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MCAT Biochem > Chapter 1 > Flashcards

Chapter 1 Flashcards

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1
Q

Amino Acid

A
  • Have two functional groups: Amino group and carboxyl group
  • a-amino acids: amino group and carboxyl group are bonded to same carbon (alpha carbon)
  • Alpha carbon also has a Hydron atom attached and a R group (specific to amino acid)
  • AAMC focuses on proteinogenic amino acids (20 a- amino acids)
  • amphoteric: can accept a proton/donate a proton
  • Reaction depends on pH of environment
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2
Q

Amino Acid Stereochemistry

A
  • In most amino acids, a-carbon is chiral center (four groups attached to it, THEREFORE most amino acids are optically active
  • Exception: glycine (hydrogen atom as R group, therefore achiral)
  • All chiral amino acids in eukaryotes are L-amino acids (amino group drawn of left in Fischer projection)
  • All have absolute configuration (S)
  • Exception: cysteine (L-amino acid with R absolute configuration because -CH2SH group takes priority over -COOH group)
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3
Q

Amino Acids with Nonpolar, Nonaromatic Side Chains

A
  1. Glycine
  2. Alanine
  3. Valine
  4. Leucine
  5. Isoleucine
  6. Methionine
  7. Proline
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4
Q

Alkyl Side Chains (1 to 4 C)

A
  1. Glycine
    * One H as side chain, therefore achiral
  2. Alanine
  3. Valine
  4. Leucine
  5. Isoleucine
    * Has chiral carbon in side chain

1 to 4 has alkyl side chains containing 1 to 4 C

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5
Q

Methionine

A
  • Contains S atom in side chain
  • Sulfar has methyl group attached
  • Makes relatively nonpolar
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6
Q

Proline

A
  • Forms cyclic amino acid
  • Amino N becomes part of side chain, forming 5 membered ring
  • Ring limits where it can appear in protein and role in secondary structure
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7
Q

Uncharged Aromatic Side Chains

A
  1. Tryptophan
    * Double-ring containing N
    * largest
  2. Phenylalanine
    * Benzyle side chain (Benzene ring plus -CH2 group)
    * smallest
    * Nonpolar
  3. Tyrosine
    * OH group added to phenylalanine
    * Polar
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8
Q

Polar Side Chains (NOT aromatic)

A
  1. Serine & Threonine
    * OH groups in side chains
    * Highly polar
    * Threonine has chiral carbon in side chain
  2. Asparagine & Glutamine
    * Amide side chains
    * Amide N doesn’t gain/lose protons with changes in pH
    * Don’t become charged
  3. Cysteine
    * Thiol (SH) group in side chain
    * S is larger and less electronegative than O, so S-H bond is weaker than O-H bond
    * Thiol group is prone to oxidation
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9
Q

Negatively Charged (Acidic) Side Chains

A

At pH of 7.4
1. Aspartic Acid (Aspartate)
* Related to Asparagine
2. Glutamic Acid (Glutamate)
* Related to glutamine

Aspartate and Glutamate have carboxylate (COO-) groups in side chains NOT amides
Aspartate and Glutamate are deprotonated form of acids

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10
Q

Positively Charged (Basic) Side Chains

A

Side chains with positively charged nitrogen atoms
1. Lysine
* Terminal primary amino group
2. Arginine
* 3 N atoms in side chain
* Positive charge delocalized over all 3 N atoms
3. Histidine
* Aromatic ring (imidazole) with 2 N atoms
* One N is protonated and other isn’t
* Under acidic conditions, second N can be protonated giving side chain + charge

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11
Q

Hydrophobic & Hydrophilic Amino Acids

A
  1. Hydrophobic
    * Long alkyl side chains
    * Ex: Alanine, isoleucine, leucine, valine, phenylalanine
    * Found in interior of protein
  2. Hydrophilic
    * Charged side chains (positive and negative)
    * Ex: Histidine, arginine, lysine, glutamate, aspartate, glutamine, asparagine
    * Found on surface of protein

All others are in the middle and not particularly hydrophobic or hydrophilic

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12
Q

Alanine

A

Ala
A

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13
Q

Arginine

A

Arg
R

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14
Q

Asparagine

A

Asn
N

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15
Q

Aspartic Acid

A

Asp
D

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16
Q

Cysteine

A

Cys
C

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17
Q

Glutamic Acid

A

Glu
E

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18
Q

Glutamine

A

Gln
Q

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19
Q

Glycine

A

Gly
G

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20
Q

Histidine

A

His
H

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21
Q

Isoleucine

A

Ile
I

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22
Q

Leucine

A

Leu
L

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23
Q

Lysine

A

Lys
K

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24
Q

Methionine

A

Met
M

25
Q

Phenylalanine

A

Phe
F

26
Q

Proline

A

Pro
P

27
Q

Serine

A

Ser
S

28
Q

Threonine

A

Thr
T

29
Q

Tryptophan

A

Trp
W

30
Q

Tyrosine

A

Tyr
Y

31
Q

Valine

A

Val
V

32
Q

Amino Acid Behavior

A
  • Ioniable group usually gain protons under acidic and lose protons under basic
  • pKa of group is pH where, usually half of molecules are deprotonated
    Protonated version of ionizable group = deprotonated version of ionizable group
  • If pH < pKa majority will be protonated
  • If pH > pKa majority will be deprotonated
33
Q

Amino Acid pKa

A

Have at least two groups that can be deprotonated so have two pKas
1. pKa 1: Carboxyl group
* Usually ~ 2
2. pKa 2: Amino group
* Usually ~ 9 - 10

For amino acids with ionizable side will have 3 pKa values

34
Q

Positively Charged under Acidic Conditions

A

At pH 1: lots of protons
* Below pKa of amino group, so amino group becomes fully protonated THEREFORE + charged
* Below pKa of carboxylic acid group, so COOH is fully protonated THEREFORE neutral

35
Q

Zwitterions at Intermediate (Blood, 7.4) pH

A

At pH 7.4: above pKa of carboxyl below pKa of amino group
* Carboxyl group will deprotonate becoming COO-
* Amino group will protonate becoming NH3+

Dipolar Ions/Zwitterions: Molecule that has both positive and negative charge, overall neutral

36
Q

Negatively Charged under Basic Conditions

A

At pH 10.5: above pKa of both groups
* Carboxylate group already deprotonated, so remains as COO-
* Amino deprotonates becoming -NH2

37
Q

Isoelectric Point (pI)

A

pH where a molecule is electrically neutral
* When molecule is neutral titration curve will be vertical

Amino acids with acidic side chains have low pI
Amino acids with basic side chains have high pI

38
Q

pI Acidic Amino Acid

A

Amino acids with charged side chains
* Ex: Glutamic acid, lysine
* Titration curve has extra step
* First deprotonating: proton from main carboxyl group
* Second deprotonating: side chain carboxyl group

39
Q

pI Basic Amino Acid

A

Two amino groups one carboxyl group
* Ex: lysine
* Loses carboxyl proton
* Loses proton from main amino group
* Loses proton on amino group in side chain

40
Q

Peptide Bond Formation

A

Condensation/Dehydration Reaction
* Removal of water molecule
* OR acyl substitution reaction (can occur in all carboxylic acid derivatives)

41
Q

Peptide Bond Resonance

A
  • Due to amide groups delocalizable pi electrons they can exhibit resonance
  • Resonance restricts rotation of protein backbone around C-N amide bonds THEREFORE more rigid protein

Amino Terminus/N-Terminus: Free amino end
Carboxy Terminus/C-Terminus: Free carboxyl end
N-terminus drawn on left and C-terminus drawn on right

42
Q

Peptide Bond Hydrolysis

A

Break apart amide bond by adding H to amide N and an OH to carbonyl C
* Catalyzed by hydrotic enzymes (trypsin and chymotrypsin)
* Only cleave at certain points in peptide chain (trypsin cleaves at carboxyl end of arginine and lysine, chymotrypsin cleaves at the carboxyl end of penylalanine, tryptophan, and tryosine)

43
Q

Residues

A

Amino acid subunits that makeup peptides

44
Q

Dipeptides

A

Two amino acid residues

45
Q

Tripeptides

A

Three amino acid residues

46
Q

Olgiopeptide

A

Small peptides with up to 20 residues

47
Q

Polypeptides

A

Longer chains of greater than 20 residues

48
Q

Peptide Bond

A

Special amide bond between -COO- group of an amino acid and NH3+ of another amino acid

49
Q

Proteins

A

Polypeptides that are a few up to thousands of amino acids in length
Four levels of structure:
1. Primary (1˚)
2. Secondary (2˚)
3. Tertiary (3˚)
4. Quaternary (4˚)

50
Q

Primary Structure (1˚)

A

Linear arrangement of amino acids
* Listed from N-terminus (amino end) to C-terminus (carboxyl end)
* Stabilized by covalent peptide bonds between adjacent amino acids
* Encodes all information needed for folding
* Can be determine via sequencin (easiest way is using DNA tha coded for the protein, also possible from protien)

51
Q

Secondary Structure (2˚)

A

Local structure of neighboring amino acids
* Result of hydrogen bonding between close amino acids

Two common types:
1. a-helices
2. B-pleated sheets
Stability for these structures comes from formation of intramolecular H bonds between different residues

52
Q

a-Helices

A

Rodlike structure where a peptide chain coils clockwise
* Stabilized by intramolecular H bonds between carbonyl O and amide H four resides down the chain
* Side chain point away from helix core
* Important in keratin (structural protein in skin, hair, and fingernails)

53
Q

B-Pleated Sheets

A

Peptide chains lie along side each other forming rows/strands
* Parallel or antiparallel
* Held together by intramolecular hydrogen bonds between carbonyl O one one chain and amid H in adjacent chain
* Have pleated sheet to have as many hydrogen bonds as possible
* Side chains point above/below plane

54
Q

Proline

A
  • Rigid cyclic structure
  • Rarely found in a-helices except when crossing cell membrane
  • Rarely found in B-pleated sheets
  • Usually found in turns between chains of B-pleated sheet and kinks at start of a-helix
55
Q

Tertiary Structure (3˚)

A

Secondary structures form first and then hydrophobic interactions and hydrogen bonds cause the protein to collapse into proper 3D structure
* Determined mainly by hydrophilic/hydrophobic interactions between R groups of amino acids
* Hydrophobic wants to be on interior of protein
* Hydrophilic bonds in polypeptide chain pulled in by hydrophobic residues
* Hydrogen bonds stabilize from inside
* Never found on surface of protein

Subtypes:
1. Hydrophobic interactions
2. Acid-base/salt bridges
3. Disulfide links

56
Q

Disulfide Bonds

A

Bonds that form when two cysteine molecules become oxidized forming cystine
* Requires loss of two protons and two electrons (oxidation)

57
Q

Denaturation

A

When a protein loses its tertiary structure thus losing its function
* Occasionally reversible
* Unfolded, can’t catalyze reactions
* Usuallly heat (increased kinetic energy enough to overcome hydrophobic interactions) and solutes (disrupting elements of 1˚/2˚/3˚/4˚ structure) caused

58
Q

Entropy

A

Why hydrophobic residues occupy interior of a protein
* Moving to interior increases entropy by allowing water on the surface to have more possible positions/configurations
* + ∆S makes ∆G < 0
* Stabilizes protein

59
Q

Quaternary Structure (4˚)

A

Interaction between seperate subunits of a multisubunit protein
* Only exist for proteins with more than one polypeptide chain
* Group of subunits
* Represents function form of protein
* Ex: hemoglobin (4 disgtinct subunit, that can each bind with an 0)

Purpose:
1. More stable
2. Reduce DNA needed to encode
3. Catalytic sites brought closer
4. induce cooperativity/allosteric effects

MCAT Biochem (7 decks)

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