Lab chapter 6: Biochemical reactions, Enzymes 1 Flashcards
(38 cards)
Ribozymes are:
RNA molecules that act as enzymes
Roughly one ounce of pure pepsin is capable of digesting/hydrolyzing two metric tons of ovalbumin in a matter of a few hours. This is an example of ____
an enzyme/catalyst speeding up a rxn which would otherwise be slow as fuck.
The 3D shape of an active site is determined by:
the arrangement of the enzyme’s constituent amino acids
Each amino acid consists of three groups, which are:
the central/alpha carbon is attached to the three groups: amino/NH2, carboxyl group, and side chain/R group
What is the primary structure of a polypeptide?
the linear sequence of amino acids in a polypeptide chain
Amino acids are linked together in a covalent bond referred to as a
peptide bond
The secondary structure is made up of ____ bonds, which are formed between the ___ group of one amino acid and the ____ acids of another amino acid
hydrogen
hydrogen of amino + oxygen of carboxyl group
The tertiary structure results from interaction of _____
side chains of its constituent amino acids and the surrounding solution
ex. water or a np substance
A quaternary structure exists in proteins consisting of
more than one polypeptide chain
The tertiary structure of a polypeptide or the quaternary structure of a protein are stabilized by three things, which are:
1.
2.
3.
1) hydrogen bonding between polar side chains
2) ionic bonds between positively charged and negatively charged polar side chains
3) covalent bonds between the sulfurs found in the side chains of two cysteine monomers (also known as disulfide bridges).
Describe how a polypeptide will fold in water
will maximize interaction between nonpolar side groups, folding closer within the molecule
The folding of a polypeptide in water results in the formation of
an active site having a specific size and shape. Note that the polar side chains are what makes up this active site because the nonpolar have folded in on themselves.
Once the proper substrate has bound, an enzyme usually undergoes a conformational change known as
induced fit
what occurs during induced fit?
puts stress on exisiting bonds within substrate that must be broken while fostering new bonds that must be made in order for a substrate to be converted into its product
The amount of product in this experiment can be followed by
The amount of product formed can be quantified by
followed colorimetrically using a spectrophotometer
quantified by a standard curve
describe what occurs in this experiment’s reaction,
The enzyme, acid phosphatase, binds p-nitrophenyl phosphate in its active site which allows a water molecule to be introduced between the phosphorus atom and the oxygen atom that links the phosphate group to the benzene ring, breaking (hydrolyzing) the covalent bond
Describe the general procedure of the time course section
- known amnt susbtrate placed into tube with acidic buffer solution
- enzyme added at “time zero” then quickly mixed and a small sample (aliquot) is withdrawn
- aliquot placed in alkaline solution, which stops reaction of that sample
the longer the enzyme is allowed to work in the reaction vessel, the more product is formed over time, so long as
substrate concentration is not a limiting factor
If aliquots of the reaction mixture are withdrawn at set time intervals and stopped as described above, one would expect
the color in each successive sample tube to be more yellow than previous
The amount of product within each sample tube is directly proportional to
the amount of light absorbed by the tube’s contents.
If one compares the amount of light absorbed by a sample tube to that of tubes containing known amounts of product, one can
quantify the amount of product contained within that particular tube. This comparison is simpli-fied by producing a graph known as a “Standard Curve.”
Describe the important of the second time course
A second time course is run concurrently; this tube is identical to the first in all respects except that enzyme is not added. In place of the enzyme, an equal volume of deionized water is added to the tube. The second time course serves as a “control” (mentioned above) of enzymatic activity for any product in the control tube did not come about from the action of an enzyme!
Describe general procedure of the “standard curve” exercise
a stock solution with a known product concentration is used to create a series of tubes in a process known as “serial dilution.” The contents of each of these tubes will absorb a different amount of a wavelength of light from the blue part of the visible spectrum.
Using a spectrophotometer, one can obtain a number which corresponds to the percentage of the initial light that is absorbed by a solution as it passes through.
Once absorbencies are obtained for a series of known concentrations of product, a graph of those results can be plotted. This allows the user to obtain a product concentration for any absorbance value that falls within the range of that graph
you obtain an absorbance value for a given tube in the time course, you
can determine how much substrate was converted to product within that time period by using your standard curve.
