Biochemistry Test one
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what amino acid does not have a free amino group but one attached to a side chain and a cyclic structure?
what are the consequences of not having a freee amino group?
forms a kink in the bond and its only compatible with a unique proline helix.
Proline is "sticky" and seeks out other polyprolines because------
because it is hydrophobic
Proline seeks out polyprolines and forms very important proteins for------
proline can also act as a molecular switch because
they have double bonds in the middle of the chain and the energy difference in proline allows it to flip back and forth between cis and trans.
All peptid bonds except for proline strongly favor ------ conformation
what does selinocysteine have attached to it?
what creates one of the termination codons
what does selinocysteine do?
has no genetic code
creates one of the termination codons
used in a number of redox enzymes
Proline has a lot of-----
what are Primary structures?
amino acid sequence
how are the electrons shared between carbon and oxygen dispersed?
they are dispersed between the carbonyl and a peptide bond
How does the peptide bond get partial double bond like characteristics?
Sometimes we see peptide bond where the second electron is dispersed between the carbonyl and peptide bond.
What conformation is it when the chains in front of the bond and behind it are facing on opposite sides?
What conformation is it when the chains in front of the bond and behind it are on the same side?
In general which conformation is less?
Trans, so all peptides not involving proline are in trans.
Cis can reach up to ------- of these peptide bonds involving proline
Only time you will see a stable Cis conformation is....
Trans is only --------kilocalorie per mole than the cis when it is on the amino side of the proline
when do ionic bonds occur?
between oppositely charged species
if you double the distance of an ionic bond what happens to the energy? why is this when ionic bonds are strong?
the weaker the bond, it would cut the energy in half.
Because it is neutralized by its own strength.
van der waals forces are-------
non-covalent bonds between electrically neutral molecules
what bond attracts water and acquires a sphere of hydration that interferes with the bond?
where do you usually see conserved ionic bonds?
places like the interface between proteins, where you can basically exclude water
Where do dipole-dipole bonds occur?
Between the carbonyls
the bond between two carobnyls is how much energy compared to an ionic bond?
it would by -9.3 kj/mole almost 1/10th the energy in an ionic bond
what happens to the energy if you double the distance of the dipole-dipole bond?
If you double the distance between the two species with the bond the energy goes from 1/10th the energy in an ionic bond to 1/8th the energy.
when does dispersion occur?
when you have two aromatic rings that involves the interatcion of the P orbitals.
when do hydrogen bonds occur and what is the strength of the bonds?
Hydrogen bonds occur when a hydrogen is shared between groups. the bond is ntermediate in strength (-20 to -30 kj/mole)
what is one of the most important bonds to proteins?
what is the length of a fixed hydrogen bond?
How many types of secondary structures are there?
What is random structure very important in?
in binding in molecular assembly and also in protein modification
1/3 to 1/2 of eukaryotic proteins have at least--------amino acids
what is another name for the random structure in eukaryotic proteins?
intrinsicially disordered peptides
when would it be difficult for modifying enzymes to get to the site on the protein?
if the protein was very tight, so most often these sites are on loose sections of the protein.
what is the advantage of random structures when it comes to molecular recognition? (2 things)
there is more versatility and the structure can recognize ligands
it has a larger capture radius which means that the kinetics of association are much faster
upon modification random structures receive------
stability but these regions can also function exclusively as random structures
what are entropic chains?
functioning random structures.
What are entropic spring used for?
They are used by entropic chains to keep proteins apart.
what is the largest protein in the body?
where is Titan located?
found in the sarcomere
what are titans?
It is random structure that can elongate and shorten without disrupting the structure of the overall protein.
what runs from the M line to the Z line?
What are entropic clots?
the ends of peptide chains that close channels (nervous system). they are random structures.
What bond does beta structure use?
chains of amino acids share hydrogens between their nitrogen and the oxygen of the adjacent chain are called------
anti-parallel beta sheet
what does a beta-pleated sheet look like?
The R groups of the protein chains get in the way so that the chain has to 'pucker' to throw the R groups above or below the sheet.
why can't the R groups be between the beta-pleated sheet?
Because they would interfere with hydrogen bonding
when can't you have a pure beta sheet?
when you have a parallel beta sheet
what is the one way you can have a pure beta structure?
if the beta strand is circular
T/F Beta structures are very rich in hydrophilic amino acids
where do you often see beta structures?
in the center of globular proteins because they are hydrophobic
you have reached the limit in protein structure when----
a protein has only one binding domain
hemoglobin consists of --------- helixes
what has four helixes that line up together to form an alpha helical bundle
The way secondary domains fold on each other is known as----
what is the difference between secondary and tertiary structures for fibrous proteins like silk and intermediate filaments?
both the same except for the globular proteins have multiple domains that fold on one another.
Biochemistry Test one