Lab 3: Biochemistry

Question 1

Learning objectives

Answer 1

• > Diagram how a mutation in DNA can lead to a change in protein sequence
• > Demonstrate a salt bridge and disulfide bond using the amino acid kit
• > Describe CPK coloring
• > Distinguish hydrophobic and hydrophilic side chains
• > Model the effect of pH and temperature on enzyme structure
• > Properly use tools, such as the spectrophotometer
• > Perform an experiment to test the rate of reaction of an enzyme
• > Use a standard curve to convert from absorbance to molarity

Question 2

central dogma of molecular biology

Answer 2

DNA -> transcription-> mRNA-> translation-> protein-> trait

review how to go from DNA-> mRNA

Question 3

ACh

Answer 3

• > chemical signal for muscle contraction
• > nerve endings in muscle
• > ACh is rapidly broken down by acetylcholinesterase

Question 4

how can we detect acetylcholinesterase activity?

Answer 4

we will test AChE indirectly by using thiocholine and DTNB (ellman’s reagent)–> (produces yellow color)

Question 5

how will you convert from absorbance concentration of thiocholine?

Answer 5

use the spec20 and test tubes containing “L-cysteine + DTNB” to measure the absorbance based on the concentration of cysteine.

• > graph the concentration of cysteine against the absorbance from each tube to produce a standard curve
• > use slope equation from the standard curve to convert absorbance to {thiocholine} for your experiment

Question 6

what is the molarity for an absorbance of .36 for your AChE reaction?

Answer 6

.04

Question 7

Enzymes are biological catalysts that speed up biochemical reaction rates—they share the common feature of lowering activation energies required for metabolic reactions.

Answer 7

true

Question 8

organophosphates

Answer 8

large class of pesticides that target the protein AChE

-> AChE is a very important enzyme in insects because it is responsible for “stopping” the communication between the nerve and muscle cells. How do these pesticides inhibit the activity of AChE? Organophosphates bind to the active site of AChE and block the substrate (i.e., ACh) from binding. Some insects have evolved resistance to organophosphates through the mutation of one amino acid in the active site of AChE. This mutation still allows ACh to bind to the AChE, but it does not allow the organophosphate to bind to the AChE.

Question 9

CPK coloring scheme

Answer 9

• > carbon is GRAY
• > Oxygen is Red
• > Nitrogen is blue
• > hydrogen is white
• > sulfur is Yellow

Question 10

carbon

Answer 10

gray

Question 11

oxygen

Answer 11

red

Question 12

nitrogen

Answer 12

blue

Question 13

hydrogen

Answer 13

white

Question 14

sulfur

Answer 14

yellow

Question 15

chemical properties of side chain

Answer 15

• > hydrophobic side chains are yellow
• > hydrophillic side chains are white
• > acidic side chains are red
• > basic side chains are blue
• > cysteine side chains are green

Question 16

Hydrophobic side chains are composed primarily of __________ atoms.

Answer 16

hydrogen

Question 17

Acidic side chains contain two __________ atoms. (This is a carboxylic acid functional group.)

Answer 17

oxygen atoms

Question 18

Basic side chains contain __________ atoms. (This is an amino functional group.)

Answer 18

nitrogen

Question 19

Hydrophilic side chains have various combinations of __________.

Answer 19

charged and polar atoms

oxygen, nitrogen, sulfur, and carbon