Chapter 4: Proteins Flashcards
primary structure (3)
what it is+determines+can show
- The amino acid sequence
- determines the 3D structure of the protein, 3D structure determines function
- can show evolutionary history
Explain the formation of a peptide bond
In trans omega torsion is —— In Cis omega torsion angle is —-
- 180
- 0
Peptides bonda are (2)
stability+what it is
- kinectically stable
- colvalent bond that links amino acids together
Oligopeptide
a polypeptide with a small number of amino acid residues
ex: dipeptide, tripeptide, tetrapeptide (4- aa)
Average weight for an AA residue is
- 110g/mol
Proteins typically consist of —– amino acids
50 to 2000
Secondary structure
The three dimensional structure resulting from a regular pattern of hydrogen bonds between the NH and the CO components of the amino acids in the polypeptide chain.
Teriary Structure
When the R groups of amino acids that are far apart in the primary structure bond with one another.
This level of structure is called —- structure and is the highest level of structure that an individual polypeptide can attain.
tertiary
The final three-dimensional structure of a protein is determined simply by the —-.
amino acid sequence of the protein
peptide bond (amide bond)
The linkage joining amino acids in a protein formed by linking the α carboxyl group of one amino acid to the α-amino group of another amino acid.
The formation of a dipeptide from two amino acids is accompanied by —–
the loss of a water molecule
Explain the biosynthesis of the peptide bonds
The equilibrium of this reaction lies on the side of hydrolysis rather than synthesis under most conditions. Hence, the biosynthesis of peptide bonds requires an input of free energy. Nonetheless, peptide bonds are quite stable kinetically because the rate of hydrolysis is extremely slow; the lifetime of a peptide bond in aqueous solution in the absence of a catalyst approaches 1000 years.
a residue
each amino acid unit in a polypeptide
By convention, the amino end is taken to be the beginning of a polypeptide chain, so the sequence of amino acids in a polypeptide chain is written starting with the —- terminal residue
amino
Why is the polypeptide backbone rich in hydrogen-bonding potential?
Each residue contains a carbonyl group (C═O), which is a good hydrogen-bond acceptor, and, with the exception of proline, an amino group (N—H), which is a good hydrogen-bond donor. These groups interact with each other and with the functional groups of side chains to stabilize particular structures.
a dalton
- Used to describe mass of protein
Disulfide bond (2)
formed by+ can form btwn
- formed by the oxidation of a pair of cysteine residues.
- Disulfide bonds can form between cysteine residues in the same polypeptide chain, or they can link two separate chains together.
The resulting unit of two linked cysteines is called .
cystine
3D structure/ traits of peptide bonds (3):
struture+ resonance+ charge
- six atoms lie in the same plane (planar): the α-carbon atom and CO group of the first amino acid and the NH group and α-carbon atom of the second amino acid
- the peptide bond has considerable double-bond character owing to resonance structures: the electrons resonate between a pure single bond and a pure double bond. This partial double-bond character prevents rotation about this bond and thus constrains the conformation of the peptide backbone
- peptide bond is uncharged, allowing polymers (petide chains) of amino acids linked by peptide bonds to form tightly packed globular structures that would otherwise be inhibited by charge repulsion.
Almost all peptide bonds in proteins are —. This preference can be explained by the fact that there are —- between R groups in the —– configuration but not in the —- configuration.
- trans
- steric clashes
- cis
- trans
Steric exclusion
- the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle
Phi (ϕ) (2)
What the angle is between + comparing which?
- The angle of rotation about the bond between the nitrogen and the α-carbon atoms
- comparing angle between the 2 carbonyl atoms
psi (ψ) (2)
What the angle is between + comparing which?
- the angle of rotation about the bond between the carbonyl carbon and the α-carbon atoms.
- Comparing the angle between the two Nitrogen atoms
In trans conformation the torsion angle is —-, in cis, omega torsion angle is —-
omega torsion angle: the half double bond between Nh and Co
- 180
- 0 degrees (right ontop of eachother)
Alpha helices, β pleated sheets, and turns are formed by
- a regular pattern of hydrogen bonds between the peptide NH and CO groups of amino acids that are often near one another in the linear sequence, or primary structure
α helix (4)
the shape+ side chain+ residues+ chirality
- a rodlike structure with a tightly coiled backbone.
- The side chains of the amino acids composing the structure extend outward in a helical array towards the amino end
- The CO group of each amino acid forms a hydrogen bond with the NH group of the amino acid that is situated four residues ahead in the sequence (same side of helix) C=O pointed downwards to c terminal
- Helix are right handed due to chirality of the amino acids
Proline in alpha helixes
No in the middle, maybe at end due to psi, phi angles
In α helix each residue is related to the next one by a rise, also called translation, of —- along the helix axis and a rotation of —– degrees, which gives —– amino acid residues per turn of helix.
- 1.5 A
- 100
- 3.6
amino acids spaced —- apart in the sequence are situated on opposite sides of the helix and so are unlikely to make contact.
two
The pitch of the α helix
the length of one complete turn along the helix axis and is equal to the product of the translation (1.5Å) and the number of residues per turn (3.6), or 5.4 Å
α helix amino acid breakers:
Branching at the β-carbon atom, as in valine, threonine,
and isoleucine, tends to destabilize α helices because of steric clashes. Serine, aspartate, and asparagine also tend to disrupt α helices because their side chains contain hydrogen-bond donors or acceptors in close proximity to the main chain, where they compete for main-chain NH and CO groups. Proline also is an α helix breaker because it lacks an NH group and because its ring structure prevents it from assuming the ϕ value to fit into an α helix.
a helix 36 amino acids long would form —- turns
10
the rise
the distance between amino acids: it’s a distance of 1.5 angstroms.
β strand
extended….
is almost fully extended rather than tightly coiled as in the α helix
The distance between adjacent amino acidnresidue along a β strand is approximately —, in contrast with a distance of —- along an α helix.
- 3.5 Å
- 1.5 Å
Instead of a single polypeptide strand, the β sheet is composed of —- called β strands.
two or more polypeptide chains
Beta strand R groups
The side chains of adjacent amino acids point in opposite directions (above and below the b sheet)
Reverse turn
The carbonyl oxygen of residue i accepts a hydrogen bond from amide nitrogen of residue i+3
Adjacent β strands run in opposite directions
tell me about the H bond
- Hydrogen bonds (green dashes) between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure
Adjacent β strands run in the same direction.
Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand.
Mixed B sheet
- contains parallel and antiparallel segments
Best conformation of phi and psi Beta sheet:
Teritary structure are a result of…. such as….
- the result of interactions between the R groups of the peptide chain.
- covalent bond- disulfide bonds
- vanderwaals interactions
- H-bond interactions
- ionic interactions
motifs or supersecondary structures (3)
what it is+ ex+ often the same motif…..
- particular combinations of secondary structure found in many proteins
- ex: an α helix separated from another α helix by a turn, called a helix-turn-helix unit (DNA binding)
- Often the same motif is found in proteins with similar functions (such as proteins that bind DNA, Ca2+, etc)
A β-hairpin (3)
What is common+ what it consist of+in terms of i
- two consecutive hydrogen-bonded antiparallel β-strands connected by a loop region that typically comprises 1–5 amino acid residues.
- glycine and proline are common
- a hydrogen bond involving the carbonyl of residue i and the NH group of residue i+3
domains (2)
What it is + size
- When polypeptide chains fold into two or more compact
regions that may be connected by a flexible segment of
polypeptide chain, rather like pearls on a string - range in size from about 30 to 400 amino acid residues
subunit
Many proteins consist of more than one polypeptide chain in their functional states. Each polypeptide chain in such a protein is called a subunit
The interactions among subunits of proteins displaying
quaternary structure are usually the — interactions
discussed in Chapter 2: —-, —–, ——
- weak
- hydrogen bonds, ionic bonds, and van der Waals interactions.
dimer
two identical subunits
In most cases, the subunits are held together by —- bonds.
not peptide
noncovalent
Dihedral angle is determined by —–.
4 atoms
alpha helices have average phi angle of
-57
alpha helices have average psi angle of
-47
