Chapter 5- Primary peptide structure Flashcards
What are steric interactions?
How close two atoms can get together without repulsion . 2 atoms can’t occupy the same region of space simultaneously.
What happens when 2 atoms are very close?
- electron clouds overlap
- pauli exclusion principle applies- quantum mechanic principal that states that no two identical atoms/fermions can occupy the same quantum state simultaneously
When is repulsion highest?
When molecules are close together. Short-range repulsion has an exponential dependence on interatomic distance.
Steric interaction result in what types of folding in molecules?
Alpha helix, beta sheets
steric interaction tell us about conformational behaviour of amino acids- which bond spin and which don’t?
single bonds spin/ rotate, where as double/ triple bonds don’t.
What happens when a peptide bond is formed?
does it require energy ?
water comes on then water comes off per 2 two amino acids.
yes- because although hydrolysis is thermodynamically favoured the rate constant is small meaning that the reaction rate is slow, that is why ATP/ enzymes is needed!
The peptide bond is metastable= HYDROLYSIS is the favoured reaction at room temperature in aqueous solution. Since the uncatalyzed reaction is so slow catalysis need to happen via what?
Specific catalysis is provided by what?
Acids and bases.
proteolytic enzymes and proteases
What formation is the peptide bond usually found in?
What bond character does it have?
trans
It has 40% double bond character, (shorter than a single but longer than a double bond). the 6 atoms are always planar. N is partially positive and O partially neg
What are the numbers like in peptide bonds (angle and bond length)?
The are all different
What is the geometry of peptide bonds like?
The geometry is best represented as a hybrid of 2 structures. One structure is =O and has free rotation, the other is C=N restricted rotation. (slide 12)
What is the geometry of peptide bonds like?
The geometry is best represented as a hybrid of 2 structures. One structure is =O and has free rotation, the other is C=N restricted rotation. (slide 12)
What gives the peptide bond partial double bond character ?
delocalisation of pi elections.
Why is the peptide group rigid and planar?
resonance interactions which give the partial double bond character.
Which peptide configuration is favoured cis/ trans?
trans- more stable, especially with bulky R groups. cis= RARE
In a peptide bond where is the pi-electron delocalisation
over the O-C-N fragment.
what does the resonance stabilisation result in?
planar structure
Why are adjacent alpha carbons in trans configuration?
to prevent steric hinderance
Is hydrolysis in peptide formation thermodynamically favoured?
yes
Polypeptides are unstable so to make them want mechanism is required?
Coupling ATP hydrolysis
Are free amino acids used to make polypeptides/proteins in cells, why?
NOOOOO, because the delta G (free energy) is positive not spontaneous
What are aminoacyl-RNAs? and what are they used for?
they are the high energy intermediates used to form polypeptides
ATP+ RNA+ Amino acid>
Aminoacyl RNA+ ADP + Pi
What does the ribosome do?
promotes peptide bond formation
What is the amino end of a polypeptide called?
N terminus
what is the carboxyl end of a polypeptide called
C-teminus
What is the polypeptide structure
N with 2 H attached to a C with an H and R attached to. C=O and (OH) is attached to N with one H attached to C with H and R etc.
What is the difference between an amino acid residue and an amino acid?
A residue is inside a polypeptide chain and is missing an H on the N and the C terminus is missing OH and its bound to something because a water is removed
What is peptide bond?
The special name given to the bond between the a-carboxyl group of one amino acid and the a-amino acid of another.
an amide bond formed between 2 amid acids
What Is an alpha carbon
the central carbon bound to an amino group and carboxyl group
define oligopeptides?
peptide which a few amino acid residues 12-20
define polypeptides?
long chain peptides with many residues 20+
How is the linear sequence of amino acid written in a peptide?
N>C, in 3 or 1 letter code
eg. Glu-Gly-Ala
define peptide
A short polymer of amino acids joined by peptide bonds, classified by # of amino acids in chain
define dipeptide, tripeptide, polypeptide
a molecules containing 2 amino acids joined together by a peptide bond, 3, many
define protein
A biological macromolecule of molecular weight 5000g/ ml , consists of many polypeptide chains
Peptide are polyampholites, what does this mean?
they contain different charges
What makes a polypeptide ionizable?
the amino groups, the carboxyl groups and the r groups
Solubility, structure and function are determined by what?
pH
What is the isoelectric point?
pH which the net charge is 0
What is the primary structure of a protein?
The order of amino acid resides- sequence
how to find the combinantion of molecules amino acids can make…
20^(#of aa)
What are enkephalins?
pentapeptide that binds to opioid receptors.
What is the sequence for a leucine enkephalin?
Try-Gly-Gly-Phe-Leu
Y-G-G-F-L
What is the sequence for a methionine enkephalin?
Try-Gly-Gly-Phe-Met
Y-G-G-F-M
What encodes the amino acid sequence?
the nucleotide sequence of DNA
Explain how the MALDI Mass Spectometer works?
ions are generated by a laser firing at the target plate, the time of firing of the laser and the arrival time of ion at detector are known , the relative masses can be calculated. Only single charged ions are generated.
Explain solid-phase peptide synthesis.
the c terminus is covalently bound to a solid support/ resin then 3 chemical reaction are repeated for each added amino acid.
- deprotection
- activation
- coupling
What happens during coupling?
the active ester from an amide bon with the deprotected amino group at the end of the peptide chain then a new cycle begins. When synthesis is complete chemical cleavage removes side chain protecting groups from the peptide and synthetic peptide from the resin support.
What is reaction to from a peptide bond?
condensation
