Chapter 2 - Biochemistry

Short Free Response Questions

1. Water has a high specific heat

Explain what high specific heat means and state one way it favorably affect living things
Explain the Chemical property of water responsible for this Characteristic
Specific heat is the amount of heat needed to raise the temperature of one gram of a substance by 1 Co. Water
has
a high specific heat due to its strong hydrogen bonds

2. Water is known as a universal solvent. Explain why so many substances are soluble in water
Water polarity allows it to dissolve all polar and ionic compounds. Only lipids are left undissolved.
 Long Free Response Questions

1. Describe the structure and function of enzymes

Enzymes form a lock and key structure. They bind to substrates that fit in only their own lock. They act as catalysts
and speed up reactions.

2. The unique properties of water make life on earth possible. Select four characteristics of water and:
a) High cohesion tension
b) High specific temperature
c) High heat of vaporization
d) Excellent solvent
e) When frozen, it is less dense than water
 A. Identify one characteristic of water and explain how the structure of water relates to this property
The molecules in ice are for tightly bound and rigid compared to water.

B. Describe one example of how this characteristic affects living organisms

Floating ice lets the water below exist beneath the frozen surface, thus allowing organisms to leave below
during
cold seasons..

Chapter 3 - The Cell

Short Free Response Questions

1. Compare and contrast two human cells; one a liver cell and one a fat cell
They have the same organelles but the liver cell has more smooth endoplasmic reticulum to use as a detoxer, while
the fat cell has larger vacuoles to store fat.

2. You prepare a slide of living elodea leaf and look at the cells under 40X magnification. You see many rectangular
shaped cells filled with green chloroplasts. While you are observing the tissue, you carefully place three drops of 4%
salt solution next to the right side of the coverslip and draw the solution across the slide by holding a piece of paper
towel on the left edge of the cover slip. You notice that suddenly the chloroplasts have clustered to the middle of
every cell and are surrounded by a membrane. The cell wall remain unchanged. Explain what has occurred and the
mechanism behind it.
Salt water is hypertonic to the elodea cells, so water diffuses in and out. High concentration to low.
 Long Free Response Questions

1. Compare and contrast the characteristics of prokaryotic and eukaryotic cells.

They both have DNA, endoplasmic reticulum and, and a cell wall. But prokaryotes carry out carry out more simple
metabolic processes. Prokaryotes are smaller, dont carry organelles, have circular DNA,. They are unicellular,
possess no cytoskeleton, and have no internal membrane.. Metabolism in prokaryotes can be anaerobic or aerobic
while eukaryotes can only have aerobic. Eukaryotes have elaborate cytoskeletons.

2. Living cells are highly organized and regulated

A. Describe the structure of the plasma membrane
Its highly regarded as a fluid mosaic model, and is a dynamic fluid structure that hs a continuous double
phospholipid bilayer. The phospholipids are amphipathic. (hydrophilic heads, hydrophobic tails) Proteins are
dispersed in the lipid bilayer. Peripheral proteins can only be on a specific face and cannot go into the
hydrophobic side. However, integral membrane proteins are amphipathic and can float everywhere.
 B. Explain how the plasma membrane contributes to the regulation of the cell
Lipid bilayer of plasma membrane is a selectively permeable membrane. It allows water and small nonpolar
molecules to pass through. The protein component carries out the other stuff. Channel proteins let specific
molecules with a certain size and charge to pass through. Carrier proteins are life membrane bound enzymes,
they
they transport specific molecules across a membrane.

Chapter 4 - Cell Respiration

Short Free Response Questions

1. Predict what would happen to the level of ATP production if you made the cristae membrane permeable to
protons, and why?
Production of ATP would cease. Too much of an acidic environment.

2. If chloroplasts and mitochondria were once free-living prokaryotes, what structures would you expect to find in
the plasma membranes of living prokaryotes, and explain your answer.
ATP synthase in living prokaryotic membranes. They would produce ATP the same way or in a familiar way.
 Long Free Response Questions

1. Membranes are important structural features of cells

A. Describe the structure of a membrane
Its highly regarded as a fluid mosaic model, and is a dynamic fluid structure that has a continuous double
phospholipid bilayer. The phospholipids are amphipathic. (hydrophilic heads, hydrophobic tails) Proteins are
dispersed in the lipid bilayer. Peripheral proteins can only be on a specific face and cannot go into the
hydrophobic
side. However, integral membrane proteins are amphipathic and can float everywhere.

B. Discuss the role of membranes in ATP synthesis.

Cristae membrane is folded a lot to increase surface area, to allow for more reactions. It has an ETC, which which
has a bunch of molecules, most of them are proteins that carry electrons from high to low energy levels. The
exergonic flow of electrons pumps protons to the cristae outer compartment of mitochondria to create protein
gradients. But because the cristae membrane doesnt allow to diffuse through the membrane, The protons then
diffuse through the ATP synthase, resulting in chemiosmosis.

Chapter 5 - Photosynthesis

Short Free Response Questions

1. Isolated chloroplasts are placed in an illuminated solution with the appropriate chemicals to carry out ATP
production. Predict what would happen to the rate of glucose production if a compound is added to the solution
that makes membranes permeable to protons. Explain your answer.
It would stop photosynthesis because there would be no production of ATP. There would be no ATP because for
chemiosmosis to happen you must have a proton gradient, within the grana. But if the grana becomes permeable to
protons then no gradient would be able to form, hence no ATP.
2. Explain why a poison that inhibits an enzyme in the Calvin Cycle would also inhibit the light reactions.
Protons go from light dependent to the Calvin Cycle (independent) by the use of NADP+. These coenzymes
combine with O2 to produce glucose. Once ATP is used up in the calvin cycle, the lower energy ADP goes back up
to the light dependent cycle to later become phosphorized to become ATP once more. But because for light
dependent cycles to keep functioning you need ADP and NADP+, if a poison were to affect them, light dependent
reactions would cease.

Ilovethespecificheatcapacit yofWater!Actuallywhat?
Long Free Response Questions

1. The rate of photosynthesis varies with different environmental conditions such as light intensity, wavelength of
light, temperature, and so on.
A. Devise an experiment to demonstrate that ONE environmental conditions such as light rate of
photosynthesis.
An experiment that could e carried out is whether wavelengths of light could alter the rate of photosynthesis or
not. The organism being elodea (easy to take care of.)
B. State your hypothesis, the procedure, how you would collect the data, the results you would expect
Youd set up 500 mL beakers of freshwater, containing the same number of elodea. Place the four beakers into
four individual large boxes that dont allow light. This controls the amount of wavelengths that goes into each
elodea. Place one light source in each box. All light sources must be the same distance away fromt the elodea.
You
would then place a heat sink between the beaker and the light source to maintain a constant temperature. Light
must be of the same of the same intensity so as to not create differing variables. Set appropriate light filters of all
different colors so each beaker receives the same amount and of a different color. (green, blue, red, or yellow.)

Results:
The blue light would bubble.
The red and yellow would bubble, but not as much.
 Green light would produce no bubbling.

C. The scientific Theory behind your expectations

Photosynthetic organisms release oxygen gas during photolysis during the light reactions of photosynthesis. You
can measure the rate of photosynthesis by the amount of oxygen released. Amount of oxygen is measured by

bubbles. More light absorbed = greater the rate of photosynthesis.

Chapter 6 - Cell Division

Short Free Response Questions

1. This diagram shows a homologous pair of chromosomes preparing to divide.(pg. 100)

A. What type of cell/s will be produced from this process?
B. Using letters A, a, B, and b explain the characteristics of any cells that result from this cell division.
The process is Meiosis. This means that it would be producing gametes. This is shown by the homologous
chromosomes that have paired in in synapsis during prophase 1. It also describes a cross-over, shown visually as
chiasma
Gametes will show the rearrangement of alleles. The four genotypes that would come from the cross over would
be
AB, Ab, aB, and ab
2. Answer the following questions about apoptosis
A. Explain what apoptosis is and give two examples of when or where it occurs.
B. Where do the signals for apoptosis come from?
Apoptosis is the process by which a cell self destructs. This is usually done to avoid mutations and damage. All of
the organelles are disassembled and recycled to be digested by enzymes and other cells.

Apoptosis is triggered via signal transduction pathways originating from internal sources and external ones as well.
This process can be used to get rid of unnecessary body parts after birth. For example it is the process by which a
tadpole's tail can be reabsorbed into its body. When cells and tissues are no longer needed in the human body they
are disposed of through this process.

Long Free Response Questions

1. An organism is heterozygous at two gene loci on different chromosomes.(pg. 100)

A. Explain how these alleles are transmitted by the process of mitosis to daughter cells
B. Explain how these alleles are distributed to gametes by the process of meiosis
This process creates daughter cells that are genetically identical to the cell from which they came. First the DNA
Replicates in order to prepare for PMATC. The nuclear membrane dissolves and the DNA forms into
chromosomes. They line up in the middle of the cell and pulled apart by the spindle fibers which are controlled by
the centrioles of the cell. Cytokinesis occurs pulling the cells apart and splitting the cytoplasm and then the two
daughter cells are complete.
 Chapter 7 - Heredity

Short Free Response Questions

1. By convention, one map unit distance on a chromosome is the distance within which recombination occurs 1% of
the time. The rate of cross-over gives no information about the actual distance between genes, but it tells us the
order of the linked genes on a chromosome
A. Construct a linkage map and give the order of genes on a chromosome from the following recombination
rates for genes A, B, C, D (pg. 125)
B. How would you calculate the recombination rate for B to C

The distance
between C
and B is 44%

Long Free Response Questions

1. A person with Turner's Syndrome has a genotype of XO, while a person with Klinefelter's syndrome has the
genotype XXY. Explain how these two mutations come about.
Both of these conditions, Turner's and Klinefelter's syndrome, are mutations that arise as a result of nondisjunction.
Normally, during anaphase 1 of meiosis, homologous pairs separate, with one homologue going into each of two
daughter cells. Occasionally, one homologous pair does not separate as it should during anaphase 1. As a result, both
homologues go into one of the daughter cells, giving it an extra chromosome, while leaving the other daughter cell
missing one chromosome. Klinefelter's syndrome results when an egg with two X chromosomes fuses with a sperm
carrying a Y chromosome. The resulting zygote has the genotype XO, where O means missing chromosome. A
person with Turner's syndrome has 45 chromosomes, while a person with Klinefelter's syndrome has 47
chromosomes.
2. Scientists understand that comparatively few genes are inherited in a simple Mendelian fashion. The expression
of most genes is altered by many things, including other genes or the environment. Choose five of the terms below
and explain what they mean. (pg. 125)

C
odominance - When on trait can be controlled by multiple allelic variants and the resulting phenotype is a
combination of the two.
Incomplete Dominance - This is characterized by a Gene containing two dominant parts resulting in the blending
of
the genes
Multiple Alleles - This is when there are more than two alleles that control one gene
Pleiotropy - One gene that controls multiple traits
Epistasis - Two separate genes that control one trait.

Chapter 8 - The Molecular Basis of Inheritance

Short Free Response Questions

1. In what way does pre-RNA differ from m-RNA? Explain why the two are different
RNA processings final transcript is shorter than the original pre-mRNA. It also has added lengths of bases at the
ends. Pre-RNA only becomes mRNA after its processed. Modified guanine nucleotides are added to the 5 end of
the molecule. This cap helps RNA bind to the ribosome during translation. Adenine nucleotides (poly-A tail) are
added to the 3 end of the molecule. This poly tail protects the RNA strand from degradation from the hydrolytic
enzymes. It also helps the release of m-RNA from the nucleus to the cytoplasm. Lastly, non-coding regions of
mRNA , introns (intervening sequences) are excised by SnRNPs and spliceosomes, leaving the final transcript.
2. What is ncRNA and what is its role?
Genome sequencing reveals that protein coding DNA accounts for only 1.5% of the entire genome. 90% of
remaining DNA is transcribed to non-protein coding RNAs also called noncoding RNA or ncRNA. This noncoding
RNA has miRNA (microRNA) and siRNA (small interfering RNA), and that binds to mRNA and will either
degrade it or stop it from translating new polypeptides. So technically, ncRNAs regulate functions of mRNA.
 Long Free Response Questions

1. Explain the process by which DNA makes proteins

The process whereby DNA makes proteins has been worked out i great detail. To summarize, the triplet code in
DNA is transcribed into a codon sequence in messenger RNA (mRNA) inside the nucleus. Next, this newly formed
strand of RNA is processed in the nucleus. Then the codon sequence is translated into an amino acid sequence in
the cytoplasm at the ribosome by tRNA.

First stage is transcription, where DNA makes mRNA that carries the message directly to the ribosome into the
cytoplasm. Transcription consists of three stages: initiation, elongation, and termination. During initiation, the
enzyme RNA polymerase recognizes and binds to DNA at the promoter. Once RNA polymerase is attached to the
promoter, DNA transcription of the DNA begins. The next step, elongation, continues as RNA polymerase adds
nucleotides to the 3 end of a growing chain. RNA polymerase pries the two strands of DNA apart and attaches
RNA nucleotides according, to the base-pairing rules: C with G and A with U. The stretch of DNA that is
transcribed into an mRNA molecule is called a transcription unit and consists of triplets of bases called codons that
code for specific amino acids. When RNA transcribes a termination sequence, the process stops. Before the newly
formed transcription unit is shipped, out to the ribosome from the nucleus, it is altered or processed by a series of
enzymes. A 5 cap is added to the 5 end, which helps protect the RNA strand from degradation, by hydrolytic
enzymes and which also helps the RNA strand bind to the ribosome in the cytoplasm. In addition, the poly A tail, is
added to the 3 end to protect the RNA strand from degradation by hydrolytic enzymes and to facilitate the release
of the RNA into the cytoplasm. A major part of the processing is the removal of introns (noncoding regions) from
the transcription unit by SnRNPs (small nuclear ribonucleoproteins) in spliceosomes. With processing complete,
only exons, expressed, move out to the ribosome for translation.
Translation is the process by which the codons of an mRNA sequence are changed into an amino acid sequence.
Amino acids present in the cytoplasm are carried by tRNA molecules to the codons of the mRNA strand at the
ribosome according to the base pairing rules. One end of the tRNA molecule bears a specific amino acid, and the
other end bears a nucleotide triplet called an anticodon. Some tRNA molecules have anticodons that can recognize
two or more codons. This is because the base pairing rules of for the third base of a codon are not as strict as they
are for the first two bases. This relaxation of the first two base pairs is called a wobble. For examples, codons UCU,
UCC, UCA, and UCG all code for the amino acid serine. The process of translation occurs in three stages: initiation,
elongation, and termination. Translation of the mRNA is complete when the ribosome reaches one of the
termination or stop codons. The mRNA is broken down, the tRNA is reused, and the polypeptide is free from the
ribosome.

2. By using techniques of genetic engineering, scientists are able to learn more about the human genome and to use
these techniques for the betterment of humankind. Describe these techniques or procedures below, and explain
how each contributes to our understanding of the human genome or for what practical purpose it can be used.
(156)
Polymerase Chain Reaction
Devised in 1985, polymerase chain reaction is a cell-free, automated technique by which a piece of DNA can be
rapidly copied or amplified. Billions of copies of a fragment of DNA can be produced in a few hours. The DNA
piece that is to be amplified is placed into a test tube and Taq polymerase, along with a supply of nucleotides and
primers necessary for DNA synthesis. Once the DNA is amplified, these copies can be comparison with other DNA
samples. The PCR technique has limitations. First, some information about the nucleotide sequence of the target
DNA must be known in advance in order to make the necessary primers. Second, the size of the piece that can be
amplified must be very short. Contamination is a major problem. Third, a few skin cells from the technician
working with the sample could make obtaining studied or used in a taining accurate results difficult or impossible.

Restriction Length Polymorphisms

A restriction fragment is a segment of DNA resulting from treatment of DNA with restriction enzymes. When
scientists compared noncoding regions of human DNA across a population they discovered that the restriction
fragment pattern is different in every individual. These differences have been named restriction fragment length
polymorphisms or RFLPs. A RFLP analysis of someone's DNA gives a human DNA fingerprint that looks like a bar
code.
Each person's RFLPs are unique, except in identical twins, and are inherited in a mendelian fashion. Because they
are inherited this way, they can be used very accurately in paternity suits to determine, with absolute certainty, if a
particular man is the father of a particular child. In addition, RFLPs are routinely used to identify the perpetrator in
rape and murder cases. DNA from the crime scene and the victim are compared against DNA from the suspect.
Because of the accuracy of RFLP analysis, these cases can be solved with a high degree of certainty, and some
suspects have been convicted on DNA evidence alone. By contrast, several incidents have occurred where men who
have been jailed for years for violent crimes were proven innocent by DNA evidence and released.

Gene Cloning
The potential uses of recombinant DNA or gene cloning are many . Here are several.
- To produce a protein product such as insulin or human growth hormone, in large quantities as an expensive
pharmaceutical
- To replace a non-functioning gene in a persons cells within a functioning gene by gene therapy. Scientists
are currently conducting clinical trials in this area with disappointing results. If scientists can master this
technique, many lives will be improved
- To prepare multiple copies of a gene itself for analysis. Since most genes exist in only one copy of a cell, the
ability to make multiple copies is of great value
- To engineer bacteria to clean up the environment. Scientists have engineered many bacteria; one can even
eat toxic waste
In order to clone a gene, you must first isolate a gene of interest, for example the gene for human insulin. Next
insert the gene into a plasmid. Then insert the plasmid into a vector, a cell that will carry the plasmid, such as a
bacterium like E. Coli. To accomplish this, a bacterium must be made competent, be able to take up a plasmid. As
the bacteria reproduce themselves by fission, the plasmid and the selected gene are also being cloned.

3. All humans are almost genetically identical. However, every person has a unique DNA fingerprint. Explain this
contradiction.
Genetically, all humans are almost identical. We can say this because only about 3% of all DNA contains genes that
code for proteins. Furthermore, all the genes for a particular trait are identical. For example, everyone's gene for
brown eyes is identical, and all genes for normal hemoglobin are identical. If all genes for a particular trait are
identical, then how can each person have a unique DNA fingerprint? The answer lies not in DNA that codes for
genes but in the DNA that does not code for proteins -- the introns, junk and repetitive sequences. Scientists have
identified certain non coding regions of DNA that are highly variable from one individual to the next. These regions
are referred to as polymorphic regions. By analyzing many polymorphic regions, scientists have identified and
agreed upon certain standard regions to analyze. This standardized analysis produces the DNA fingerprint that
looks like a bar code and that is unique for every individual.