Biological Molecules II Flashcards
1
Q
Biopolymers
A
- 𝝰-amino acids, largest constituent of cells
- Chemical properties are determined by constituent amino acids
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
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
4
Q
Cysteine
A
- R configuration but it is always L amino acid
5
Q
All L amino acids
A
- Classified by the properties of R group particularly the polarity
6
Q
Amino acids with hydrophobic R group
A
- 3D structure of protiens side chains of amino acids cluster together mainly hydrophobic residue
7
Q
OH on Ser and thr
A
- Can be phosphorylated regulating activity and attach to polysaccarides
- Attach to polysaccarides to form glycoprotiens
8
Q
Amino acid with charged chain
A
- pKa close to neutral 50 % prortonatioated and physological pH
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-
10
Q
Amphoteric
A
- Has both acidic and basic NH3+ and basic COO- depends on the pH
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
12
Q
OH on Trp and Tyr
A
More polar compared to alanine due to hydrogen bond also side chain with water
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
14
Q
Glycine
A
- Smallest R group
- No contribution to hydrophobic effect in flexible area
15
Q
Proline
A
- Cyclic secondary amine
- Ridgid conformation reduces flexibility of protien region
- Found at bends of protien region
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
17
Q
Essential amino acids
A
- Arg, Val, His, Met, Leu, Thr, Lys, Phe, Trp, Iso
- Hydroxylated versions of amino acids in collegen
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
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
Strecker synthesis
- Addition of NH3 and HCN to alderhyde
- Catalysed by water to form amino nitrile then add H3O to form amino acid (Hydrolysis reaction)
26
Esterification of carboxyl group
- Amino acid (Non-interfereing) + alcohol = Amino ester (Protecting COOH) + water
27
Peptide bond
- Amines and acids condense with loss of H2O to form amides
- Acid +amines = salt add heat is amide
28
Amide link
- 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
Peptide
- 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
N-terminus suffix
-yl suffix of acyl groups except the last arginine
31
Disulphide linkage
- Addition of 2 thiols making a disulphide bridge
- Formation of oxytocin and insulin
32
Characteristics of peptides
- 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
Features of peptide bonds
- Ridgid planes with consecutive plans that rotate around C which limits range of conformations available
34
Why are peptides usually trans?
- Due to conformational restrictions point towards the opposite sides
- Cis has greater steric hinderance
35
L-proline structure
- Proline residue protiens are in the cis configuration
36
Protiens structure
- 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
Secondary structure
- 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
Alpha helix link
- 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
Helical wheel
- Alpha helix where 1 and 4 form a salt bridge stablising the helix
- Right handed or left handed most stable left
40
Beta pleated sheet
- 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
Antiparallel beta sheet
- Adjacent beta strands have opposing amino to carboxyl groups where hydrogen bonding occours
42
Parallel
- Adjacent beta strands have the same amino to carbonyl orientation H bonds are not in-line
43
Secondary structure loops and turns
- 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
Tertiary structure
- 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
Quaternary structure
- Contains more than 1 polypeptide 2 forms a dimer, 3 is trimer and 4 is tetramer
46
Oligomer
- Protien suunit held together my non-covalent interactions
- Heamoglobin - heterotetramer
