L3 Protein Structure Flashcards
structural features of an amino acid
- central carbon atom
- amino group
- side chain (R/R-group)
- carboxyl group
what are the three different categories based on chemical properties of the R group
- neutral (uncharged) and nonpolar
- neutral and polar
- charged – acidic (negative) or basic (positive)
polypeptide structure - what is a peptide bond
- covalent links between amino acid residues in a polypeptide
- form through a condensation reaction ( one water molecule is expelled)
- happens between one carboxyl group (O-) and an amino group (H)
- it has partial double-bond characteristics bc electrons are shared (makes the bond very strong and rigid)
polypeptide structure - what are carbonyl groups
- C=O
- with the carbon atom bonded to two other atoms
polypeptide structure - what are amide groups
- N-H
- functional group where a carbonyl carbon atom is directly linked to a nitrogen atom
polypeptide structure - carbonyl and amide groups
- they are nearly coplanar and form the amide plane
- it is always in the trans configuration
polypeptide structure - what is trans configuration
- most common arrangement of a peptide bond bc it is sterically favorable
- the amino acid side chains are on opposite sides of the bond
polypeptide structure - what is cis configuration
- not common arrangement bc there is r group interference
- the side chains are on the same side
define conformation
the arrangement of chemically bonded atoms in three dimensions
what does the polypeptide chain conformation consist of?
- three repeating covalent bonds
1) between the amide group (N-H) and central carbon (C alpha)
2) between central carbon (C alpha) and the carbonyl group (C=O)
3) a peptide bond between carbonyl group (C=O) and amide group (N-H)
polypeptide chain conformation - rotational angle of bond
- amide group (N-H) and central carbon (C alpha) = phi (φ)
- central carbon (C alpha) and carbonyl group (C=O) = psi (ψ)
- peptide bond: amide group (N-H) and central carbon (C alpha) = omega (ω)
polypeptide structure - what amino acids have unique properties?
- glycine
- proline
- cysteine
unique properties - glycine
- not chiral (a type of molecule that has a non-superposable mirror image)
- has great conformational freedom (free to rotate its bonds however)
unique properties - proline
- reduced hydrogen bonding potential due to absence of N-H
- least conformational freedom
unique properties - cysteine
- it can form a disulfide bond by oxidation to then form cystine
- this happens bc the extracellular space has the redox potential that favors disulfide bond formation
- its common in extracellular domains of membrane proteins and in small secreted proteins (hormones)
unique properties - cysteine and human insulin
- L-cysteine inhibits (restrains) insulin release
- D-cysteine controls insulin secretion
what are the levels of protein structure
- primary structure
- secondary structure
- tertiary structure
- quaternary structure
levels of protein structure - primary
1-D sequence of amino acids
levels of protein structure - secondary
- 3-D arrangement of a short, local stretch of amino acid residues
- can be an alpha helix or a beta sheet
levels of protein structure: secondary - alpha helix
- always right handed
- its stabilized by hydrogen bonds of the main chain, between the carbonyl group of one residue and amide group of another one 4 positions down
levels of protein structure: secondary - beta sheet
- a pleated structure stabilized by hydrogen bonds between the main chains of amide and carbonyl groups
- the groups project laterally
- R groups project alternatively to either side of the backbone
- the strands run in parallel or anti-parallel arrangement
levels of protein structure - tertiary structure
- overall 3-D folded arrangement polypeptide chain adopts under physiological conditions
- stabilized by interactions involving R groups
levels of protein structure: tertiary structure - what are the R group interactions
- hydrogen bonds (OH-O or OH-N)
- hydrophobic interactions
- disulfide bonds (S-S)
- ionic bonds
levels of protein structure - quaternary structure
manner in which individual folded chains associate with themselves
explain how protein structure is heirarchial
- quaternary structure is based on tertiary structure, which is based on secondary structure
- all three higher order structures depend on primary structure
what are some examples of post-translational modifications
- phosphorylation
- lipidation
- ubiquitination
- disulfide bond
- acetylation
- glycosylation
post-translational modifications - phsophorylation
- can activate the protein by adding a phosphate via kinase
- can turn off the protein by cleaving it off via phosphatase
why is protein folding important
the amino acid sequence of a domain determines its table, functional (or native) structure
protein folding - explain Anfinsen’s experiment (1960s)
- studied the folding of Ribonuclease A (has 8 cystine residues that form 4 disulfide bonds)
Anfinsen experiment (1960s) - what was the question asked
- can the protein refold after being denatured outside of the cell
- if yes, then everything needed to fold the protein is in the primary structure
Anfinsen experiment (1960s) - how do you unfold Ribonuclease A
- you will need a:
1) denaturant to disrupt hydrogen bonding (urea, guanidine hydrochloride, etc.)
2) reducing agent to disrupt the disulfide bridges (beta-mercaptoethanol, etc.)
Anfinsen experiment (1960s) - what happened in the experiment
1) used urea and beta-me to denature the protein
2) then either removed denaturant and reducing against together or separately
Anfinsen experiment (1960s) - results of taking out reducing agent then denaturant
- the cysteine (disulfide) bonds reform first then the hydrogen
- this is a problem bc it brought it back to the tertiary structure first
- results in a scrambled protein
Anfinsen experiment (1960s) - results of taking out reducing agent and denaturant together
- hydrogen bonds form first
- results in native conformation
Anfinsen experiment (1960s) - was the hypothesis correct
- yes, the protein will refold outside of the cell
- so everything needed is within the primary structure
- but you need to allow the protein to form the secondary structure first
Anfinsen experiment (1960s) - significance of results
1) Emphasizes hierarchical nature of protein structure
2) Polypeptides can fold correctly without additional cellular machinery
3) Nucleic acid sequence specifies not only amino acid primary sequence, but also the tertiary structure and ultimately the function of the protein
explain why protein misfolding is important
- it can be “infectious”
- the abnormal version (prion) induces a conformational change in the normal protein to adopt its infectious shape
protein misfolding - what is a prion
- “proteinaceous infectious particles”
- they are improperly folded forms of normal protein
- the amino acid sequence does not differ
