Download Homework/class-work Unit#3 Organic compounds

Name: ______________________________
Homework/class-work Unit#3 Organic compounds and DNA synthesis (25 points)
Think and try every question. There is no reason for a blank response or an I don’t know. Any blanks will receive a zero.
Every assignment must be done on a separate piece of paper. Each assignment must be complete, neat, in complete sentences
and done on time for full credit. Any assignment may be used as a take home or pop quiz at any time. One missing or late
assignment will lose 5 points, 2 will lose 15 points, 3 will be considered incomplete and given a zero.
1. Organic compounds reading:
Date: __________________
Organic compounds
The chemical compounds of living things are known as organic compounds because of their association with organisms. Organic
compounds, which are the compounds associated with life process, are the subject matter of organic chemistry. Among the numerous
types of organic compounds, four major categories are found in all living things: Carbohydrates, lipids, protein, and nucleic acids.
Carbohydrates
Almost all organisms use carbohydrates as sources of energy. In addition, some carbohydrates serve as structural materials.
Carbohydrates are molecules composed of carbon, hydrogen, and oxygen; the ratio of hydrogen atoms to oxygen atoms is 2:1.
Simple carbohydrates commonly referred to as sugars, can be monosaccharides if they are composed of single molecules, or
disaccharides if they are composed of two molecules. The most important monosaccharide is glucose, a carbohydrate with the
molecular formula C6H12O6. Glucose is the basic form of fuel in living things. It is soluble and is transported by body fluids to all
cells, where it is metabolized to release energy. Glucose is the starting material for cellular respiration, and is the main product of
photosynthesis.
Three important disaccharides are also found in living things: maltose,
sucrose and lactose. Maltose is a combination of two glucose units
covalently linked. The table sugar sucrose is formed by linking glucose to
another monosaccharide called fructose. (The figure below shows that in
the synthesis of sucrose, a water molecule is lost. The process is therefore
called dehydration synthesis. The reversal of the process is hydrolysis, a
process in which the molecule is split by adding water to the molecule.)
Lactose is composed of glucose and galactose units.
Complex carbohydrates are known as polysaccharides. Polysaccharides
are formed by linking innumerable monosaccharides. Among the most
important polysaccharides are the starches, which are composed of
hundreds or thousands of glucose units linked to one another. Starches
serve as a storage form of carbohydrates. Much of the world’s human
population satisfies its energy needs with the starches of rice, wheat, corn,
and potatoes.
Two other important polysaccharides are glycogen and cellulose. Glycogen is also composed of thousands of glucose units, but the
units are bonded in a different pattern than in starches. Glycogen is the form in which glucose is stored in the human liver. Cellulose
is used primarily as a structural carbohydrate. It is also composed of glucose units, but the units cannot be metabolized by most
species of organisms. Wood is composed of cellulose, as are plant cell walls. Cotton fabric and paper are commercial cellulose
products.
Lipids
Lipids are organic molecules composed of carbon, hydrogen, and oxygen atoms.
The ratio of hydrogen atoms to oxygen atoms is much higher in lipids than in
carbohydrates. Lipids include steroids (the material of which many hormones are
composed) waxes, and fats.
Fat molecules are composed of a glycerol molecule and three fatty acid
molecules (see figure). The fatty acids in a fat may be all alike or they may all be
different. They are bound to the glycerol molecule by dehydration synthesis (the
removal of water).
Certain fatty acids have one or more double bonds in their molecules. Fats that
include these molecules are unsaturated fats. Other fatty acids have no double
bonds. Fats that include these fatty acids are saturated fats. In most human
health situations, the consumption of unsaturated fats is preferred to the
consumption of saturated fats.
Fats stored in cells usually form clear oil droplets called globules because fats do
not dissolve in water. Plants often store fats in their seed, and animals store fats in
large, clear globules in the cells of adipose tissue. The fats in adipose tissue contain much concentrated energy. Hence, they serve as
a reserve energy supply to the organism. The enzyme lipase breaks down fats into fatty acids and glycerol in the human digestive
system.
Proteins
Proteins, among the most complex of all organic compounds, are
composed of amino acids (see figure), which contain carbon, hydrogen,
oxygen, and nitrogen atoms. Certain amino acids also have sulfur
atoms, phosphorous, or other trace element such as iron or copper.
Many proteins are immense in size and extremely complex. However, all proteins are composed of long chains of relatively simple
amino acids. There are 20 kinds of amino acids. Each amino acid has an amino group, a carboxyl group, and a group of atoms called
an R group. The amino acids differ depending on the nature of the R group (see figure).
The removal of water molecules links amino acids to form a protein. The process is
called dehydration synthesis, and a byproduct of the synthesis is water. The links
between the amino acids are peptide bonds.
All living things depend on proteins for their existence. Proteins are the major
molecules from which living things are constructed. Certain proteins are dissolved
or
suspended in the watery substance of the cells, while others are incorporated into
various structures of the cells. Proteins are also found as supporting and
strengthening materials in tissues outside of cells. Bone, cartilage, tendons, and
ligaments are all compose of protein.
One essential use of proteins is in the construction of enzymes. Enzymes catalyze
the
chemical reactions that take place within cells. They are not used up in a reaction;
rather, they remain available to catalyze succeeding reaction.
Every species manufactures proteins unique to that species. The information for
synthesizing the unique proteins is located in the nucleus of the cell. The genetic
code specifies the amino acid sequence in proteins. Hence, the genetic code
regulates the chemistry taking place within a
cell.
Nucleic acids
Like proteins, nucleic acids are very large
molecules. The nucleic acids are composed of
smaller units called nucleotides. Each
nucleotide contains a carbohydrate molecule, a
phosphate group, and a nitrogen containing
molecule that because of its properties is a
nitrogen base.
Living organisms have two important nucleic
acids. One type is deoxyribonucleic acid, or
DNA. The other is ribonucleic acid, or RNA.
DNA is found in the nucleus of the cell, while
RNA is found in both the nucleus and the
cytoplasm, a semi-liquid substance that
composes the foundation of the cell.
DNA and RNA differ from one another in their
components. DNA contains the carbohydrate
deoxyribose, while RNA has ribose. In
addition, DNA contains the base thymine, while
RNA has Uracil.
Discovering the double helix
During the 1950s, a tremendous explosion of biological research occurred, and the methods of gene expression were elucidated. The
knowledge generated during this period helped explain how genes function, and it gave rise to the science of molecular genetics. This
science is based on the activity of deoxyribonucleic acid (DNA) and how this activity brings about the production of proteins in the
cell. Genetic material is packaged into DNA molecules. DNA molecules relay the inherited information to messenger RNA
(mRNA) which, in turn, codes for proteins. This chain of command is represented as:
The flow of information from DNA to protein is known as the Central Dogma of
Molecular Genetics.
In 1953, two biochemists, James D. Watson and Francis H.C. Crick, proposed a
model for the structure of DNA. (In 1962, they shared a Nobel Prize for their
work.) The publication of the structure provided valuable insight into how genes
operate and how DNA can reproduce itself during mitosis, Thereby passing on
hereditary characteristics. Not only did the new research uncover many of the
principles of protein synthesis, but it also gave rise to the science of biotechnology
and genetic engineering.
DNA structure
As proposed by Watson and Crick, deoxyribonucleic acid (DNA) consists of two
long nucleotide chains. The two nucleotide chains twist around one another to
form a double helix, a shape resembling a spiral staircase. Weak chemical bonds
between the chains hold the two chains of the nucleotides to one another.
A nucleotide in the DNA chain consists of three parts: a
nitrogenous base, a phosphate group, and a molecule of
deoxyribose. The nitrogenous base of each nucleotide
chain are of two types: purines and pyrimidines. Purine
bases have two fused rings of carbon and nitrogen atoms,
while pyrimidines have only one ring. The two purine bases
in DNA are adenine (A) and guanine (G). The pyrimidines
bases in DNA are cytosine (C) and thymine (T). Purines
and pyrimidine bases are found in both strands of the
double helix.
The phosphate group of DNA is derived from a molecule
of phosphoric acid. The phosphate group connects the
deoxyribose molecules to one another in the nucleotide
chain. Deoxyribose is a five carbon carbohydrate. The
purine and pyrimidine bases are attached to the deoxyribose
molecules, and the purine and pyrimidine bases are opposite
one another on the two nucleotide chains. Adenine is
always opposite thymine and binds to thymine. Guanine
is always opposite cytosine and binds to cytosine.
Adenine and thymine are said to be complementary, as are
guanine and cytosine. This is known as the principle of
complementary base pairing.
DNA
Replication
Before a cell
enters the
process of mitosis, its DNA replicates itself. Equal copies of the DNA pass into the
daughter cells at the end of mitosis. In human cells, this means that 46 chromosomes
(or molecules of DNA) replicate to form 92 chromosomes. The process of DNA
replication begins when specialized enzymes pull, or “unzip” the DNA double helix.
As the two strands separate, the purines and pyrimidines on each strand are exposed.
The exposed bases then attract their complementary bases. Deoxyribose molecules
and phosphate groups are present in the nucleus. The enzyme DNA polymerase joins
all the nucleotide components to one another, forming a long strand of nucleotides.
Thus, the old strand of DNA directs the synthesis of a new strand of DNA through complementary base pairing. The old strand then
unites with the new strand to reform a double helix. This process is called semiconservative replication because one of the old
strands in conserved in the new DNA double helix.
DNA replication occurs during the S phase of the cell cycle and ensures that the molecular material passes to the offspring cells in
equal amounts and types.
Answer the following based on your reading:
1. What is the difference between a monosaccharide and a disaccharide? Name one of each.
2. What is a polysaccharide? Name two polysaccharides and compare and contrast them.
3. What are the different types of fats and how do they differ?
4. What do almost all organisms use carbohydrates for?
5. What are the differences between DNA and RNA?
6. Describe the process of DNA replication (synthesis). Include all important molecules and locations.
7. What are the building blocks of proteins? How many different building blocks are there?
8. What are organic compounds? Name the four categories of organic compounds.
9. What is the process that makes disaccharides by bonding two monosaccharides together? How is it reversed?
10. What are the two types of nucleic acids? How do they differ?
11. What is the composition of a lipid?
12. What type of bond holds amino acids together?
13. Completely describe the structure of DNA. Include a drawing of your own to accompany your answer.
14. During which process does DNA replicate itself?
15. What is meant by complementary base pairing?
16. What is meant by semiconservative replication?
17. What is the most important monosaccharide?
18. What are the building blocks of nucleic acids?
19. What are the parts of a nucleotide?
20. What makes amino acids different from each other?
2. Organic compounds questions:
Date: _______________________
1. Why is carbon used as the backbone for lipids, proteins, carbohydrates, and nucleic acids?
2. Explain the difference between hydrophobic, hydrophilic, polar and non-polar.
3. What is the difference between an autotroph and a heterotroph? Give one example of each.
4. What are the four classes of macromolecules?
5. What is the process by which two sugars are bonded? What is lost?
6. What is a polymer and what is a monomer?
7. Compare and contrast the processes of hydrolysis and dehydration synthesis.
8. What are lipids and how are they used in the human body?
9. Describe what it takes to be a complete lipid.
3. Learning from pictures and tables:
1. Completely
describe this
molecule.
B.
Date: _______________________
2. Describe
what is
happening in
the picture and
in what type of
macromolecule
this is occurring
3. What is this
molecule and how
.can you tell? Be
specific and give
at least 2 reasons.
Copy and complete the table by checking the correct column for each description:
Description
4. Made up of nucleotides
5. Most consist of three fatty acids bonded to a glycerol molecule
6. DNA and RNA
7. Contain peptide bonds
8. Produce proteins
9. Commonly called fats and oils
10. Made up of amino acids
11. Used for long term energy storage, insulation and protection
12. Contain carbon, hydrogen, oxygen and nitrogen
Lipids
Proteins
Nucleic acids
4. Macromolecules advanced questions:
Date: ______________________
1. What makes one protein different from another?
2. For each class of macromolecules list their purpose in the human body.
3. For each class of macromolecules discuss the different molecules that fall under each category (be specific).
4. Describe the different structural parts of an amino acid. How many different amino acids are there? What kind of bond holds one
amino acid to the next?
5. Describe the different structural parts of a nucleotide? How do these make DNA different from RNA?
6. Name the purines and the pyrimidines and tell me if they will be found in DNA, RNA or both.
7. What are the structural differences between DNA and RNA?
8. Name the subunits (building blocks) of each of the 4 classes of macromolecules.
9. What is a protein? A Lipid? A carbohydrate? A nucleic acid?
10. Name 3 monomers and 5 polymers?
11. During times of extreme malnutrition (starvation) the human body will utilize macromolecules in the following order: blood
carbohydrates (blood sugar or glucose), Liver carbohydrates (glycogen), lipids and proteins. Explain how each is used and why this
order exists.
5. Making a flow chart:
Date: ______________________
Construct a flow chart for macromolecules. It must include all the categories, their properties and specific compounds.
6. DNA replication questions:
Date: _______________________
1. What is the purpose of the lagging DNA polymerase? What would happen to species if this enzyme did not exist?
2. Why do the differences between DNA and RNA exist?
3. Complete this DNA molecule ATCGGGCTATTCAGG.
4. What is an origin of replication? What is the purpose of having thousands of them?
5. DNA replication takes the same amount of time to occur in all cells of the human body. Explain why this is true.
6.Look at this complete section of DNA- AT
Take it through DNA replication to make two strands. During each phase
describe what is occurring and the role of any enzymes involved.
GC
AT
CG
CG
TA
7. What is the role of hydrogen bonds in the structure of DNA? How does this ensure that A always bonds to T and G always bonds
to C?
8. With your understanding of complementary base pairing, if a piece of DNA has 45,000 adenine nucleotides what can you deduce
about the thymine nucleotides?
9. Compare and contrast the 3 forms of DNA?
10. Use these four words: Gene, Trait, DNA and Protein in one sentence that explains their relationship.
11. Describe everything that is occurring in this picture
including the name of the process, all enzymes used
and the end product.
12. Here we have two pictures of DNA. Describe what is
happening in each picture. Is it the same process? How can you
tell? Be specific as possible.
review:
Date: ____________________
7. Organic compounds
1. Name in order from most energy to least energy, the 4 classes of macromolecules.
2. There are 4 classes of macromolecules. Name them and the building blocks they are made of.
3. Name the type of bond that links amino acids together.
4. Name the process that links monosaccharides together and tell me what molecule is lost during the process.
5. Name the three things that make up a nucleotide in DNA.
6. Name the three things that make up a nucleotide in RNA.
7. Name the 3 structural differences between DNA and RNA.
8. Name two polysaccharides.
9. Name an important monosaccharides.
10. What is the picture?
11. Name two general things that proteins do in the human body.
12. Which macromolecule is never used to make energy?
13. Name two purines.
14. Name two pyrimidines.
15. Cytosine always bonds to:
16. Fill in the blank. Make a numbered list and fill in the blanks using the
words given.
thymine
strand
protein
DNA
uracil
nucleic acid
double helix
codon
proteins
replication
guanine messenger
hydrogen bond bases
sugar
three-base
phosphate
amino acid
transcription
In the living world there are millions of different kinds of ________. How are these made by cells? It has been found that protein
synthesis in a cell is controlled by a complex macromolecule called ____. This is not a protein but a __________ . A nucleic acid is
made up of three parts: a 5-carbon ______ molecule, a nitrogen _____, and a _________ group. DNA looks like a ladder twisted into
a shape known as a __________ Each side of the “ladder” is a long strand made of connecting nucleotides. Each base is joined by a
weak ______________ to a base on the other strand forming “rungs” on the ladder. The bases form complementary pairs: adenine
bonds to _______; cytosine bonds with _______. During DNA __________, the hydrogen bonds break. In the nucleic acid, RNA,
adenine always pairs with ______. There are 3 kinds of RNA. ___________ RNA carries genetic information from the nucleus to the
cytoplasm. During _____________, information is transferred from DNA in the nucleus to mRNA. The DNA molecule opens up
and the mRNA forms a single ______. The four bases of RNA can be combined into 64-different ______ combinations. Each triplet,
known as a _____, codes for one specific __________. The order of the amino acids determines the _________ synthesized.