7 Protein Structure MBS
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What is the R group of glycine?
Are amino acids chiral?
Yes, the central alpha carbon is generally except for glycine
R groups rich in ___________ are HYDROPHOBIC
R groups with ___________, ___________ and ______ ________ are hydrophilic
oxygens, nitrogens & ESPECIALLY charged groups
What are the components of amino acids (4)
- • Alpha carbon (usually chiral)
- • Hydrogen
- • R group - gives AA its properties
- • Amine group - NH3+ at neutral pH
- • Carboxylate acid group - COO- at neutral pH
- • the smallest amino acid side chain
- • allows for sharp bends in chains & for chains to come close to each other (eg. hairpin bend in p53 protein)
- • can be hydrophilic or hydrophobic due to its minimal H side chain
contains a ring that limits its flexibility and makes it incompatible with alpha helix formation
tyrosine & tryptophan
- • both absorb UV light (280 nm) and makes protein detection easy
- • tryptophan has a non-polar R group
- • tyrosine has a polar R group
can form disulfide bonds between S's at the end of their R group
- the amount of activity per amount of purified protein
- eg. catalyzes light production: how much light is produced for x amount of protein
the stability of a protein's folded state results from:
- the sum of the weak interactions
- -weak forces: 1-7 kcal/mol
- -covalent forces: > 50 kcal/mol
transmembrane protein of the ATP Binding Cassette family
What are the 5 domains of the CFTR protein?
- • TM1, TM2: 2 transmembrane domains that are groups of 6 alpha helices that form a chloride channel
- • NBD1, NBD2: 2 cytoplasmic nucleotide binding domains that bind & hydrolyze ATP
- • R domain: a regulatory domain modified by phosphorylation
Describe how CFTR is activated:
- Activation of CFTR
- • when the R domain is phosphorylated activates the channel
- • ATP hydrolysis by NBD domains changes channel conformation and allows passage of Cl- ions through the PM
What does the drug Kalydeco do?
It is a treatment for CF patients with the G551D mutation
a polypeptide connection involving four lysines, but only in elastin (a connective tissue protein that is springy)
tough fibers rich in cysteine; contains tightly wound alpha-helices that are difficult to digested
- increased acidity in the blood and other body tissue; can result in bone formation issues, cognitive problems; often times the treatment is ingesting bicarbonate
- • causes problems in protein function because if not at the right pH, a protein has wrong charges on some of its side-chains & may not function
isoelectric point (pI)
the pH as which a compound is electrically neutral, aka the net charge is zero
to find, average the two pKa's surrounding the isoelectric species
The pKa is the pH at which the concentration of the acid form of a molecule is equal to the concentration of the base form of the same molecule (aka half molecules are in acid form, half in base form)
At what pH will a buffered solution be most resistant to changes in the pH after the addition of acid or base?
When the pH is close to the pKa value, the pH is most resistant to change upon addition of OH- (or H+). Relatively large additions in the amount of base (or acid) produce only small changes in pH, representing maximal buffering capacity.
Which amino acid is capable of forming disulfide bonds?
Cysteine: disulfide bonds are most often found in oxidizing environments such as outside of the cell
What is the main buffer in blood?
Carbonic acid/bicarbonate (H2CO3/HCO3-)
What is the main buffer inside cells?
- Phosphate ions
- H2PO4- --> H+ + HPO42-
In terms of buffering the blood: when CO2 is released from the body, the pH ________, meaning the environment is more ________
when CO2 is released, the pH INCREASES, meaning the environment is more BASIC
In terms of buffering the blood: when CO2 is NOT released from the body, the pH ________, meaning the environment is more ________
when CO2 is NOT released, the pH DECREASES, meaning the environment is more ACIDIC
pulmonary obstruction causes:
an increase in carbon dioxide, therefore a decrease in pH (makes it more acidic)
At pH values lower than the pKa, the ________ form of the molecule predominates. At pH values higher than the pKa, the ________ form of the molecule predominates.
Aspirin is a weak acid at low pH and has a pKa of 3.5. Per unit surface area, will more aspirin be absorbed in the stomach (pH 1.5) or in the intestine (pH 6.5)?
At a pH below its pKa, aspirin will be in its acid form (RCOOH). At a pH above its pKa, aspirin will be in its base form (RCOO-). Since non-ionized molecules cross cell membranes passively whereas ionized molecules do not, more aspirin will be absorbed in the stomach than in the intestine
What kind of bond links the amino acid residues of a protein to one another?
Peptide bond; forms between an amino and a carboxyl group; backbone of the peptide
What is a polypeptide?
A polypeptide is a chain of amino acids linked together by peptide bonds
What is meant by primary, secondary, tertiary, and quaternary structure of a protein?
- Primary: the amino acid sequence
- Secondary: helices, beta sheets, and turns
- Tertiary: the way the secondary structure elements come together in 3D space.
- Quaternary: the way multiple proteins come together to form a complex.
What determines most of the structural and functional properties of a protein?
The protein's amino acid side chains, which are also called R-groups
Which amino acids are positively charged at neutral pH?
arginine, lysine, and histidine
Which amino acids are negatively charged at neutral pH?
aspartate and glutamate (ate = negatively charged)
Which of the 20 standard amino acids are aromatic?
phenylalanine, tryptophan, and tyrosine (all have benzene rings)
The amino acid R-groups of water soluble proteins that face the exterior of the protein are usually ________, and those that face the interior of the protein are usually ________.
Regions of proteins that interact with DNA are usually ___________ charged:
Positively charged because DNA carries a negative charge
What technique can a scientist use to measure the purity of a protein in a sample?
Define specific activity of a protein:
It is the activity per amount of protein
A scientist inserts a sample of protein in a spectrophotometer and calibrates the instrument to detect absorbance of the sample at a wavelength of 280nm. What is the scientist measuring?
The content of tryptophan and tyrosine residues in the protein. Absorbance at 280nm is frequently used to determine protein concentration of a purified protein.
How may the activity of a DNA-binding protein be determined?
By the ability of the protein to band-shift DNA.
What type of bond has the most significant influence on how proteins fold?
Weak non-covalent bonds. The energy contribution from each individual bond is small, but the net contribution from all the non-covalent interactions is large.
an open state protein folding intermediate
catalyze the folding of some proteins; do not appear to influence the final structure of the protein
Name two common secondary protein structure elements:
Alpha-helix and beta-sheet
Describe the hydrogen bonding pattern between amino acid residues in an alpha-helix:
Hydrogen bonds in an alpha-helix occurs between the oxygen of a carbonyl group and the HN of an amino acid that is four residues down the polypeptide chain
Which amino acid cannot fit in an alpha-helix?
Proline: this amino acid has a five-member ring and is referred to as the 'helix breaker'
Describe the hydrogen bonding pattern between amino acid residues in a beta-sheet
In a beta-sheet, hydrogen bonding occurs between backbone atoms within stretches of amino acid residues. At least two (and frequently more) extended polypeptide chains are involved.
Which amino acid has the smallest side chain?
Glycine; its side chain is a hydrogen atom
Proteins make a significant contribution to the buffering capacity in cells and plasma. What part of proteins allows them to act as buffers?
Titratable groups on the amino acid side chains. Note that the pKa of these groups differ depending on the side chain. Also, since the protein concentration in cells and plasma is quite high, proteins have a considerable buffering capacity.
Describe the pathogenesis of inherited Creutzfeldt-Jakob disease:
The disease is caused by a single amino-acid mutation. This mutation causes prion proteins to switch their conformation from soluble alpha-helices to insoluble beta-sheets. The insoluble beta-sheets can form aggregates that in turn lead to neurological symptoms.
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