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Biochemistry Basics

What concepts from chemistry are helpful in studying biology?

Why?

Typically chemistry is a prerequisite course for advanced biology courses. This is because everything in your body, everything in a plant, everything in a virus, etc. is made of atoms. The structures and properties of the molecules in an organism determine the features and properties of the organism. Which molecules are polar, which are nonpolar? Which molecules have acidic properties, which have basic prop- erties? A quick review of these concepts at the beginning of your advanced biology course will help you to understand the molecular basis for life.

Model 1 – Molecular Drawings

Ball-and-stick model of

Lewis structure of 1-pentanol

Line drawing of 1-pentanol

1-pentanol

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

H

H

 

H

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

OH

 

H C

C

C C

C O H

H3C

 

 

 

 

 

H

H

H

 

H

H

 

 

 

 

 

Ball-and-stick model of glucose

Lewis structure of glucose

 

Line drawing of glucose

 

 

 

 

H

 

 

 

 

 

 

OH

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

C

OH

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

O

 

 

 

 

 

C

 

O

 

 

 

 

 

 

 

 

 

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

 

 

 

 

 

H

 

 

OH

 

 

 

 

 

C

 

 

 

C

 

 

 

 

 

 

 

 

HO

 

OH

 

H

 

OH

HO

 

OH

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

C

 

C

 

 

 

 

OH

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

 

OH

 

 

 

 

 

 

Ball-and-stick model of

Lewis structure of unsaturated

Line drawing of unsaturated

unsaturated fatty acid

fatty acid

 

 

 

 

 

 

fatty acid

 

 

 

 

 

H

H

 

H

 

H

 

O

 

 

 

 

 

 

H

C

H

C

H

C

H

C

 

 

 

 

H

 

C

 

 

 

 

 

O

 

 

C

 

C

 

C

 

C

OH

 

 

 

C

 

H

H

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

 

H H H

H

 

H

 

H

 

 

 

 

 

H C

C

C

C

H

 

 

 

 

 

 

CH3

OH

 

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

H

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

1.Name the three molecules that are illustrated in Model 1.

2.Name the three types of drawings that are used to illustrate the molecules in Model 1.

Biochemistry Basics

1

3. How many bonds are typically formed by each of the following atoms:

Carbon

Hydrogen

Oxygen

4.Which types of drawings in Model 1 provide more accurate images of the shape of a molecule? Justify your reasoning.

5.Refer to Model 1.

A. Symbols or atoms of what element(s) are missing from the line drawings?

B. In reading a line drawing, how do you know where atoms of these elements are in the struc- ture if they are missing from the drawing?

6.Locate the carbon and hydrogen atoms in the line drawing of isoleucine shown below and draw them in as if the drawing were a Lewis structure.

CH3 O

H3C

OH

NH2

Isoleucine

7.Isopropyl alcohol is a three-carbon molecule with an –OH group attached to the middle carbon atom. Draw this molecule using all three types of drawings.

8.If you were asked to write the chemical formula for one of the compounds in Model 1, which type of the drawing would be the easiest to use? Justify your reasoning.

9.What is the advantage to a scientist in using a line drawing rather than a ball-and-stick model or Lewis structure?

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POGILActivities for AP* Biology

Model 2 – Properties of Biological Molecules

 

Polar Molecules

 

 

 

Nonpolar Molecules

 

(hydrophilic)

 

 

 

(hydrophobic)

 

Acidic

 

 

O

 

Acidic

 

 

 

O

 

H3C

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

OH

 

 

 

 

 

 

 

OH

 

H3C

 

 

 

OH

 

 

 

 

 

 

 

 

Lactic acid

 

 

 

 

Fatty acid

 

Neutral

 

 

O

 

Neutral

 

 

 

 

 

 

CH3

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H3C

CH3

 

H3C

 

 

OH

 

 

 

CH3

 

 

 

NH2

 

 

 

 

CH3

CH3

Valine (amino acid)

 

 

 

 

 

 

 

 

 

 

OH

 

 

 

 

 

 

 

H

 

O H

HO

 

 

 

 

 

OH H

H

 

 

 

 

Cholesterol

 

 

HO

 

 

OH

 

 

 

 

 

 

H

 

OH

 

 

 

 

 

 

 

 

Glucose

 

 

 

 

 

 

 

 

 

 

 

OH

CH

 

CH

CH

 

 

 

 

 

H C

 

 

 

 

 

 

 

 

 

OH

 

H

 

O OH

 

 

 

 

 

 

 

 

 

 

 

 

OH

 

 

 

OH H

H

 

 

 

 

 

 

 

 

 

 

HO

O

O

 

 

H

 

 

CH

 

OH H

 

 

 

 

 

 

 

H

 

 

 

 

 

 

 

 

H

 

OH

 

 

Vitamin A

 

 

 

 

 

 

 

 

H

 

H

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H

OH

 

 

 

 

 

 

 

 

 

 

Lactose

 

 

 

 

 

 

Basic

 

 

OH

H

 

 

 

 

OH

 

 

 

 

 

 

 

 

 

HO

 

 

 

N

 

 

 

CH3

 

 

 

 

 

 

 

 

 

 

 

 

 

CH3

 

 

CH3

 

 

 

 

 

 

 

 

 

 

HO

 

 

 

 

 

 

 

 

 

 

Adrenaline

 

 

 

 

 

 

HO

 

 

 

NH2

O

 

 

 

 

 

 

 

 

 

 

Testosterone

 

HO

 

 

 

 

 

 

 

 

 

 

Dopamine

 

 

 

 

 

 

 

 

 

NH2

 

 

 

 

 

 

 

N

N

 

 

 

 

 

 

 

 

 

 

 

 

 

 

NH

N

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Adenine

 

 

 

 

 

 

Biochemistry Basics

 

 

 

 

 

 

 

3

10.Consider the polar molecules in Model 2.

A. In general, the presence of atoms of what element(s) makes a molecule polar?

B. What property do atoms of these elements have that helps make the molecules they are in polar?

C. Can nonpolar molecules also have atoms of these elements? If yes, what distinguishes a non- polar molecule from a polar molecule?

11.In chemistry there is a saying “like dissolves like,” which means things will mix with or dissolve into each other best when their polarities are similar.

A. Is water polar or nonpolar?

B. Is oil polar or nonpolar?

C. Which of the substances in Model 2 would dissolve well in water? Justify your reasoning.

D. Which of the substances in Model 2 are more likely to dissolve well in oil? Justify your reasoning.

E. Which class of substances in Model 2, polar or nonpolar, is more likely to be found in high concentrations in the bloodstream of a vertebrate? Justify your reasoning.

12.Refer to Model 2.

A. What is another term for a polar molecule?

B. What is another term for a nonpolar molecule?

C. Give the literal translation for the terms you gave in parts A and B above.

4

POGILActivities for AP* Biology

13.Functional groups are key groups of atoms in biological molecules. Describe the carboxyl func- tional group that both acidic molecules in Model 2 have in common.

14.Recall the definition of an acid that you learned in chemistry. Explain how the reaction below illustrates the acidic properties of lactic acid.

OO

H3C

OH

OH + H2O

 

H3C

 

 

 

O

+ H3O+

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

OH

Lactic acid

Lactate ion

15.Describe the functional group, called an amine group, that the basic molecules in Model 2 all have in common?

16.Recall the definition of a base that you learned in chemistry. Explain how the reaction below illustrates the basic properties of adrenaline.

OH

H

 

HO

N

HO

 

CH3

 

+ H2O

 

 

HO

 

HO

 

 

Adrenaline

H

+

 

 

 

N

 

CH3

 

 

 

 

 

 

H

+

OH

 

 

 

17.Predict the approximate pH (pH = 7, pH > 7 or pH < 7) of fairly concentrated aqueous solu- tions of the following compounds from Model 2.

Lactic acid

____________

Dopamine

____________

Amino acid

____________

Lactose

____________

Biochemistry Basics

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18.In chemistry you learned that covalent bonds are one type of intramolecular bond. They occur between nonmetal atoms in a molecule. You may have also learned about a type of intermo- lecular bond called a hydrogen bond. Hydrogen bonds are weak attractive forces between polar molecules containing strong polar bonds such as H-O, H-N or H-F.

H O H H O H

H O

N H

H O

O H

H H O H

A. Label at least two covalent bonds in the diagram above.

B. Label at least one hydrogen bond in the diagram above.

19.Which of the molecules in Model 2 would form hydrogen bonds with itself (that is, other mol- ecules of the same type) or with water molecules if in a solution?

6

POGILActivities for AP* Biology

Extension Questions

20.Although amino acids have “acid” in their name, some are acidic in water solutions, some are basic, and others are neutral. Propose an explanation for this observation based on the structures and descriptions of the amino acids below.

Neutral amino acids

OO

H3C

OH HO OH

NH2NH2

Acidic amino acid

 

Basic amino acid

O

 

O

 

 

O

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

H2N

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

HO

 

 

 

 

OH

 

 

 

OH

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

NH2

 

NH

 

 

 

 

 

 

 

 

2

 

 

 

 

21.The structure shown below is a line drawing of noncyclic AMP, an important messenger mol- ecule in molecular communication systems.

A. Draw the missing carbon and hydrogen atoms on the molecule.

 

 

 

 

NH2

 

 

 

 

N

N

 

 

O

 

 

 

 

 

 

 

 

O P

O

N

N

 

 

 

 

 

 

O

 

 

 

O

 

 

 

 

OH OH

B. Write the chemical formula for a molecule of noncyclic AMP.

Biochemistry Basics

7

22.The phosphate functional group in the noncyclic AMP molecule of Question 21 contains “acidic hydrogens.”

A. Explain what this phrase means.

B. Draw the noncyclic AMP molecule after it has dissolved in water.

8

POGILActivities for AP* Biology

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