BIOCHEM 2EE3 Lecture Notes - Lecture 8: Cyan, Epitope, Peptide

51 views8 pages

purplehound890

8 Dec 2017

School

Department

Course

Professor

For unlimited access to Class Notes, a Class+ subscription is required.

Document Summary

1. 1 module 4 video 1 - protein folding. Let"s start with enzymes as the majority of enzymes are proteins and enzymes play a vital role in our lives. This means that they make biochemical reactions go faster and since they are catalysts, the enzymes themselves do not get used up in the reaction. There are many ways in which enzymes act as catalysts. They typically speed up reactions based on acid/base catalysis, covalent catalysis, electrostatic catalysis in order to perform the reaction much faster. Of course, when discussing catalysis we must introduce the energy-level diagram for a chemical reaction whereby we want our substrate to be converted to our product. In this diagram the y-axis represents the free energy of the reaction and the x-axis the course of the reaction - this variable changes with the type of reaction we are looking at.

Related Questions

Please help! Not sure about these questions..thanks

QUESTION 1

An example of an endergonic reaction is

	A.	Polymerizing a protein from amino acids.
	B.	Breaking a protein down into amino acids.
	C.	Breaking down ATP into ADP and P.
	D.	Breaking down glucose (using oxygen) to make CO2 and H2O.

QUESTION 2

When ATP breaks down to supply energy for cellular reactions, it often transfers its 3rd phosphate to another molecule. This is called ______, and makes the other molecule _______ reactive.

	A.	catalysis . . . more
	B.	phosphorylation . . . more
	C.	phosphorylation . . . less
	D.	polymerization . . . less

QUESTION 3

Which is true of enzymes?

	A.	They are highly specific in the reactions they catalyze.
	B.	Chemically, most are carbohydrates.
	C.	They accelerate reactions by adding energy.
	D.	They break down and are used up as they catalyze reactions.

QUESTION 4

What is peristalsis?

	A.	Rings of muscle that can contract to close off the stomach at each end.
	B.	A gland that secretes saliva.
	C.	Coordinated muscle contractions that move the contents of the GI tract.
	D.	A stomach enzyme that breaks down proteins.

QUESTION 5

Which is not a component of gastric juice?

	A.	H2O
	B.	acid
	C.	pepsin
	D.	amylase

QUESTION 6

What does the enzyme pepsin do?

	A.	Completely breaks down proteins into individual amino acids.
	B.	Completely breaks down carbohydrates into monosaccharides.
	C.	Partially breaks down proteins into smaller polypeptides.
	D.	Partially breaks down fats into fatty acids.

1.When something appears blue, it is absorbing all colors except__________.

yellow

blue

red

green

orange

2.During heavy exercise, lactic acid can build up in ourmuscles. Why? How does this resemble the metabolism of bacteria andyeast?

lactic acid is results from insufficient oxygen during sugarmetabolism; it is fermentation

lactic acid accumulates when we are dehydrated; bacteria andyeast use the same pathway

lactic acid is built up from carbon dioxide; bacteria and yeaststore energy in this way

3.Why must a cell keep a similar concentration of dissolvedsubstances with the fluid surrounding them?

to avoid dilution of potential energy

to avoid osmotic imbalance and rapid gain or loss of water

to maintain the correct amount of dehydration and hydrolysis

4.What is entropy?

the amount of energy in a system

the amount of disorganization

the amount of organization

5.Burning a log is the reverse reaction found in photosynthesis.What products would be formed in burning a log?

carbon dioxide and water

glucose and oxygen

oxygen and carbon dioxide

oxygen and water

6.The main reason that cellular respiration needs to occur stepby step instead of a single, big reaction is

cells don't store enough oxygen

too much energy would be released for the cell to harness

cells don't have many mitochondria.

cells produce the enzymes needed for cellular respiration veryslowly

7.Enzymes are catalysts because they operate to:

raise activation energy

lower activation energy

supply activation energy

supply the reactants

8.When ATP powers a reaction it becomes ADP. The ADP

can reform ATP by an exergonic reaction

is a waste product for lysosomal breakdown

can reform ATP by an endergonic reaction

can reform ATP by an oxidation reaction

can reform ATP by an equilibrium reaction

9.The energy source that drives photosynthesis is

water

glucose

carbon dioxide

oxygen

sunlight

10. What is the process by which enzymes regulate their ownactivity?

osmosis

self-propulsion

feedback inhibition

11.Coupled reactions are reactions in which a

endergonic reaction drives a spontaneous reaction

exergonic reaction drives a spontaneous reaction

endergonic reaction drives an exergonic reaction

exergonic reaction drives an endergonic reaction

12.How is water used in photosynthesis?

as a substrate for ATP synthase

as an electron donor

to combine with ADP forming ATP

as an electron acceptor

13.Why are the âDark Reactionsâ of photosynthesis referred to asâDarkâ?

they do not require light

they can only occur at night

they generate excess sugar and the leaves turn brown

14.What is the difference between potential and kineticenergy?

potential is stored, kinetic is being used

potential is being used, kinetic is ready to be used

potential is negative, kinetic is positive

15.The products of cellular respiration are

carbon dioxide, water, and ATP

glucose, water, and ATP

glucose, carbon dioxide, and ATP

oxygen, ATP, and water

carbon dioxide, glucose, and water

16.All of the following are correct about energy except:

The biological world gets its energy from the sun.

Chemical bonds store potential energy.

A boulder perched on a hill has kinetic energy.

Energy is defined as the ability to do work.

All forms of energy can be converted to heat.

17.What is needed for the end product of glycolysis, pyruvate,to enter the citric acid cycle?

More glucose for energy

ATP

Oxygen

Carbon dioxide

18.The enzyme that forms a transmembrane channel in mitochondriaand phosphorylates ADP

a carrier protein

ATP synthase

acetyl CoA

19.Fermentation is most common in

plants

microorganisms

animals

20.During adsorption of sunlight by photosystems, H+ ions aregenerated. Where do they come from? What are they used for?

from the breakdown of sugar; they help form water

water; they help form sugar

from carbon dioxide; they help dissolve NaCl

21.Glycolysis

does not use oxygen

uses oxygen

uses carbon dioxide

22.Photosynthesis is

not dependent on chlorophyll

a process that produces glucose and oxygen

a process that produces water and carbon dioxide

23.Breakdown of glucose generates many ATP molecules, each ofwhich can be used independently. Why is ATP ideally suited to powerbiological reactions?

ATP has many hydrogen bonds

ATP has enough energy to power one biological reaction

ATP readily dissolves in water

24.Objects that are not actively moving but have the capacity todo so are said to possess:

kinetic energy

entropy

potential energy

living energy

25.The first stage of cellular respiration, called ___________,takes place in the cytoplasm of the cell and needs no oxygen.

photorespiration

citric acid cycle

glycolysis

oxidation

26.Diffusion

requires energy

utilizes proteins to move molecules across a membrane

moves molecules against a concentration gradient

does not require energy

cannot occur without a membrane present

27.What is the name of the molecule on which an enzymeworks?

substrate

monomer

polymer

28.ATP contains

phenylalanine

two phosphate groups

three nitrate groups

three phosphate groups

29.How does chlorophyll function in photosynthesis?

by absorbing carbon dioxide

by absorbing the sun's energy

by absorbing water

30.Objects that are moving are said to possess:

living energy

potential energy

entropy

kinetic energy

31.The respiration pathway that evolved first is probably

glycolysis

aerobic respiration

citric acid cycle

32.The energy source for the process of photosynthesis is

oxygen

sunlight

carbon dioxide

chlorophyll

glucose

33.Burning wood generates heat and light. What type of reactionis this?

exergonic

kinetic energy

endergonic

potential energy

equilibrium

34.What is meant by a âcoupled reactionâ in terms of energy?

many poymers are built simultaneously

energy released by one reactions powers another reaction

some reactions occur in the same organelle

35.The First Law of Thermodynamics states:

energy is constantly being created by entropy events

energy can be changed from one form to another, but cannot becreated or destroyed

energy can be used and then destroyed because of entropy'sactions on it

energy can be destroyed while it is producing entropy

36.How do we dispose of the carbon derived from the glucose thatis metabolized during respiration?

by breathing out

via our urine

it is broken down in lysosomes

37.Both plant and animal cells have mitochondria because theyboth

carry on respiration

carry on photosynthesis.

require water

38.What is Activation Energy?

the energy needed to initiate a reaction

the energy that transports water into cells

potential energy

39.If you put a plant in a chamber and shine a light on it

oxygen will decrease and carbon dioxide will increase

oxygen will increase and carbon dioxide will decrease

oxygen and carbon dioxide will increase

oxygen and carbon dioxide will decrease

40.What are the inputs and the output molecules for the overallphotosynthetic process?

input sugar and oxygen; output carbon dioxide and water

input oxygen and water; output sugar and carbon dioxide

input carbon dioxide and water;output sugar and oxygen

41.What kind of reaction is photosynthesis?

endergonic

kinetic energy

exergonic

potential energy

equilibrium

42.In the process of glycolysis, glucose is cleaved into a pairof three-carbon molecules called

lactate

pyruvate

acetyl CoA

ATP

alcohol

43.Entropy is

order

disorder

complexity

Both order and disorder are correct

Both complexity and disorder are correct

44.Glycolysis takes place in the _____________ and the citricacid cycle and electron transport chain take place in the___________.

cytoplasm; endoplasmic reticulum

mitochondria, chloroplast

mitochondria; cytoplasm

cytoplasm; mitochondria

45.The organelle that carries out photosynthesis in plants isthe

mitochondria

chloroplast

ribosome

chlorophylllysosome

46.The energy to power the Calvin cycle comes from

cellular respiration

oxygen

the light reactions of photosynthesis

47.Which of the following can be broken down into intermediateproducts that enter cellular respiration?

Proteins

Lipids

Carbohydrates

All of these.

48.When cellular product levels get too high, the responsibleenzyme is inhibited. This is an example of

promotion

denaturation

equilibrium

a coenzyme

feedback inhibition

49.How is respiration the opposite of photosynthesis?

respiration breaks sugar down to carbon dioxide; photosynthesisbuilds sugar from carbon dioxide

respiration builds sugar from carbon dioxide; photosynthesisbreaks sugar down to carbon dioxide

respiration requires energy input; photosynthesis gives offexcess energy

50.The molecule that absorbs sunlight for photosynthesis is

oxygen

carbon dioxide

chlorophyll

glucose

sunlight

amaranthbear841

Creat Testable Question?

Not all questions are testable!!

A testable question asks. . .

"What is the effect of the Independent Variable on the Dependent Variable?"

Creat a Hypothesis?

A hypothesis is a prediction of the outcome of the lab. Your prediction is based on your understanding of the scientific concept.

It answers your testable question. Use the following pattern:

IF the (IV- how it is changing), then the DV- how you think it will change), BECAUSE (why do you think this is happening.

Example- If the IV increases, then the DV will decrease because....

6.Creat a Procedures ?

Procedures are a list of materials used in the experiment and the steps in performing the experimental part. Procedures are the recipe you follow in order to perform the experiment. Write these in order, in paragraph form, and using your own words. Do not simply copy and paste from the student lab guide.

7. Creat Data Table ?

Data is recorded during the procedures. You need to a data collection table for your experiment. Below is an example Data collection table. you need your own collection table using labels with the names of your variables and the correct units you are measuring.

{Insert name of Independent Variable} (insert units)

{Insert name of Dependent Variable} (insert units)

Average { Insert name of Dependent Variable }(insert units)

Trial 1 *

Trial 2 *

Trial 3*

Control

{Insert Treatment 1 Name}

{Insert Treatment 2 Name}

{Insert Treatment 3 Name}

Project Guide

Introduction from Vernier

Almost all chemical reactions that occur in living organisms are catalyzed by enzymes. Enzymes are globular proteins, responsible for most of the chemical activities of living organisms. They act as catalysts, substances that reduce activation energy, or the energy it takes to get a reaction started. Enzymes are not destroyed or altered during the process. They are extremely efficient and may be used over and over again. One enzyme may catalyze thousands of reactions every second. Many factors in a cell's environment, like temperature, pH, concentration and salinity, affect the action of an enzyme. Changes in these conditions may change the shape of the enzyme making it useless, a process called denaturation. In this investigation, you will conduct an experiment to determine the effect of a variable on an enzyme catalyzed reaction.

In every cell of the body, hydrogen peroxide, H₂O₂, is produced as a waste product. However, hydrogen peroxide kills living cells. Although H₂O₂ is toxic to most living organisms, many organisms are capable of enzymatically destroying the H₂O₂ before it can do much damage. H₂O₂ can be converted to oxygen and water, as follows.

2H₂O₂ â 2H₂O + O₂

Because your liver is responsible for detoxifying your blood, your liver cells contain a lot of catalase to break down H₂O₂ into harmless H₂O and O₂. Yeast cells also contain catalase, so we will use them as an easy and inexpensive source of catalase in this lab.

When the H₂O₂ encounters the yeast catalase, it bubbles, as the gaseous O₂ escapes. We will measure the amount of O₂ being produced using a gas pressure sensor. The more O₂ that is produced, the greater the pressure in the tube will become. An increase in pressure tells us that the catalase is effective at breaking down the H₂O₂.

The results of your experiment will be shared in an experiment report due week 15. This lab gives you hands on practice with the Vernier sensors. Use of the sensors will be required in other courses for the Natural Sciences Degree Program. The hands on procedure is detailed step by step below.

After reading through the direction make sure to watch the video showing the procedure in action.

Safety Precautions

Make sure to wear safety goggles. Keep a close eye on your pressures and make sure your gas sensor does not get wet (this will ruin the sensor)

Lab Materials

1 Vernier LabQuest

1 Vernier Gas pressure sensor w/ tubing set

1 Vernier Logger Pro (installed on computer)

1 Lab goggle (from HOL kit)

10 mL graduated cylinder (from HOL kit)

200 mL beaker (from HOL kit)

Tap water

4 cups (any kind)

1 Bottle FRESH 3% H₂O₂ (hydrogen peroxide)

3 18 x 150mm test tubes)

1 Test tube rack (create using cardboard, legos etc.)

1 packet of yeast

3 pipets (from HOL kit)

1 Thermometer (any kitchen or medical thermometer will work)

IMPORTANT NOTES:

You must use fresh hydrogen peroxide and yeast for this lab to yield decent results. Yeast can be bought at any grocery store (look at the expiration date closely) and hydrogen peroxide can be bought at any pharmacy or grocery store. You should buy a couple of packs of yeast in case you make an error in preparing the yeast solution If peroxide is kept in the refrigerator, it must be brought to room temperature before the lab.

Set out a large container of water so the water equilibrates to room temperature overnight.

Make sure you are using metric units on your thermometer. You can always run conversions from Fahrenheit to Celsius.

You must run a test on the catalase (yeast) to make sure that the yeast suspension is at the right concentration/activity before testing it with your independent variable. You should prepare the solution when you are ready to test your independent variable. The solution will serve as your control in the experiment

To make yeast suspension as seen in the included video, add the following into a cup :

100 ml warm water (37-40C, but no hotter or the yeast will die or enzymes will denature).

1 packet of yeast (approx 7g)

1 packet of sugar (the little packets they give at restaurants) (or make a 2% sugar solution by adding 4 g sugar to 250 ml water, then add a packet of yeast to 100 ml of this solution. You can use your scale provided in the HOL kit to weigh the sugar)

Let the solution sit for 10 minutes before testing.

Follow lab procedure steps 1 & 2. Add 2 drops of the yeast suspension and measure following lab procedure steps 4-9. (Make sure to read the lab steps before adding the yeast suspension. It is time sensitive and must be measured quickly after being dropped in the test tube.)

The room temperature reaction with two drops of suspension should produce around 130 kPa (1.3 atm) in 40-60 seconds. Pressures above 130 kPA will cause the stoppers to pop off. Pressures above 210 kPA may damage the sensor so keep a close eye on your numbers!

If your numbers are too high, add more warm water, to dilute the suspension. Start by adding a small increment of water (10 mL) and repeat the test. Continue adding water until you reach 130kPa in 40-60 seconds.

If the solution isn't strong enough, add 1 more drop to the test tube (3 drops instead of 2 for example). Continue to increase the number of drops until you get results near 130 kPA after 1 minute. Record the number of drops needed and use that number of drops as the control for the experiment. *With the exception of enzyme concentration, that will be the number needed for each test tube. If you are doing your experiment on enzyme concentration and it for example it takes 4 drops instead of 2 you will need to double the number of drops for all of your concentrations.

Variables:

You can modify this lab to test the effect of enzyme concentration, temperature, sugar source, enzyme source or salinity. Choose 1 independent variable to test. Below are lists of variables and some ideas on how to test them:

Enzyme: With 3ml H₂O₂ and 3ml H₂O in each tube, add 1 drop of enzyme suspension. Repeat with different numbers of drops. Make sure none of the enzyme solution touches the sides of the test tube and mix before measuring. These must be measured quickly after the drops have been added.

Temperature: With 3ml H₂O₂ and 3ml H₂O in each tube, add 2 drops of enzyme suspension. Fill cups with water of different temperatures. Set each test tube in the water for 5 minutes before recording data.

Salinity: With 3ml H₂O₂ and 3ml H₂O in each tube, add 2 drops of enzyme suspension. Add drops of 1M NaCl. To make 1M NaCL, dissolve 58.44grams of table salt in 1 liter of water. Repeat with different numbers of drops. These will also need to be measure quickly after the enzyme and NaCL solution are added.

Sugar source: Make the yeast suspensions with various types of sugars (brown sugar, granulated, powdered, glucose, fructose, lactose, etc). Measure quickly after yeast suspension is added to test tubes.

If you have an idea for another variable not on this list that you would like to test, please send me a message for pre-approval.

Procedure

Place test tubes in a rack and label them 1, 2, 3 etc. You can improvise a rack by cutting holes in a cardboard box. You just need something that will keep the test tubes vertical and easy to distinguish.

Add 3 mL of 3.0% H2O₂ and 3 mL of tap water to each test tube (Use a plastic pipet/dropper to easily dispense the water and H2O₂âdon't mix up the pipets!).

Conduct your experiment according to which variable you have chosen to test. Make sure to follow the time guidance for each variable as directed on page 3. For example if you were testing temperature you would place your tubes in water of different temperatures (pictured below), for salinity you would add drops of saline solution etc. If you have questions about how to test your chosen variable please send me a message.

To collect data connect the plastic tubing to the valve on the gas pressure sensor.

Connect the sensor to CH1 on the LabQuest.

Connect your Lab Quest to your computer. (You can conduct this experiment just using the Lab Quest but it is nice to use Logger Pro because you can easily export the graphs and tables for use in your report. ) Turn on Logger Pro (cd included with Vernier equipment, very easy to install on your computer and generates great graphics for your report)

In Logger Pro click Open â Experiments â Biology w Vernier â(Pressure)Enzyme.cmbl

Once Logger Pro is open to the Pressure Enzyme lab you should have all the lab settings pre-set so that the sensor will collect for the correct duration of time.

Turn the LabQuest on.

For your control, add 2 drops (or more depending on calibration) of the enzyme solution and put the stopper on the tube and GENTLY swirl the tube to mix the contents.

Start data collection by pressing the green play icon on your computer screen. The test will run for 180 seconds.

Disconnect the stopper from the test tube. Rinse out the test tube and leave it to dry.

Processing the DATA

There are several options for processing the Data. I recommend running through the steps listed in the experiment procedure on the Lab Quest. You can also follow the steps below to analyze the slope. The slope, m, tells us the pressure generated every minute, so the units would be kPa per minute, or kPa/min. Kilopascals, or kPa, are just a unit of pressure; you may have heard of other units of pressure like pounds per square inch (PSI) in car tires or atmospheres (atm) or millimeters of mercury (mmHG) for weather pressure. For example, if m is 0.00376 our rate of gas production is 0.00376 kPa/min. The larger the slope, the more oxygen is generated and the more active the enzyme is at those conditions.

Choose Curve Fit from the Analyze menu. Check mark Pressure.

Choose Linear Fit to get an equation in the form y=mx+b

Record the slope of the line, m, in your data table. Select OK.

Store the data from the first run.

Repeat steps 2-16 for each of your treatments.

Tap Run 3. Select All Runs. All three runs will now be on the same graph.

BIOCHEM 2EE3 Lecture Notes - Lecture 8: Cyan, Epitope, Peptide

Document Summary

Get access

Related Documents

BIOCHEM 2EE3 Study Guide - Final Guide: Catabolism, Hydrolysis, Acid Catalysis

BIOCHEM 2EE3 Study Guide - Final Guide: Opsin, Pyridoxal, Pantothenic Acid

BIOCHEM 2EE3 Chapter Notes - Chapter 1: Francis Crick, Stanley Miller, Polymer

Related Questions