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MCAT - Biology > MCAT Biology Ch15: Amino Acids, Peptides and Proteins Kap > Flashcards

MCAT Biology Ch15: Amino Acids, Peptides and Proteins Kap Flashcards

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1
Q

Amino Acids

A
  • an amine group and a carboxyl group to a single carbon atom (the alpha carbon)
  • alpha hydrogen and R group
  • alpha carbon, chiral (stereogenic) center –> optically active
  • naturally occurring (20) are all L-enantiomers, amino group on the left
  • S config (except for cysteine, R, priority by sulfur)
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2
Q

R group

A

attached to alpha carbon

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3
Q

glycine

A

simplest AA, not chiral

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4
Q

acid-base characteristic

A
  • basic amino group (pos when protonated) and acidic carboxyl group (neg charge when depro) –> amphoteric
  • depend on terms and conditions
  • pH –> lots of protons –>AA as base (vice versa)
  • try to achieve equilibrium
  • since two diff locations, can either be pro or depro, having least two diff disso. constants Ka1 and Ka2, to pH, or Kb1 and Kb2, pOH
  • neutral AA in acidic sol –> fully protonated –> amino pro easily than carboxyl (need fairly acidic)
  • if even basic solution, become fully depro, easilly for carboxyl group than amino group.
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5
Q

amphoteric

A

-species acting both acids and bases (ex: h20)

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6
Q

zwitterion

A

both charged on amino and carboxyl at same time –> neutralize –> so at neutral pH –> internal salts

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7
Q

isoelectric point (pI)/isoelectric pH

A
  • intermediate pH, which AA exists as zwitterion (uncharged)

- between pKa1 and pKa2 (pKa is pH which disasso. occurs)

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8
Q

titration of amino acids

A
  • looks like a combo of two or three monoprotic acids (three is acidic or basic R group)
  • when add base, carboxyl group deprotonates first, than amino group
  • two moles of base to deprotonate one mole of most amino acids
  • buffering capacity greatest at or near pH of two diss. constants, pKa1 and pKa2; at isoelectric point, capacity is min., vertical line
  • some have acidic or basic side chains, to find pI, avg two acidic pKa;s if side chain acidic, two basic pKa’s if basic
  • can perform by adding acid to base, sequence is reversed.
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9
Q

henderson-hasselbalch equation

A
  • relationship by relating the pH to the ratio of CA to CB
  • when pKa known, ratio at particular pH can be determined
  • can prepare effective buffer solutions of AAs; buffering regions of AA within one pH unit of pKa or pKb.
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10
Q

amino acid side chains

A

-side chains (R groups) give character and give proteins distinguishing features

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11
Q

types of amino acid side chains

A

nonpolar, polar (uncharged), acidic, basic

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12
Q

nonpolar amino acids

A
  • most R groups are saturated hydrocarbons –> hydrophobic –>dec the solubility in water –> prefer bured inside proteins away from aq. cell enviwronment
  • tryptophan has N atom w/ lone pair, resonated through aromatic ring –> doesn’t exhibit basic properties –> nucleating residue when proteins fold
  • often found at core of globular proteins or transmembrane regions of proteins in contact w/ hydrophobic portion of phospholipid membrane
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13
Q

polar amino acids

A

-uncharged polar R- groups that are hydrophilic –> inc. solubity in water –> surface of proteins

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14
Q

acidic amino acids

A
  • R-group has carboxyl group, neg charge at physiological pH (7.4) so exist in salt form in body
  • roles in substrate-binding site of enzymes, require proton transfer
  • name ends in -acid
  • have three distinct pKa’s; has three groups (two COOH (overlap) and one NH3+), because of add. carboxyl group, isoelectric point shifted towards acidic pH, founding by avg. both acidic pKa’s
  • 3 moles of base needed for deprotonation
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15
Q

basic amino acids

A
  • side chain is amino group
  • net pos charge at pH 7.4
  • add. amino group, three disso. constant (amino’s overlap)
  • pI towards alkaline pH, avg two basic pKas
  • three moles of acid
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16
Q

Predicting AA charge

A

using pI:

  • pH < pI –> pos
  • pH > pI –> neg
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17
Q

peptides

A
  • amino acid subunits , sometimes called residues
  • carboxyl one end, amino at other –> combine is peptide bond
  • small proteins, < 50 residues
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18
Q

residues

A

amino acid units for peptides

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19
Q

peptide bond

A

two amino acids combine –> amine bond forms between them

20
Q

dipeptide

A

two amino acids joined

21
Q

tripeptide

A

three amino acids joined

22
Q

polypeptide

A

many amino acids

23
Q

rxns, forming peptide bonds

A
  • condensation rxn occurs (water is lost)
  • reverse, hydrolysis (cleavage by adding water), catalyzed by an acid or base
  • certain enzymes digest specific peptide linkage (given in passage)
24
Q

properties of peptides

A

-terminal amino acids
1. free alpha amino group - amino terminal, N terminal
2. free carboxyl group - carboxy-terminal, C terminal
read from N to C (left to right)

-amides have two resonance structures, w/ partial DB character between N and C –> C-N bond restrict (rigid and stable) of backbone of proteins

25
Q

amino terminal, N terminal

A

free alpha amino group of terminal amino acid

26
Q

carboxy-terminal, C terminal

A

free carboxyl group of terminal amino acid

27
Q

proteins

A
  • polypeptides
  • range in length
  • many functions
    1. hormones
    2. enzymes
    3. membrane pores
    4. receptors
    5. elements of cell structures
    6. main actors of bio system

-ther are four levels

28
Q

primary structure of protein

A
  • structure coded in DNA of organism
  • sequence of AA, from N-term to C-term, linked by peptide bonds
  • most fund. structure, seq. determines higher levels of protein structure (2,3,4 most energetically favorable)
  • determined in lab through sequencing, easily done on DNA that produced protein
29
Q

sequencing

A

1st structure determined in lab this way, easily done on DNA that produced protein

30
Q

secondary structure

A
  • local structure of neighboring AAs
  • result of H bonding between AAs
  • two most common types are alpha helix and beta pleated sheet
31
Q

alpha helix

A
  • rodlike structure, peptide chain coils clockwise about central axis
  • helix stablized by intramolecular H bonds between carbonyl oxygen atoms and amide H atoms foru residues away from each other (n +4 H bond)
  • side chains point away from helix core, interacting w/ cell environment
  • typical protein w/ structure is keratin
32
Q

keratin

A

fibrous structural protein; hair and fingernails

33
Q

B pleated sheet

A
  • may be parallel or antiparallel
  • peptide chains lie alongside each other, forming rows
  • chains held by intramolecular H bonds, between carbonyl O atoms on one peptide chain and amine H atom on another
  • rippled, or pleated, shape
  • R-groups of amino residues point above and below plane
  • ex: silk fibers
34
Q

tertiary structure

A
  • 3D shape
  • determined by hydrophobic and hydrophilic between R groups of amino acids
  • also determined by distribution of disulfide bonds (create loops)
  • proline –> ring –> can’t fit every location of alpha helix –> kink in chain
  • two major classifications: fibrous proteins and globular proteins
35
Q

cysteine

A

disulfide bonds results when these two moleculse become oxidized to from cystine

36
Q

fibrous proteins

A

like collagen, as sheets or long strands

37
Q

globular proteins

A

like myoglobin, are spherical

38
Q

two major classifications of tertiary structures

A

fibrous and globular proteins

39
Q

quarternary structure

A
  • more than one polypeptide subunit
  • refers way these subunits arrange themselves yield functional protein
  • ex: hemoglobin
40
Q

hemoglobin

A
  • O2-transporting machines –> fill red bloodcells

- composed of 4 diff. globular protein subunits

41
Q

Conjugated Proteins

A
  • part of function from covalently attached molecules called prosthetic groups
  • proteins w/ lipid, carb, and nucleic acid prosthetic groups: lipoproteins, glycoproteins, nucleoproteins.
  • major roles in determining function of their respective proteins
  • Hemoglobin’s subunit (also myoglobin) have heme group
42
Q

prosthetic roups

A
  • conjugated proteins get part of function from these covalently attached molecules.
  • can be organic (vitamins) or even metals ions
43
Q

heme group

A

-prosthetic group of hemoglobin (cooperative) (and myoglobin subunits
(inactive w/o)
-composed of organic porphyrin ring w/ iron atom in center

-binds to and carrier oxygen

44
Q

denaturation of proteins

A
  • also known as melting

- protein loses 3D structure and revert to a random-coil state

45
Q

random-coil

A
  • state achieved after protein loses 3D structure
  • completely functionless, damage usually permanent; gentle denaturing agent (urea) don’t permanently
  • methods: detergent, change in pH, temp, or even solute concentration; removing reagent might renature (regain structure and function)
  • weak intermolecular forces –> protein stable and function –> disrupted
  • reversible
46
Q

renature

A

removing reagent that denatures protein brings to this state

MCAT - Biology (16 decks)

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