biochem lec 3 B
what is a peptide bond
a specific amide linkage that connect two amino acids together in proteins btween the carboxyl group and amino group
two amino acids joined by one peptide form a
dipeptide
polypeptide vs oligopeptide
oligo: large number of amino acids, synthetic
poly; large chain produced naturally
what is a protein
a large polypeptide ( or >1 polypeptide) with a biological function
is there only one form of a dipeptide containing met and arg
no in can be arg-met or met-arg which has different directionality and structure but same molecular weight
what charges stay in a peptide
only the terminal amino and carboxylate groups in a peptide retain their charge, others are eliminated by the formation of peptide bonds
side chains retain their charge (if they have one)
what is the primary structure of a polypeptide
the sequence of amino acids , every protein has a uniqiue sewuence
what are the 3 properties of peptide bonds
electrons in pepetide bonds are somewhat delocalized generating 2 resonances
peptide bonds therefore exhibit partial double bond character with no rotation around the C-N bond
the functional groups in peptide bonds are potential h bond acceptor or donor
how many charged functional groups are present on the peptide below at physiological ph 7
arg-asp-cys-tyr-gln-val-glu
5
arg ++, Asp-, Glu --
how many charged side chains are present on the petide below at physiological ph 7
asn-trp-cys-tyr-lys-val-glu
lys +, glu, -
2
rotation around the c alpha-c and n- c alpha bonds can occur to a certain degree, the c-n bond cannot freely rotate just like a double bond, so the atoms of the bond lie in the same plane, what does this mean for its chemical structure
the bond has a rigid, flat (planar) structure while rotaion is only possible around the alpha carbons on either side
what are the levels of proteins structure
primary--> the sequence of amino acid residues which determine 3d which determines function
secondary--> the spatial arrangement of the polypeptide backbone
tertiary structure--> the three dimesnional structure of an entire polypeptide including all its side chains
quaternanry structure--> the spatial arrangement of polypeptide chains in a protein with multiple sub units
why is the rotation of polypeptide back bone limited
peptide bonds stay flat proteins can only bent at N- calpha nd calpha-c
are peptide bonds polar? can h bond?
yes the chemical groups in the peptide bonds are highly polar the carbonyl groups are h bond acceptor and nh groups are h bond donor
what is secondary structure
the local 3d folding patterns in polypeptide chain formed by h bonds between backbone atoms (not side chains)
what are the 2 regular patterns that occur in secondary structures
alpha helic and beta sheet
what is the alpha helic formation
carbonyl oxygen forms h bond with the backbone nh group 4 residues downstream. c1-n5
the only ones that arent bonded are the amino acid residues at either end
right handed coil, twists like spiral
how do the amino acids sit in alpha helix formation
amino acids project outwards, residues 3-4 apart in the primary structure are close in the secondary structure
can neighbouring alpha helix residues and residues located in the same alpha helix form hydrogen bonds with ser residues in the middle of an alpha helix
yes both can
the following sequence of amino acids is very unlikely to fold into a stable alpha helix at ph 7, why? asp-glu-ser-asp-glu-glu-arg-val-asp-ala-glu-asp
alot of acidic side chains, lots of - side chains
electrostatic repuslion among side chains
b sheets are often drawn as arrows, explain this
the arrows are show pointing from the n terminal end to the c terminal end, so antiparallel or paralelel sheets (arrows same way)
what is the b sheet
backbone stretches into strands that align side by side
h bonds between c=o and n-h of adjacent strands (can be parallel or antiparallel)
strands joined by loops or other structures
where are side chains located on b sheet structure
located above and below the plane of the sheet (alternating)
what stabilizes a helix vs b sheets
both are stabilized by h bonds between backbone CO and NH groups except
a helix: in the same helice
b sheets: of neighbouring strands
a helices and b sheets are regular secondary structures, what does this mean
the peptide backbone has the same conformation for every amino acid within the secondary structure
what are irregular structures
distinct elements of regular secondary structures are linked together by polypeptide loops of various sizes ranging from simple hairpins to longer loops--> irregular structures
non repeating, connecting regular segments (loops turns coils)
does irregular mean disordered
no, polypeptide loops typically have a backbone of irregular secondary structure
what is tertiary structure
arrangement of all atoms in a single polypeptide
--> arrangement of secondary structures in relation to one another, positions of amino acid sidechains, location of prosthetic groups
what two general morphologies can tertiary structures be classified into
fiborous (elongated) or globular (compact)
(3) what are fiborous proteins
1. pratically insoluble in aq solutions
2. form long protein filaments (limtied reisdues with repeats)- often linear/extended
3. usually structural or connective proteins
ex. collagen
2- what are globualr proteins
1. basically soluble in aq solution
2. fold into compact structures with non polar cores and polar surfaces
examples of globular proteisn
hemo (globin), my(globin)
lactate dehydrogenase, chymotrypsin, hexokinase, lysozyme
where do loops tend to be located in the interior of folded proteins
on the surface
how does the hydrophobic effect affect protein folding
the shape of globular proteins depends on the relative position of hydrophobic amino acids in the proteisn primary structure
this effect is the driving force via which soluble globular proteins adopt and maintain their tertiarty structure
how can hydrogen bodns stabilize protein secondary and teritary structures
secondary: h bonds between backbone C=O and N-H stabilize alpha helices and beta sheets
tertiary: H-bonds between polar side chains help maintain the overall 3d fold
what are salt bridges (ion pairs)
electrostatic interactions between closely-positioned formal charged groups. helps fine tune and stabilize secondary and teritary structures
can form between + and - charged groups
what are disulfide bonds/bridges
covalent bonds between closely- positioned cysteines, form stabilizing crosslinks for extracellular proteins (or proteins in the lumen)
why does ribonuclese (an extracellular protein) form disulfide bonds, but cytosolic proteins do not
bc disulfide bonds form only in oxidizing environments. ribonuclease, secreted outside the cell, form stable cystine (S-S) links that hold its tertiary structure in the reducing cytosol, cysteine as SH, preventing disulfide formation
oxidizing= cystine (S-S)
reducing= cysteine (SH)
what is a domain
a polypeptide segment that has folded into a single structural unit with a hydrophobic core, proteins may contain more than one domain
what is a motif
motif a short region of polypeptide with a recognizable 3d shape, zinc fingers is an example, may be found in many contexts
helix loop helix, coiled coil, helix. bundle, BaB unit, hairpine, b meander, greek key, B-sandwhich are examples of what
structural motifs.
what is zinc finger
an example of a structural motif including a prosthetic group
what is a prosthetic group
a non peptide component that is permamemtly incorporated into a protein. these provide structure (ex. zinc fingers) and functional chemical groups (ex. heme in hemoglobin)
what are globular proteins stabilized by
weak non covalent forces and are easily unfolded or dentatured
what forces do these conditons break: heat, changes in ph, salt, detergents
heat --> h-bonds/hydrophobic interactions
changes in pH--> salt bridges/H bonds
salt--> salt bridges/ion pairs
detergents--> hydrophobic interactions
how can we disrupt disulphide bridges
reducing agents (DTT)
what is quaternanry structure
proteins composed of more than one polypeptide chain, each polypeptide chain is called a subunit.
how quaternary structures named
by number and type of subunits,
ex. 2 subunits: dimer
identical subunits: homodimer
non identical subunits: heterodimer
3 subunits: trimer
what stabilzies quartnary structures
the same forces as the teritary structure
hydrophobic interactions, h bonds, ion pairs "fine tune"