Name _________________________
Course_________________________
Problem Set #1: Evolution of Cells & Atoms and Bonding
Cell structure and function
1. What structures do all cells have in common?
2. Choose one cell in your finger. Where did that cell come from? ___________ Did your body ever consist of
a single cell?
Explain:
Where did this cell come from?
3. According to the cell theory where do all cells come from? ______________________________________
Are new cells originating spontaneously at present?_____________________________________________
4. The simplest cell is the _____________ cell. These kinds of cells do not have a _____________ like more
complex cells. The ancient form of these cells lived in a ___________________atmosphere where there was
no _________________________ present.
5. Why are cells so small?
6. Eukaryotic cells contain membrane bound structures called ______________.
7. How does the plant cell differ from the animal cell?
8. Matching : Use these choices for the next 8 items.
A. MITOCHONDRION
B. CHLOROPLAST
C. BOTH
______ Can make ATP using energy.
______ Capture sunlight energy to make sugar
______ Convert sugar energy into ATP energy.
______ Have DNA and ribosomes.
______ Have chlorophyll and other pigments.
______ Function in photosynthesis and starch storage
______ Have an internal membrane system plus a double outer membrane
______ Is almost as complex as an independent cell.
9. More Matching
_______ 9 + 2 structure
_______ actin
_______ 2 subunits
_______ Golgi
_______ Tonoplast
b.
c.
d.
e.
a. plant vacuole
ribosomes
eukaryotic flagella and cilia
part of endomembrane system
moves cytoplasm
10. In your own words describe the function for each of the following cell structures.
Ribosomes
Lysosomes
Flagella and cilia
Nucleus
Rough ER
Cytoskeleton
Know the difference between viruses, virion, and prions.
I Periodic table
A. Periods - explain the relevance of the number of shells
- explain the significance of each period
B. Groups - explain the octet rule
- explain how it refers to bonding
- explain how the group number represent valence electrons
C. Atomic # and Atomic mass/weight. How do you determine neutorons?
D. Bonding- Name types of bonds. Why do atoms bond?
Activity
1. Which of the following are molecules:
N CO
NaCl
Na
H2 2H
C6H12O6 Co
2. Which of the following is an atom, molecule, or compound, then tell how many atoms are present:
Na Fe CO Co 2H NaCl KOH C6H12O6 H2 MgCl2
3. Using a periodic table, determine the number of protons, neutrons, electrons, and mass number for
the following. Then draw the electron configurations of each
(a) Calcium (b) Bromide (c) Lithium (d) Phosphorus
II Bonding
a Bonding – explain the types of bonds: Covalent and Non-covalent
- explain the significance of valence electrons and bonding
b Noncovalent – explain the different types of noncovalent bonds
- give examples and explain in detail about the kinds of bonds
- what can you do to break bonds?
c. Describe the difference between Polar and Nonpolar bonds. Give examples.
d. Water – Explain the characteristics of water, the nature of their hydrogen bonds, and their importance in
water to life.
Activity
1. List the properties of water. Draw the cohesion of 6 water molecules. Show hydrogen bonds.
2. Draw the bonds of NaCl, CaCl2 , Ba(OH)2, then tell what type of bond is present.
3. What is the bond angle of water compared to that of the tetrahedron, methane?
III Acids, Bases, and Buffers
A. Acids, Bases, and Buffers – Explain acids, bases and buffers
-Explain the amphoteric activity of buffers
-Explain the importance of buffers in blood
D. Acids – Explain the pH range of Acids and explain how acids reduce the pH of solution
E. Bases – Explain the pH range of bases and explain how base increase the pH of solution
Activity
(1) Draw the electron configurations of the following acids and bases, then tell which ones are acids or
bases. (a) NaOH (b) H2SO4 (c) KOH (d) HNO3 (e) HCl
(2) Write an equation showing the ionization of the acids and bases in #1.
(3) What is the equation to determine pH and POH?
(4) What is pH? What are the pH and pOH for solutions with: [OH] of 1.0 x 10-12 M,
[H+] of 1.0 x 10-2 M, [OH] of 1.0 x 10-5 M and [H+] of 1.0 x 10-7 M
II. Draw the following structures in the branched form based on the octet rule.
A. CH3CH(OH)CH3 B. CH3COCH2NH2 C.CH3CH2COH D. CH3CH2CO2H
III. Circle which group does not follow the octet rule: A. CH3CH3CH(CH3)CH3 B.
CH3CH(NH3)COCH2 C.CH2CH2CH(COH)CH3 D. CH3CH3
COCH2CO2H
Functional Groups
Functional groups impart certain sets of properties to compound. Example of such a functional groups are
hydroxyl, ketone, carboxyl, aldehyde, ester, amino, and sulfhydryl groups.
I
Alcohols
The OH group in an ionic compound is called a hydroxide ion NaOH—> Na+ OH-(ionic)
The OH group in a covalent compound is called and alcohol group; it does not ionize.
Q.
Does a NaOH solution form electrolytes? ________
Given that CH3- = methyl, CH3CH2- = ethyl, CH3CH2CH2- = propyl, draw an alcohol of each form.
Q.
Is the solution of this compound an electrolyte? __________
The OH group has the bonds -O-H. It is frequently written as OH with the bond between hydrogen and
oxygen being understood and not written. Note that the oxygen atom still has two bonds attached to it. Which
are alcohols? What are the others?
(a) CH3CH2CH2CO2H
(b) KOH
(c) CH3CH(OH)CH3
Glycerol C3H8O3 is one of the primary constituents of fats. Draw its structure of glycerol?
Q.
Is glycerol an alcohol? ____________
Why or Why not? ________________ Alcohols generally end in ____________
Draw the following alcohols:
( a) methane (1 carbon)
( b) butanol (4 carbons)
( c) octanol (8 carbons)
II
Aldehydes
A second functional group is the aldehyde group. Aldehydes contain a CHO group. Note that in the
aldehyde group the oxygen atom has a double bond attached to it. Draw the aldehydes side chain.
______________. Aldehydes form some carbohydrates called aldoses.
Draw out each of the following and tell which of the following is an aldehyde or alcohol?
CH3CH2CHO or CH3CH2CH2CH2OH or CH3CHO
III.
Ketone
Another functional group is called a ketone. A ketone contains a carbon atom attached to atom, and is
between two other carbon atoms.
An example of a ketone is acetone found in the blood stream and the urine of diabetics. Ketones also
from some carbohydrates called Ketoses.
Q.
Identify the compound below as a(n) alcohol, aldehyde, or ketone?
CH3CH(OH)CH3. If the molecule is not a ketone, draw it as a ketone
The name of most ketones ends in “one”, while sugars end in “ose” An example of a ketone is acetone. The
structure of acetone consist of a ketone group between two methl groups. Draw the structure of acetone.
Draw several other larger ketones, then draw the branched structures of glucose as a ketose sugar. What
determines if sugar is an D or L sugar? Which form do humans recognize?
IV
Carboxyl
Another functional group is the carboxyl group. A carboxyl group contains a carbon atom double-bonded to
oxygen and attached to an OH group (not hydroxyl).
Q. When a carboxyl group ionizes, the OH becomes O - + H+. the carboxyl group yields H+ ions because
it is a(n)____________. Look at amino acids aspartate and glutamate. What is the nature of these
amino acids?___________________
V
Hydrocarbons
Hydrocarbons, are functional groups which contain only carbon and hydrogen atoms. They give molecules a
non-polar nature. Why_____________________________________________________________________
VI
Fats
Fatty Acids contain hydrocarbon hydrocarbons connected to a carbons connected to a carboxyl group.
Fatty acids can be saturated or unsaturated. Fatty acids that contain single bonds are saturated. Fatty acids
that contain double-bonds are called unsaturated. Unsaturated fatty acids tend to be more liquid than
saturated fatty acids. A liquid fat is called an oil.
Q.
Increasing the number of double bonds between carbon atoms in fatty acids of fat molecule should
make the fat more___________ (solid / liquid). Draw a branched unsaturated fat containing six
carbons and three double bonds.
Q.
Which are unsaturated, fats or oils? _______________
Q.
What happens when an acid is added to an oil? Why. What happens when a base is added to a solid
fat? Why?
Q.
Decreasing the number of double bounds in fat will makes the fat more _____________ (solid /
liquid). Draw a branched six carbon fat without double-bonds.
Q.
Which is the better fat, health-wise?______________. Which is more capable of binding to structures
of the heart and blood vessels through hydrophobic interactions?
(A)
(B)
Draw a saturated fat and unsaturated fat. Then draw the structure of glycerol.
A triglyceride is made of 1 glycerol estertied to three fatty acids by dehydration synthesis. Draw the
structure of a triglyceride.
A phosphoglyceride looks like triglyceride only the third fatty acid is replaced by a phosphate esterfied
to hydrophilic head.
(C)
VII Amino groups
Amino groups (-NH2) are found on amino acids, monomers for proteins. The amino group gives compounds
a basic nature. An amino acid consists of an alpha carbon bonded to an amino group, hydrogen, R group (side
chain) and a carboxyl group. Unlike sugars, humans only recognize the L form of amino acids. The (-NH2)
groups of amino acids are basic, they will accept protons to form (-NH3+) in aqueous solutions. Note that the
amino group cancels out the charge of the carboxyl group in the core amino acid structure. What happens in
the addition of one of these groups in the R group? What effects do mutations have on the structure and
function of proteins?
An amino acid sequence is the primary sequence of a protein. Draw the following amino acids structures and
connect them by a peptide bonds by dehydration synthesis to form a primary sequence.
( a) alanine ( R group= CH3)
( b) glycine ( R group=H)
( c) cysteine ( R group = CH2SH)
* Practice drawing other amino acids if you are responsible for all 20.
Secondary structures of proteins results from hydrogen bond formation that form two structures called alpha
helices (derived from non-polar amino acids) and beta-pleated sheets (derived from polar amino acids). The
folding of the protein results at this level because the amino group of an amino acid in one plane hydrogen
bonds with the carboxyl group of an amino acid in another plane. Draw hydrogen bonding of two amino
acids in different planes.
Q. What effects do heat and bases have on this structure. Do acids have any effect on this structure?
VI
Sulfhydryls
Q.
A compound that contains an -SH Group is a Sulfhydryl. Sulfhydryl groups are important in forming
the 3 D structure of protein by forming disulfide bridges ( S- S) Draw the compound cysteine, one of
the essential amino acids._______________
Q.
When sulfhydryl groups of two amino acids are joined, a _____________bridge is formed. These
bridges are found in the tertiary and quaternary structures of proteins? How are they different? Since
methionine contain sulfur, can it also form these bonds? Draw a protein depicting tertiary and
quaternary structures.
Q.
How do heat and acids affect quaternary structures? Do reducing agents have any effect on these
structures?
Noncovalent bonds
Draw a cartoon structure of a protein and show the following non-covalent bonds: hydrogen, ionic, then show
the following covalent bond: disulfide bonds.
Problems
1.
A solution went from an [-OH] of 1.0 x 10-12 M to an [H+] 1.0 x 10-8M after an unknown substance
was added. The substance added was most likely a(n):
A. Acid
C. Buffer
B. Base
D. Both Acids and bases
2.
Which of the following functional groups tends to attract protons?
A. R-COH C. R-NH2
B. R-CO2H D. R-CO-R
3.
Which of the following functional groups is the most acidic?
A. R-COH C. R-SH
B. R-CO2H D. R-CO-R
4.
Water contains which of the following bonds:
A. Ionic
C. Polar covalent
B. Covalent D. Nonpolar
5.
How many neutrons are found in fluorine?
A. 19 B. 10 C. 9
D. 29
6.
CH3CH(OH)CH2CH3 is an example of a(n):
A. Alcohol C. Ketone
B. Acid
D. Aldehyde
7.
CH3CH2CO CH2 CH3 is an example of a(n):
A. Alcohol C. Ketone
B. Acid
D. Aldehyde
Dehydration Synthesis
Dehydration Synthesis is a process whereby two monomers through the removal of a water molecule (s). A
hydrogen is removed from on compound and a hydroxyl (OH) from the other leaving an oxygen to link the
two molecules together. The reverse reaction of breaking up polymers is accomplished by another chemical
reaction known as hydrolysis. Dehydration occurs in the formation of sugars, lipids and proteins.
1. Draw an alpha and beta glycosidic bond between two glucose monomers
2. Calculate the following:
What is the chemical formula of a sugar containing 7 glucose molecules?
a. C22H12O23 d. C42H23O33
b. C42H84O42 e. C6H12O6
c. C42H72O36
What is the chemical formula of a sugar containing 3 disaccharide sugars?
a. C12H22O11 c. C36H62O31
b. C36H66O33 d. C18H36O18
e. C36H72O36
3. Calculate how many water molecules are removed when forming 7 triglycerides?
4. Draw the following tripeptide and show the removal of water between monomers:
serine-cysteine-alanine
5. Draw the dehydration synthesis of nucleotides form the complementation of DNA
Drawing organic compounds
Make sure you know how to draw the following organic
compounds for Exam #1:
1. All Functional Groups such as Amino group, Sulfhydryl,
Carboxyl, Ketone, Aldehyde, etc.
2. The branched and ring structures of glucose
3. Aldose and ketose (D or L)
4. Two ring structure of glucose joined by an alpha or beta
glycosidic bond
5. Glycerol, fatty acids, triglycerides, phospoglycerides
6. Free amino acids and amino acids in peptide chains:
Glycine, Alanine, Serine, Phenylalanine, Tyrosine, Cysteine,
Valine, Glutamate
7. Draw branched structures of formula such as:
CH3C(NH2)2CH2COH; CH3CHOHCH2CO2H;
CH3COCH2CO2Na
Make sure you know how to draw the following organic
compounds for Exam #1:
8. Purine or Pyrimidine ribo- or deoxyribonucleotides, the
complementation of four nucleotides of DNA.
9. Electron configuration of atoms
10. Draw four nucleotides in the complementation of DNA