day 1 Flashcards
Some proteins can switch between two or more conformations. The switch often involves :
noncovalent binding of another molecule
weak bonds
noncovalent bonds
Types of noncovalent interactions
ionic, polar, LDF’s, hydrophobic exclusions
of amino acids essential for humans
9
polypeptide chain: Formation of peptide bond by energy-requiring ___ rxn
condensation
Hydrogen bonding is not involved in forming which level of protein structure?
primary
Proper folding of a newly synthesized protein is accomplished by:
the hydrophobic effect
electrostatic attractions and repulsions
Van der Waals attraction
help from chaperone proteins
Functioning proteins change between conformations when
a small molecule binds noncovalently
combustion: exer or endergonic?
exergonic
which things contribute to a proteins function?
shape
order of amino acids in primary sequence
positioning of R groups
secondary struture
The R group of which amino acid would form a covalent bond with another R group?
cysteine
Which of the following defines the polypeptide backbone?
anything that’s not an R group
how would you calculate an isoelectric point and what does it mean
- take the average of the pKa’s of its various forms
- its the point at which it stops migrating in an electric field which is equal to its average pH
aspartic acid vs serine; which is more water solube and why?
aspartic acid. COO- >> OH. ionic wins
Enzymes differ from chemical catalysts because they lose activity at high temperature or extremes of pH. This difference can be explained by
the loss of the 3-D shape of the enzyme
the loss of the shape of the active site
the loss of noncovalent interactions
the loss of ionic bonds
name an amino acid with an R group capable of hydrogen bonding
serine, threonine, tyrosine
If a crystal of NaCl is dropped into a beaker of polar solvent such as methanol, how would the electrostatic attraction of Na+ for Cl- in the salt bridge change?
The electrostatic attraction is weaker
DNA Polymerase is the enzyme involved in
Replication
are hydrophobic exclusions a true type of bond? where do they exist and what do they mainly depend on? give an example
- Not a true bond. Only exists in water
- Depends on entropy more than any binding
- Benzene: nonpolar molecule.
If you put benzene in water, benzene clusters together
T/F: membrane formation is powered by the hydrophobic effect
T
entropy of protein folding
disorder -> order
name some hydrophobic R groups
hydrophobic R groups: alanine, leucine, isoleucine
ways to denature a protein
Since proteins are held together with these weak forces, they can be unfolded fairly easily.
- Heat up to 50 degrees celcius,
- Detergent also denatures protein. (amphipathic molecule- highly polar salt bridge on one side, long hydrophobic tail on other side. Surrounds molecule- unfolds the molecule)
- Urea: has a lot of polar properties (2 dipoles) .
- Changing the pH of the system. Changes the molecules ability to ionize- titrates amino acids- lowering pH means adding H+ to the system. Swamping your negative R groups with positively charged hydrogen.
T/F: protein folding occurs via hydrogen bonding between backbone atoms and weak interactions of the R groups
True
what kinds of bonds can aspartic acid make?
ionic, hydrogen , LDF’s
Weak acids and bases are good at buffering pH changes if acid or base is added because
they easily protonate and deprotonate.
a buffer is most effective near:
its pka
Any given amino acid molecule in solution is constantly losing and gaining protons so as to shift among the forms drawn below. However, more time is spent in this form: ____ when the pH is near 7. If the pH is made very acidic (more H+) then more time is spent: ____
- zwitter ion
- with H+ on both the amine and carboxyl ends because there is more H+ available.
histidine structure- why is it special?
aromatic
STY CNQ- what group are these?
polar uncharged
what are some essential amino acids
histidien, menthionine, leucine, valine, tryptophan
secondary protein structure
‘local interactions’ alpha helix, beta pleated sheet,
hydrogen bonding between polar backbone
tertiary protein structure
overall 3-D shape. results from all R group and backbone interactions combined. can be globular or filamentous
when would you have quaternary structure?
more than one chain of polypeptides
