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PMP 102 Drugs & Medicines > Biological Molecules II > Flashcards

Biological Molecules II Flashcards

1
Q

Biopolymers

A
  • 𝝰-amino acids, largest constituent of cells
  • Chemical properties are determined by constituent amino acids
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2
Q

Function of biomolecules

A
  • Direct DNA replication, RNA transcription and protein translation
  • Catalyse the formation and transformation of various biomolecules
  • Combined with polysaccharides, they signal various processes at cellular interfaces
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3
Q

Amino acid

A
  • Amino group - Bonded to alpha carbon next to carbonyl group
  • R group is the side chain diffrent properties and determined by 3D structure and folding
  • Charged has pH 7.4
  • All naturally occouring found s configuration and classified and L amino acid
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4
Q

Cysteine

A
  • R configuration but it is always L amino acid
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5
Q

All L amino acids

A
  • Classified by the properties of R group particularly the polarity
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6
Q

Amino acids with hydrophobic R group

A
  • 3D structure of protiens side chains of amino acids cluster together mainly hydrophobic residue
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7
Q

OH on Ser and thr

A
  • Can be phosphorylated regulating activity and attach to polysaccarides
  • Attach to polysaccarides to form glycoprotiens
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8
Q

Amino acid with charged chain

A
  • pKa close to neutral 50 % prortonatioated and physological pH
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9
Q

Acid base properties of amino acids

A
  • High melting points over 2o0 degrees
  • More soluable in water than in organic solvents
  • Less acidic than most carboxylic acid and less basic than most amine, the acidic part NH3 and basic COO-
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10
Q

Amphoteric

A
  • Has both acidic and basic NH3+ and basic COO- depends on the pH
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11
Q

Peptide

A
  • Compound containing 2 or more amino acids linked by amide bonds
  • Oligopeptides - few peptites together
  • Name peptides from the the N-terminus
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12
Q

OH on Trp and Tyr

A

More polar compared to alanine due to hydrogen bond also side chain with water

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13
Q

pKa value when ionised

A
  • pKa value increases when the there is an NH3+ charge
  • Agr and Lysine are always positively charged pH 7.4
  • Asp and Glu always negatively charged at pH 7.4
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14
Q

Glycine

A
  • Smallest R group
  • No contribution to hydrophobic effect in flexible area
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15
Q

Proline

A
  • Cyclic secondary amine
  • Ridgid conformation reduces flexibility of protien region
  • Found at bends of protien region
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16
Q

Cystine

A
  • The -SH group makes it polar
  • 2 cystine residue reacts to form a disulphide bond which strengthens the protiens 3D structure - covalent but reversible
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17
Q

Essential amino acids

A
  • Arg, Val, His, Met, Leu, Thr, Lys, Phe, Trp, Iso
  • Hydroxylated versions of amino acids in collegen
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18
Q

Tritration of curve for glycine using NaOH

A
  • Half of product is converted from cationic form to zwitterionic form
  • Reaches isoelectic point halfway allong equivalence line - net charge is zero
  • Then more pH increase causing zwitterion being converted to basic form
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19
Q

R aspartic acid and glutamic acid

A
  • Acid isolectric points which is required to prevent the deprotonation of lateral carboxylic acid keeping amino acid neutral
20
Q

Basic amino acids

A
  • Arg Lys and His basic isoelectric points use basic solution to prevent protonation keeping it neutral
21
Q

Isoelectric point

A
  • pH at which the concentration of zwitterion is maximum and both cation and anion are equal
  • pH = Pka1 + Pka2/2
22
Q

Synthesis of amino acid

A
  • Hydrolyse protein seperation of amino acid mixture
  • Reductive amination adding excess NH3 to alpha-ketoacid
  • Formation of imine COO-NH4+ then add H2 forms racemic amino acid
  • Biological synthesis of amino acids - intermediate to the metabolism of carbohydrates add reducing agent forms pure L enantiomer
23
Q

Transmission and biosynthesis of amino acid

A
  • All of L-amino acids except lysine and thronine which participates in transmission reactions
24
Q

Amination of halo acid

A
  • Addition of bromine and water to carboxylic acid
  • Add large excess of NH3 forms the amino acid
25
Q

Strecker synthesis

A
  • Addition of NH3 and HCN to alderhyde
  • Catalysed by water to form amino nitrile then add H3O to form amino acid (Hydrolysis reaction)
26
Q

Esterification of carboxyl group

A
  • Amino acid (Non-interfereing) + alcohol = Amino ester (Protecting COOH) + water
27
Q

Peptide bond

A
  • Amines and acids condense with loss of H2O to form amides
  • Acid +amines = salt add heat is amide
28
Q

Amide link

A
  • Dehydration between alpha caboxylic group with one amino acid and the amino acid of another
  • Reversible reaction is thermodynamically unfavourable - Must be activated to good leaving group - Protein synthesis and translation
29
Q

Peptide

A
  • 2 or more amino acids linked by amide bond
  • Oligopeptide - Few amino acids 4-10
  • Polypeptide <5,000 amino acids
  • Protien >5,000 amino acids
  • N-terminus on left and C-terminus on right
30
Q

N-terminus suffix

A

-yl suffix of acyl groups except the last arginine

31
Q

Disulphide linkage

A
  • Addition of 2 thiols making a disulphide bridge
  • Formation of oxytocin and insulin
32
Q

Characteristics of peptides

A
  • 3D structure of peptides and protiens
  • Ridgid and planar peptide partial double bond nature strict rotation
  • 6 atoms held together ridgid in a plane
33
Q

Features of peptide bonds

A
  • Ridgid planes with consecutive plans that rotate around C which limits range of conformations available
34
Q

Why are peptides usually trans?

A
  • Due to conformational restrictions point towards the opposite sides
  • Cis has greater steric hinderance
35
Q

L-proline structure

A
  • Proline residue protiens are in the cis configuration
36
Q

Protiens structure

A
  • Covalent bonded linear structure
  • Hydrogen bonded local 3D arrangement into a helix or pleated sheet
  • Complete 3D conformation
  • Association of 2 or more peptide units forming a complex
37
Q

Secondary structure

A
  • Local spatial rearrangement of the backbone of protein segment doesn’t concider R group interaction
  • Conformational constraints in peptide sequence local portions of peptide specific 3D arrangement
  • Formation via the carbonyl interaction with hydrogen bonding to the amide
38
Q

Alpha helix link

A
  • Col-like structure which involves only one polypeptide chain
  • Stablisation of the H bonding between the CO and the NH
  • 4 amino acids towards the C-terminus
  • R-group faces outwards from the backbone
39
Q

Helical wheel

A
  • Alpha helix where 1 and 4 form a salt bridge stablising the helix
  • Right handed or left handed most stable left
40
Q

Beta pleated sheet

A
  • Polypeptide extended zig-zag structure
  • Multiple B strands side by side forming a Beta pleated sheet
  • R groups protrude from the opposite directions of 2 ridgid planes hreld together by hydrogen bonds
41
Q

Antiparallel beta sheet

A
  • Adjacent beta strands have opposing amino to carboxyl groups where hydrogen bonding occours
42
Q

Parallel

A
  • Adjacent beta strands have the same amino to carbonyl orientation H bonds are not in-line
43
Q

Secondary structure loops and turns

A
  • Polypeptide reverses indirection Beta turns which connects two adjacent segments in antiparallel beta sheets
  • 4 amino acid residue stablised by bonds requiring presance of proline - cis structural tension
  • Glycine - trans which has rotational freedom
44
Q

Tertiary structure

A
  • 3D structure of polypeptide including secondary elements interactions between regions
  • Weak interactions hydrogen bonding and wander waals forces
  • Hydrophobic effect clustering in protiens interior stablised by disulphide bonds
45
Q

Quaternary structure

A
  • Contains more than 1 polypeptide 2 forms a dimer, 3 is trimer and 4 is tetramer
46
Q

Oligomer

A
  • Protien suunit held together my non-covalent interactions
  • Heamoglobin - heterotetramer

PMP 102 Drugs & Medicines (56 decks)

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