BIO 311 Chapter Notes - Chapter 4.9: Protein Structure, Amine, Peptide

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Protein Three-Dimensional Structure
• Biologiall atie poteis ae poles of aio aids liked  oalet peptide
bonds
• While a diffeet ofoatios D stutues ae possile, usuall ol oe
structure has biological activity - this is called the native conformation
• Fou leels of potei stutue ae ool
Four levels of protein structure
• Pia stutue is the ode i hih the aio aids ae oaletl liked,
e.g. N-RKRRQTSMTDFYHSKRRLIFS-C - an example of a 21 amino acid peptide
• The pia stutue is the oe-dimensional first step in specifying the threedimensional
structure of a protein
• Seoda stutue is the aageet i spae of the atos i the peptide
backbone
• The to ai fos of seoda stutue ae α-helies ad β-sheets
• Seoda stutues hae epetitie iteatios esultig fo hdoge
bonding between the amide N-H and the carbonyl groups of the peptide
backbone
• The ofoatios of the side hais of the amino acids are not part of the
secondary structure
• I a poteis, the foldig of pats of the hai a ou idepedetl of
the folding of other parts - such independently folded portions of the protein are
referred to as domains
Four levels of protein structure
• Tetia stutue iludes the thee-dimensional arrangement of all the atoms
in the protein, including those in the side chains and any other groups (e.g.
covalently attached groups or prosthetic groups)
• A potei a also osist of multiple polypeptide chains or subunits - typically
individual subunits are encoded by distinct genes. The arrangement of subunits
with respect to one another is referred to as quaternary structure
• The iteatios etee suuits is ediated  noncovalent interactions, such
as hydrogen bonds, electrostatic interactions, and hydrophobic interactions
Summary 4-1, p. 88
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Primary (1°) Structure
• Pia stutue is the liea ode i hih the aio aids ae oaletl
linked, e.g. N-RKRRQTSMTDFYHSKRRLIFS-C
• The pia stutue is the oe-dimensional first step in specifying the threedimensional
structure of a protein
• The ode of aio aids i a potei is of etee ipotae ad defies the
three-dimensional structure of a protein
• To proteins can have the same primary amino acid composition but in a different
arrangement (20100) - these proteins will display markedly different function/
biological activity
• Chages i the pia aio aid seuee a hae ajo sigifiae fo the
activity of the protein, e.g. hemoglobin in sickle cell anemia
Sickle Cell Anemia
• Appoiatel ,-80,000 individuals in the US alone are afflicted with Sickle
cell anemia (homozygosity for the Sickle cell mutation)
• Appoiatel ,, idiiduals in the US have Sickle cell trait
(heterozygosity for the Sickle cell mutation)
• Appoiatel  i  Afia-Americans have Sickle cell anemia, and 1 in 12
have Sickle cell trait
• Appoiatel  i , Hispai-Americans have Sickle cell anemia
• The pia liial aifestatio of Sikle ell aeia is outs of hoi pai
(often referred to as Sickle cell crisis), which can last from several hours to
several months
• Sikle ell patiets ae also highl suseptile to aious ifetios - pneumonia is
the primary cause of death among children with Sickle cell anemia
Hemoglobin S - Sickle cell anemia
• A siple hage utatio i the HBB gee, that eodes the β-subunit of
hemoglobin, results in a change in the primary amino acid sequence of beta globin
(E V on the surface of the protein), leading to the production of hemoglobin S
• Noal heogloi A is esposile fo oge taspot i the lood -
hemoglobin S causes red blood cells to sickle, clump and block blood flow
Hemoglobin S - Sickle cell anemia
Summary 4-2, p. 88
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Protein Secondary (2°) Structure
• Seoda stutue is the hdoge-bonded arrangement of the backbone of
the protein
• The to ai fos of seoda stutue ae α-helies ad β-sheets
• Withi eah aio aid residue there are two bonds with reasonably free
rotation:
 the od etee the α-C and the amino N of that residue, and
 the od etee the α-C and the carbonyl C of that residue
• The oiatio of the plaa peptide od ad the to freely rotating bonds
has important implications for the 3D conformation of the protein
• A peptide-chain backbone can be visualized as a set of playing cards, each card
representing a planar peptide bond
• The ads ae liked at opposite oes  siels, representing the bonds about
which there is considerable freedom of rotation
Fig. 4-1, p. 89
Secondary (2°) Structure
• The agles φ phi ad υ psi, also alled
Ramachandran angles, are used to
desigate otatios aoud the Cα-N and
-C bonds, respectively
• The ofoatio of a potei akoe
can be described by specifying the values
of φ ad υ fo eah esidue -180° to 180°)
• To kids of seoda stutues that
occur frequently in proteins are the
epeatig α-heli ad β-sheet hydrogen
bonded structures
• The φ ad υ agles epeat theseles i
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Document Summary

The arrangement of subunits with respect to one another is referred to as quaternary structure: the i(cid:374)te(cid:396)a(cid:272)tio(cid:374)s (cid:271)et(cid:449)ee(cid:374) su(cid:271)u(cid:374)its is (cid:373)ediated (cid:271)(cid:455) noncovalent interactions, such as hydrogen bonds, electrostatic interactions, and hydrophobic interactions. Secondary (2 ) structure: the a(cid:374)gles (cid:894)phi(cid:895) a(cid:374)d (cid:894)psi(cid:895), also (cid:272)alled. Ramachandran angles, are used to desig(cid:374)ate (cid:396)otatio(cid:374)s a(cid:396)ou(cid:374)d the c -n and. 5. 4 (or angstrom = 10-10 m: p(cid:396)otei(cid:374)s ha(cid:448)e (cid:448)a(cid:396)(cid:455)i(cid:374)g a(cid:373)ou(cid:374)ts of -helical structures, ranging from a few percent to nearly 100% The -helix: f(cid:396)o(cid:373) left to (cid:396)ight, (cid:271)all a(cid:374)d sti(cid:272)k (cid:373)odel sho(cid:449)i(cid:374)g te(cid:396)(cid:373)i(cid:374)olog(cid:455); (cid:271)all a(cid:374)d sti(cid:272)k (cid:373)odel with planar groups shaded; computer generated space filling model. The -helix: the -helix makes optimal use of internal h-bonding between h of h-n and o of the c=o bond of the fourth amino acid on the amino-terminal side of that peptide bond. The -helix - hemoglobin: ri(cid:271)(cid:271)o(cid:374) diag(cid:396)a(cid:373)s: (cid:373)odel of the he(cid:373)oglo(cid:271)i(cid:374) p(cid:396)otei(cid:374), sho(cid:449)i(cid:374)g the f(cid:396)e(cid:395)ue(cid:374)t helical regions.

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