MCAT Biology Ch15: Amino Acids, Peptides and Proteins Kap Flashcards
(46 cards)
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)
2
Q
R group
A
attached to alpha carbon
3
Q
glycine
A
simplest AA, not chiral
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.
5
Q
amphoteric
A
-species acting both acids and bases (ex: h20)
6
Q
zwitterion
A
both charged on amino and carboxyl at same time –> neutralize –> so at neutral pH –> internal salts
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)
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.
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.
10
Q
amino acid side chains
A
-side chains (R groups) give character and give proteins distinguishing features
11
Q
types of amino acid side chains
A
nonpolar, polar (uncharged), acidic, basic
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
13
Q
polar amino acids
A
-uncharged polar R- groups that are hydrophilic –> inc. solubity in water –> surface of proteins
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
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
16
Q
Predicting AA charge
A
using pI:
- pH < pI –> pos
- pH > pI –> neg
17
Q
peptides
A
- amino acid subunits , sometimes called residues
- carboxyl one end, amino at other –> combine is peptide bond
- small proteins, < 50 residues
18
Q
residues
A
amino acid units for peptides
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
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amino terminal, N terminal
free alpha amino group of terminal amino acid
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carboxy-terminal, C terminal
free carboxyl group of terminal amino acid
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proteins
- 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
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primary structure of protein
- 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
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sequencing
1st structure determined in lab this way, easily done on DNA that produced protein
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secondary structure
- local structure of neighboring AAs
- result of H bonding between AAs
- two most common types are alpha helix and beta pleated sheet
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alpha helix
- 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
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keratin
fibrous structural protein; hair and fingernails
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B pleated sheet
- 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
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tertiary structure
- 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
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cysteine
disulfide bonds results when these two moleculse become oxidized to from cystine
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fibrous proteins
like collagen, as sheets or long strands
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globular proteins
like myoglobin, are spherical
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two major classifications of tertiary structures
fibrous and globular proteins
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quarternary structure
- more than one polypeptide subunit
- refers way these subunits arrange themselves yield functional protein
- ex: hemoglobin
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hemoglobin
- O2-transporting machines --> fill red bloodcells
| - composed of 4 diff. globular protein subunits
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Conjugated Proteins
- 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
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prosthetic roups
- conjugated proteins get part of function from these covalently attached molecules.
- can be organic (vitamins) or even metals ions
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heme group
-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
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denaturation of proteins
- also known as melting
| - protein loses 3D structure and revert to a random-coil state
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random-coil
- 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
renature
removing reagent that denatures protein brings to this state
