BIOC chapter 4
The α helix: Most alpha helices are
12 residues long
Short polypeptide
oligopeptide
Cysteine's R-group -CH2-SH •pKa = 8.4 therefore at physiological pH (7.4) it is
protonated
Amino acids can be classified by their chemical properties: •These classifications are made based on their
"R" groups
amino acids within the peptide are called
"amino acid residues" because only the residual atoms remain
Amino acids have 3-letter codes AND 1-letter codes.
*Most* of the time the 1-letter code is the 1st letter (a few don't) •Example: Alanine (Ala, A) however Arginine (Arg, R) b/c "A" is for alanine, we use "R" for arginine
Charge at ph 10 N-met-cys-gly-lys-glu-c
0(n)+0(met) -(cys)0(gly)+(lys)-1(glu)-(C) -2 charge
Building Blocks of Proteins:•Proteins are made up of
1 or more polypeptide chains
List the 1.) covalent and 2.)noncovalent forces that can stabilize protein structures.
1.)The primary structure is held together by covalent peptide bonds.disulfide bonds, thioester bonds, and isopeptide 2.) hydrogen bonds, ionic bonds, van der Waals interactions, zinc ions, and hydrophobic bonds.
•Most polypeptides contain
100-1000 amino acid residues
in Beta sheet, Each residue forms
2 hydrogen bonds with the neighboring strand
a single beta sheet can contain between
2 to more than 12 strands -Average = 6 strands, with 6 residues long
tertiary structure
3-d strucuture of an entire polypeptide, including all its side chains
The α helix:• ___ residues per turn of the helix, for every turn the helix rises 5.4 angstroms along its axis
3.6
Charge at ph 7 N-met-cys-gly-lys-glu-c
=+1(n)0(met) 0(cys)+0(gly)+(lys)-(glu)-(C)0 CHARGE
A polypeptide segment that has folded into a single structural unit is called a
DOMAIN •Some proteins have 1 domain, some have more!
nonpolar amino acids
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline
Identify all the hydrogen bond donor and acceptor groups in the backbone.
Hydrogen bond donor: N-H(BLUE/WHITE) Hydrogen acceptor: O(RED) The α helix. In this conformation, the polypeptide backbone twists in a right-handed fashion so that hydrogen bonds (dashed lines) form between ═ and N—H (donor) groups four residues farther along. Atoms are color-coded: Cα light gray, carbonyl C dark gray, O red, N blue, side chain purple, H white.
there are Hydrophobic and Hydrophilic Residues in
Myoglobin
Compare parallel and antiparallel β sheets.
Parallel beta pleated sheets have two polypeptide strands running in the same direction while antiparallel beta pleated sheets have two polypeptide strands running in the opposite directions.
Describe the four levels of protein structure.
Primary: the sequence of amino acids forms the polypeptide chain Secondary:the primary chain forms spirals(alpha helix) and sheets(beta sheets) Tertiary: Superimposed on the secondary structure. Alpha helices and/or beta sheets are folded up to form a compact globular molecule held together by intramolecular bonds. Quaternary structure: Two or more polypeptide chains, with its own tertiary structure, combine to form a functional protein.
•In this structure, polypeptide strands are aligned and hydrogen bonding are with neighboring strands
The beta sheet
Identify the polar amino acids that are sometimes charged.
Two of the polar amino acids (glutamic acid and aspartic acid) contain carboxylic acid functional groups and are therefore acidic (negatively charged). Two of the polar amino acids (lysine and arginine) contain amino functional groups and are therefore basic (positively charged).
zinc finger
a small protein structural motif that is characterized by the coordination of one or more zinc ions in order to stabilize the fold -Only in smaller structures 20-60 residues -Zn complexes with Cys, His, Glu, and Asp tetrahedrally to help stabilize the protein
Most proteins contain
all 20 amino acids
An entire protein structure often has a mixture of some of its backbone in the
alpha helix confirmation and some in the beta sheet confirmation
3 types of secondary structure
alpha helix, beta sheet, unstructured (bturn)
Proteins are polymers of
amino acids
negatively charged amino acids
aspartate, glutamate
charged amino acids
aspartate, glutamate, lysine, arginine, and sometimes histidine
The α helix: The carbonyl oxygen forms hydrogen bond with the
backbone NH group 4 residues ahead
a secondary proteins unique properties are important for how the
backbone folds
Polar amino acids can be in
both the surface and core
Polypeptide: chain of amino acids linked together by peptide bonds
chain of amino acids linked together by peptide bonds
acidic and basic amino acids are
charged
These amino acids are also on the surface (exterior) of protein
charged amino acids
Amino acids; All but 1 of them are
chiral
Amino acids are linked via a
condensation reaction.
Dive into the 3D structure: Regular secondary structures (alpha helix, beta sheet) are typically in the
core
pH>pKa
deprotonated
Amino acid sequence is important and
dictates shape
Some polypeptide chains align in regions with
directionality.
•Ionizable groups are ones that can
either give up or gain a proton!
Dive into the 3D structure: Irregular structure (loops) are typically found on the solvent
exposed surface
Explain why biochemists know more about globular proteins than disordered proteins.
globular proteins are usually stable by themselves in aqueous solution.
methionine is not polar
has a "S" but it's surrounded by carbons on the side chain so it's mostly nonpolar
In protein secondary structure, Polypeptide (AA chain) folds in a way to maximize
hydrogen bonding
in tertiary structures: Core is almost always
hydrophobic
pH=pKa
ionized and unionized forms are equal (50%)
•Ionization state is sensitive to
local pH changes
positively charged amino acids
lysine, arginine, and sometimes histidine
•20 standard amino acids->
most proteins contain all of these
Draw a tripeptide and identify its peptide bonds, backbone, side chains, N-terminus, C-terminus, and net charge.
net charge 0
in a tertiary structure, some polar amino acids can be in the protein interior to help
neutralize their polarity
in a tertiary structure, Charged amino acids are almost always located
next to a residue with opposite charge (interact electrostatically to form an ion pair)
Explain why proteins are not rigid.
no protein exists as a completely rigid block. All proteins are inherently flexible, because individual bonds in the polypeptide chain can rotate, bend, and stretch, and secondary and tertiary structures are stabilized by relatively weak noncovalent forces. *many proteins must undergo other types of structural changes in order to carry out their biological functions.
How does a protein fold? Protein folding and protein stabilization depend on
noncovalent forces. Key factor: the hydrophobic effect
These amino acids are mostly on the INTERIOR of the protein (not exposed to solvent)
nonpolar amino acids
•Don't often participate in any chemical reactions
nonpolar amino acids
Antiparallel= chains run in
opposite directions *The NH and C=O groups of an amino acid on one strand form H bond w/ C=O and N-H groups of the opposing amino acid on the other strand
Antiparallel b sheets align in
opposite directions (hair pin).
Formation of 3D structure:Some proteins need
other proteins (molecular chaperones) to help them fold
Name some residues that are likely to be located on the protein surface and some residues that are likely to be located in its core.
outside:polar and charged ex: histidine, aspartate interior: nonpolar ex: glycine, alanine
The α helix: Side chains extend _____ and the atoms of backbone fill the inside
outward
disulfide bonds
oxidation reaction between Cysteine
in the beta sheet Polypeptide strands can be arranged in
parallel and anti-parallel confirmation
neutral polar will be
polar
•N,O, and S on the side chain can help classify an amino acid as
polar
These amino acids mostly make up the exterior of a protein but can also be found in the interior
polar amino acids -They are exposed to solvent because they are polar! (solvent= aqueous environment)
Amino acids are linked by peptide bonds to form a
polypeptide
•The different elements of secondary structure are linked together by
polypeptide loops
•essentially the AA sequence (doesn't tell anything about shape)
primary
pH<pKa
protonated
not all proteins have this, proteins that have more than 1 polypeptide, this structure defines the spatial structure of the chains
quaternary
Properties of the backbone: C-N (peptide bond) is
rigid, meaning it doesn't move
Properties of the backbone: There is some _____ about the N-Cα and Cα-C axis
rotation
Parallel b sheets align in the
same direction
Parallel = chains run in
same direction (N - C or C - N) - an amino acid on one strand connects to two amino acids on the opposing end via hydrogen bonds *dont line up perfectly
proteins fold, the confirmation of the backbone (so not the R groups) is the 20 structure.
secondary
These polypeptide loops often link
secondary structures
primary structure of protein
sequence of amino acid residues
polar amino acids
serine, threonine, tyrosine, asparagine, glutamine, cysteine
quaternary structure of a protein
spatial arrangement of polypeptide chains in a protein w/ multiple subunits
secondary structure of protein
spatial arrangement of the polypeptide backbone:
The α helix: Hydrogen bonds along the helical axis
stabilize this structure.
complete 3D confirmation including backbone AND side chains
tertiary
•Includes regular and irregular secondary structures PLUS the spatial arrangements of the R-groups
tertiary structure
the tertiary structure lets us know what happens to
the side chains
Charge of the side chains depend on
their ionization state
Explain why a globular protein has a hydrophilic surface and a hydrophobic core.
these proteins are surrounded by water molecules, so the main driving force for folding is the packing of hydrophobic side chains into the interior of the molecule, thus creating a hydropohobic core and a hydrophilic surface.
chiral
they are asymmetric, non-superimposable, "left" and "right" handed
Overall factors that affect protein stability
•Hydrogen bonding (within the secondary structure) •Ion pairing (minimal effects) •Disulfide bonds (between cysteines) •Interaction with Zn ions (Zinc Fingers)
backbone of protein
•The backbone is planar (not including R groups, because they are not planar)
Proteins
•The workhorses of the cell •This chapter (Ch4) we will focus on their structure, next chapter will focus on their function
