

in cells: amino to carbonyl terminus

Merrifield: carbonyl to amino terminus

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12
Q

Convention for naming peptide sequences

A

N-terminus to C-terminus

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13
Q

Protein vs Peptide

A

Protein: Mr > 10,000
Peptide: Mr< 10,000

Note: Mr means molecular weight

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14
Q

Avg weight of AA in protein

A

110

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15
Q

absolute configuration

A

config of four diff substituent groups around asymmetric carbon, in relation to D- and L- glyceraldehyde (corn=L)

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16
Q

amphipathic

A

containing both polar and nonpolar domains

phospholipids in cell membrane

17
Q

amphoteric

A

capable of donating or accepting protons and therefore of being acid or base (noun form ampholyte)

makes me think of HA- form of a diprotic acid

18
Q

conjugated protein

A

protein containing one or more prosthetic groups

19
Q

prosthetic group

A

metal ion or orgainc compound (other than AA) covalently bound to a protein

essential to protein’s activity

20
Q

isoelectric pH (pI)

A

the pH at which a solute has no net electric charge and thus does not move in an electric field

21
Q

lipoprotein

A

lipid-protein aggregate that carries water-insoluble lipids in blood
-just the protein is called apolipoprotein

22
Q

metalloprotein

A

protein with a metal ion as prosthetic group

23
Q

metalloprotein

A

protein with a metal ion as prosthetic group

24
Q

oligomeric protein

A

multisubunit protein having two or more polypeptide chains

25
Q

oligopeptide

A

short polymer of amino acids joined by peptide bonds

  • really just a short peptide
  • -as opposed to a long peptide=protein
26
Q

polypeptide

A

long chain of amino acids linked by peptide bonds

Mr<10,000

27
Q

primary structure

A

covalent backbone of polymer, including sequence of monomeric subunits and any interchain and intrachain covalent bonds

//i.e. sequence of AAs

28
Q

quaternary structure

A

three-dimensional structure of a multisubunit protein, esp manner in which subunits fit together

29
Q

residue

A

single unit in a polymer

ex AA in peptide chain

30
Q

secondary structure

A

local spatial arrangement of the main-chain atoms in a segment of a polymer (polypeptide or polynucleotide) chain

ex alpha helix, beta pleated sheet

31
Q

tertiary structure

A

three-dimensional conformation of a polymer in its native, folded state

32
Q

zwitterion

A

dipolar ion with spatially separated positive and negative charges

Biochem 507 Exam 1 (10 decks)

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