Topic 2 - Molecular Biology Flashcards
(302 cards)
1
Q
Recognize common functional groups: AMINE.
A
A nitrogen atom bonded to two hydrogen atoms (-NH2)
2
Q
Recognize common functional groups: CARBOXYL.
A
A carbon double bonded to an oxygen (=O) and a hydroxyl (-OH)
3
Q
Recognize common functional groups: HYDROXYL.
A
Polar covalent bond between an oxygen and a hydrogen (-OH).
4
Q
Recognize common functional groups: PHOSPHATE.
A
A central phosphorus bonded to four oxygen atoms (-PO₄). This functional group has a negative charge.
5
Q
Outline the number and type of bond carbon can form with other atoms.
A
Carbon can form four covalent bonds with other atoms.
6
Q
List the four major classes of carbon compounds used by living organisms.
A
Carbohydrates
monosaccharides
disaccharides
polysaccharides
Proteins
amino acids
dipeptides
polypeptides
Lipids
fatty acids
sterols
triglycerides
phospholipids
Nucleic Acids
nucleotides
DNA
RNA
7
Q
Define metabolism.
A
The chemical processes that occur within a living organism in order to maintain life.
8
Q
Define catalysis.
A
The increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst, which is not consumed in the catalyzed reaction and can continue to act repeatedly. Biological catalysts are called enzymes.
9
Q
Define anabolism.
A
Constructing larger molecules from smaller subunits.
10
Q
Define monomer.
A
A small molecule that can bind with other molecules of the same type to form a large polymer.
11
Q
Define polymer.
A
A large molecule composed of many repeating monomer subunits.
12
Q
Describe condensation (dehydration synthesis) reactions.
A
A chemical reaction in which two molecules (monomers) combine to form a larger molecule with the formation of water.
13
Q
Define catabolism.
A
Catabolism is the breaking down of large molecules into smaller subunits.
14
Q
Describe hydrolysis reactions.
A
A chemical reaction in which a polymer breaks apart into smaller subunits; addition of water is used to break the bonds.
15
Q
Draw the molecular structure of urea.
A
16
Q
Describe how urea can be synthesized by living and artificial mechanisms.
A
In the liver, ammonia (NH3, a toxic byproduct of protein metabolism) is converted to urea, which is excreted from the body via the kidneys.
Urea can also be synthesis artificially in a reaction between ammonia and carbon dioxide.
17
Q
Draw the molecular diagram of ribose.
A
18
Q
Draw the molecular diagram of alpha-glucose.
A
19
Q
Draw the molecular diagram of a saturated fatty acid.
A
20
Q
Identify the carboxyl and methyl groups on a fatty acid.
A
Carboxyl = COOH
Methyl = CH3
21
Q
Draw the generalized structure of an amino acid.
A
22
Q
Label the amine group, carboxyl group, alpha carbon and R group on an amino acid.
A
23
Q
Identify a triglyceride from molecular drawings.
A
24
Q
Identify a triglyceride from molecular drawings.
A
25
Identify a sterol from molecular drawings.
26
Identify cellulose from molecular drawings.
Polymer of beta-glucose with bonds between carbons 1 and 4 of adjacent molecules
27
Identify glycogen from molecular drawings.
Polymer of alpha-glucose with many branch points.
28
Identify amylose from molecular drawings.
Amylose starch is a polymer of apha-glucose with few or no branch points.
29
Identify amylopectin from molecular drawings.
Amylopectin is a polymer of apha-glucose with some branch points.
30
Define vitalism.
Vitalism is a (non-scientific) idea that living organisms contain a "life force" or "energy" that give the properties of life separate from physical and chemical laws.
31
Explain the role of urea in the falsification of vitalism.
Up until about the 1830s, people thought that organic molecules of life could not be synthesis without the vital "life force" thought to be found in living things.
However, French chemist Wohler synthesized the organic molecule urea from inorganic components, showing that a vital "life force" was not needed.
32
Describe the structure of an atom.
Atoms are composed of protons, neutrons and electrons. Protons have a positive charge, neutrons have no charge and electrons have a negative charge.
Protons and neutrons are found in the atomic nucleus. Electrons are found in a cloud surrounding the nucleus.
33
Contrast ion with atom.
Atoms have no net charge because the have equal numbers of protons (+) and electrons (-). If an atom gains or loses an electron it will have a net charge and be called an ion.
34
Define anion.
A negatively charged ion because it has gained electrons
35
Define cation.
A positively charged ion because it has lost electrons.
36
Contrast covalent, ionic and hydrogen bonds.
All bonding involves electrons or the charges that result from the giving/taking of electrons.
Covalent bond: electrons are shared between two atoms
Ionic bond: attraction between cation and anion (no sharing of electrons)
Hydrogen bond: an attraction (not a true bond) between two polar molecules.
37
Write the molecular formula for water.
Water is H2O
38
Define "polar" in relation to chemical bonding.
Polar means a molecule has regions of slight charge due to the unequal sharing of electrons in a polar covalent bond. One of the atoms has more of a tug on the electrons that another, making it slightly negatively charged.
39
Describe the cause and effect of the polar nature of water.
In water, the oxygen has a greater "pull" on the shared electrons than the hydrogen atoms. As a result, there is unequal sharing of the electrons, with the electrons drawn closer to the oxygen.
As a result, the oxygen has a slightly negative charge and the hydrogens have a slightly positive charge.
40
Describe where and how water is able to form hydrogen bonds.
Water forms hydrogen bonds between the partial positive hydrogen of one water molecule and the partial negative oxygen of ANOTHER water molecule.
One water molecule is capable of forming up to four hydrogen bonds with other water molecules.
41
Define adhesion.
Water molecules bonding to non-water molecules through hydrogen bonding or attraction to an ionic charge.
42
Define cohesion.
Water molecules attaching to other water molecules through hydrogen bonding.
43
Outline an example of the cohesive property of water being of benefit to life.
Water cohesion allows for surface tension, allowing some insects to stay on the surface of the water.
Water cohesion creates a chain of water molecules that allows for the transport of water from the roots to the leaves of plants.
Water cohesion is responsible for the high heat capacity of water, maintaining a relatively stable internal temperature and external environment for living organisms.
44
Outline an example of the adhesive property of water being of benefit to life.
Adhesion is needed for water to move from the roots to the leaves of plants. Water sticks to the sides of the xylem wall through adhesion.
45
Outline a benefit to life of water's high specific heat capacity.
It takes a relatively large amount of heat energy to raise the temperature of water. This is a benefit because the temperature of large bodies of water remains relatively constant, protecting life from potentially lethal temperature fluctuations.
46
Outline a benefit to life of water's high latent heat of vaporization.
It takes a relatively high amount of heat energy to vaporize water (convert from liquid to gas) because hydrogen bonds must be broken.
As the water evaporates, the surface it leaves becomes cooler. This is called evaporative cooling and allows organisms to cool with sweating.
47
Outline a benefit to life of water's high boiling point.
Water boils at a relatively high temperature for a compound made of such light elements; this is due to the hydrogen bonding between water molecules causing them to resist being pulled apart (which is what happens when water boils to become a gas).
Without this, water would not be a liquid over much of the surface of the Earth and we would not have a liquid ocean.
48
Explain why is water such a good solvent.
Water is a good solvent because it can form hydrogen bonds with a variety of different substances. Water is called the "universal solvent" because it dissolves more substances than any other liquid.
49
List the types of molecules that water will dissolve.
Water will dissolve substances that are polar or ionically charged.
50
List types of molecules that are hydrophilic.
Water is a polar molecule that attracts other polar or ionic substances, making them hydrophilic.
51
List types of molecules that are hydrophobic.
Nonpolar or non-ionic molecules are hydrophobic.
52
Given a diagram of a molecular structure, determine if the molecule is hydrophilic or hydrophobic: PHOSPHATE GROUP.
The negative charge found on a phosphate group makes it an ION. Water is attracted to ions, making them hydrophilic.
53
Given a diagram of a molecular structure, determine if the molecule is hydrophilic or hydrophobic: HYDROXYL GROUP.
There is a polar covalent bond between the O and H in a hydroxyl group. As a result, water is attracted, making molecules with many hydroxyl groups hydrophilic (such as glucose).
54
Given a diagram of a molecular structure, determine if the molecule is hydrophilic or hydrophobic: HYDROCARBONS.
If there are no charges and no polar covalent bonds, then water will not be attracted, making the molecule hydrophobic.
55
Define hydrophobic.
A molecule or substance that is NOT attracted to water.
56
Define hydrophilic.
A molecule or substance that is attracted to water.
57
Explain why water and methane have different thermal properties based on their molecular structures.
Methane is nonpolar whereas water is polar.
Because water is polar, it is able to form hydrogen bonds with many types of molecules.
As a nonpolar molecule, methane does not form hydrogen bonds with other molecules.
58
Compare the physical properties of methane and water.
Methane (CH4)
Gas at room temperature
Lower heat capacity
Water (H2O)
Liquid at room temperature
Higher heat capacity (more energy to change temp)
59
Explain sweating as a mechanism to cool the body.
Sweat is mostly water. When the water evaporates from the surface of the skin, it takes heat with it. With the loss of the heat energy, the skin feels cooler.
60
State if the following molecule is hydrophobic or hydrophilic: glucose.
Hydrophilic
Glucose has many polar -OH groups which are able to form hydrogen bonds with water.
61
State if the following molecule is hydrophobic or hydrophilic: amino acids.
Generally Hydrophilic
Although variable, many amino acids have polar or ionic "R" groups which are able to form hydrogen bonds with water.
62
State if the following molecule is hydrophobic or hydrophilic: cholesterol.
Hydrophobic
Cholesterol is primarily a non-polar hydrocarbon and does not form hydrogen bonds with water.
63
State if the following molecule is hydrophobic or hydrophilic: fats.
Hydrophobic
Fats are primarily non-polar hydrocarbons and do not form hydrogen bonds with water.
64
State if the following molecule is hydrophobic or hydrophilic: oxygen.
Gaseous oxygen does not react with water. It is water soluble depending on temperature and pressure conditions.
65
State if the following molecule is hydrophobic or hydrophilic: sodium chloride.
Hydrophilic
The ions are able to dissolve in water.
66
Outline the mechanism of transport of glucose in the blood.
Blood is primarily water. Because it is hydrophilic, glucose can dissolve and be directly transported in the blood.
67
Outline the mechanism of transport of amino acids in the blood.
Blood is primarily water. Because most are hydrophilic, amino acids can usually dissolve and be directly transported in the blood.
68
Outline the mechanism of transport of cholesterol in the blood.
Blood is primarily water. Because it is hydrophobic, cholesterol must be transported in the blood within "sacs" called lipoproteins. Lipoproteins are a group of soluble proteins that combine with and transport fat or other lipids in the blood plasma.
69
Outline the mechanism of transport of fats in the blood.
Blood is primarily water. Because it is hydrophobic, fats must be transported in the blood within "sacs" called lipoproteins. Lipoproteins are a group of soluble proteins that combine with and transport fat or other lipids in the blood plasma.
70
Outline the mechanism of transport of oxygen in the blood.
Oxygen is transported in the blood by binding to a protein transport molecule (hemoglobin) within the red blood cells.
71
Outline the mechanism of transport of sodium chloride in the blood.
Blood is primarily water. Because they are hydrophilic. sodium and chloride ions can dissolve and be directly transported in the blood.
72
State why scientists cannot prove without a doubt that hydrogen bonds exist between water molecules.
A scientific theory is a well supported explanation of some aspect of the natural world that is supported through repeated observation and experimentation.
Because H-bonds have yet to be directly observed, their presence can not be proven, however H-bonding does mathematically, chemically and observationally explain the properties of water.
73
Define monosaccharide.
The simplest form of carbohydrate; "one sugar."
74
Define disaccharide.
The sugar formed when two monosaccharides are joined; "two sugar."
75
Define polysaccharide.
Long chains of bonded monosaccharides; "many sugars."
76
List three examples of monosaccharides.
Glucose (C6H12O6)
Ribose (C5H10O5)
Deoxyribose (C5H10O4)
Fructose (C6H12O6)
Galactose (C6H12O6)
77
List three examples of disaccharides.
Maltose (glucose + glucose)
Sucrose (glucose + fructose)
Lactose (glucose + galactose)
78
List three examples of polysaccharides.
Starch: polymer of alpha-glucose (amylose and amylopectin)
Cellulose: polymer of beta-glucose
Glycogen: polymer of alpha-glucose
79
Draw the formation of maltose from two glucose monomers.
Carbon #1 of one glucose binds to carbon #4 of the other glucose
80
Explain a condensation reaction connecting two monosaccharides in the formation of a disaccharide.
Condensation is a chemical reaction in which two molecules are joined to make a larger molecule with the loss of water.
An -H from the hydroxyl on carbon #1 of one monosaccharide combines with an -OH from the hydroxyl on carbon #4 of the other monosaccharide. The -H and _OH combine to form water. A bond is formed with a C-O-C bridge between the two monosaccharides.
81
Describe the differences between saturated and unsaturated (mono- or poly-) fatty acids.
Saturated fatty acids have only single carbon-to-carbon bonds (therefore the carbons are saturated with hydrogen atoms)
Unsaturated fatty acids have one ("mono") or more ("poly") carbon-to-carbon double bonds.
82
Define "isomer."
Isomers are molecules that have the same molecular formula but a different arrangement of atoms.
83
Describe the differences between cis- and trans- fatty acids.
Cis and trans fatty acids have the same molecular formula but different arrangements of H- atoms relative to the C=C.
Trans: H atoms are on the opposite sides of the C=C
Cis: H atoms are on the same side of the C=C.
84
Outline the difference between fats and oils.
Fats
Solid at room temperature
Typically from animal sources
Contain more saturated fatty acids
examples: butter and lard
Oils
Liquid at room temperature
Typically from plant sources
Contain more unsaturated fatty acids
examples: olive oil
85
Explain a condensation reaction connecting fatty acids and glycerol to form a triglyceride.
Three molecules of fatty acid combine with one molecule of glycerol with the removal of three molecules of water. The resulting compound is called a triglyceride.
86
State two functions of triglycerides.
-source of energy
-storage of chemical energy
-thermal insulation
-waterproofing
-protection
87
State the structural difference between alpha and beta glucose.
The only (but significant) difference between alpha and beta glucose is the orientation of the hydroxyl group (-OH) relative to carbon #1 of the molecule.
Alpha glucose: the -OH goes "down"
Beta glucose: the -OH goes "up"
88
Describe the structure and function of cellulose.
Cellulose is a straight chain (unbranched) polymer of beta glucose molecules that forms the plant cell wall. Hydrogen bonds form between cellulose chains.
89
Describe the structure and function of amylose.
Amylose consists of a linear chain of roughly 500 to 20,000 alpha-glucose monomers linked together. Amylose is a energy storage molecule found in plants.
90
Describe the structure and function of amylopectin.
Amylopectin consists of a branching chain of roughly 1-2 million alpha-glucose monomers linked together. Amylopectin is a energy storage molecule found in plants.
91
Describe the structure and function of glycogen.
Glycogen consists of a highly branched chain of alpha-glucose monomers linked together. Glycogen is a energy storage molecule found in animals.
92
Outline the use of trans-fats in food.
Trans fat, also called trans-unsaturated fatty acids or trans fatty acids, are a type of unsaturated fat that occur in small amounts in nature but became widely produced industrially from vegetable fats starting in the 1950s for use in margarine, snack food, and packaged baked goods and for frying fast food. Use of trans fats in food is now banned in the USA.
93
Outline the health risks of trans-fats and saturated fats in food.
There is a direct, strong correlation between intake of trans-fats and saturated fats in food and:
1. all causes of mortality
2. cardiovascular disease
3. coronary heart disease
4. stroke
5. type II diabetes
94
Compare the energy storage of lipids to that of carbohydrates.
Lipids
Slow release of energy
Able to store chemical energy long term
≈ 2X the energy per gram compared to carbs
Insoluble, so easier to store
Carbohydrates
Fast release of energy
Quickly digested and used
≈ 1/2 the energy per gram compares to lipids
Soluble, so easy to transport by blood
95
Describe how health claims can be evaluated.
Health claims can be evaluated using a systematic analysis of the claim:
Does scientific research support the claim?
-How strong is a correlection?
-Is a result determined to be statistically significant?
-How much variation is there between people?
What are the limitations of the research?
-Was there a large sample size?
-Were relevant variables controlled?
-How accurate are the measurement techniques?
Are there financial reasons for making a claim?
-Is the claim maker trying to sell a product?
96
Identify carbon, hydrogen and oxygen atoms by color in molecular visualization software.
Carbon = black
Hydrogen = white
Oxygen = red
97
Describe how molecular visualization software is used to compare molecules.
Molecular visualization software (like Jmol) allows molecule models to be viewed, rotated, zoomed and manipulated.
98
Outline the use of the body mass index (BMI).
The a body mass index (BMI) is a weight-to-height ratio, calculated by dividing one's weight in kilograms by the square of one's height in meters and used as an indicator of obesity and underweight.
99
Given weight and height, calculate the BMI.
BMI = weight / (height X height)
if weight = 77 kg and height = 1.9 m
then BMI = 77 / (1.9x1.9)
BMI = 77 / 3.61 = 21. 3
100
Given weight and height, use a nomogram to determine the BMI.
Connect the weight and height with a straight line. BMI is the point at which the line crosses the center scale.
101
Outline effects of a BMI that is too high or too low.
A high BMI can be an indicator of obesity, which correlates to health problems, including:
- Type II diabetes
- Gallstones
- Hypertension
- Heart disease
A low BMI can be an indicator of malnourishment.
Note, use of BMI has limitations because it doesn't distinguish mass from fat, muscle or bone. Might misclassify healthy people as obese and visa versa.
102
Describe how the effect of lipids on health can be assessed scientifically.
The effects of lipids on health can be assessed using scientific investigations, including:
-determining correlations between dietary lipids and health effects using large databases of population statistics
-performing controlled experiments with human volunteers or animal models.
103
Describe polypeptide chain formation in terms of the formation of peptide bonds and condensation reactions.
Condensation is a chemical reaction in which two molecules are joined to make a larger molecule with the loss of water.
An -OH from the carboxyl on one amino acid combines with an -H from the amine of the other amino acid. The -H and _OH combine to form water. A peptide bond is formed with a C-N bridge between the two amino acids.
104
Determine the number of peptide bonds given the number of amino acids in a polypeptide.
of bonds is the number of amino acids minus 1
of waters created = the number of peptide bonds
Ex: a polypeptide with 784 amino acids has 783 peptide bonds and formed 783 water molecules
105
Define dipeptide.
A molecule containing two amino acids joined by a single peptide bond
106
Define oligopeptide.
A molecule that contains a relatively small number (2-20) of amino-acids joined by peptide bonds.
107
Define polypeptide.
A linear polymer consisting of a large number of amino-acids bonded together in a chain, forming part of (or the whole of) a protein molecule.
108
Draw the structure of a generalized amino acid.
109
State the number of amino acids used by living organisms to make polypeptides.
There are twenty amino acids that are commonly used by living organisms to make polypeptides.
R groups give the polypeptide its character, because of their differences, the twenty amino acids are chemically diverse.
110
Given an image of an amino acid, classify the amino acid chemical properties based on R group properties.
Look at the variable ("R") group
If the R group has -OH or =O then it is polar and the amino acid will likely be HYDROPHILLIC
If the R group is a hydrocarbon, then it is non-polar and the amino acid will likely be HYDROPHOBIC
If the R group has a charge (+ or -) then the amino acid will likely be HYDROPHILLIC
111
Calculate the possible number of amino acid sequences given n amino acids in the chain.
There are innumerable ways that amino acids can combine to form polypeptides.
The general formula for the number of theoretically possible different amino acid sequences of length n is 20^n.
112
Outline the relationship between genes and polypeptides.
Three bases of a gene ("triplet") code for one amino acid. The DNA is transcribed into mRNA (3 mRNA bases is a "codon"). The mRNA is then translated at a ribosome with one codon coding for one amino acid. The amino acids are bound together to form a polypeptide.
113
Distinguish between a polypeptide and a protein.
When a polypeptide folds into a specific three-dimensional structure that determines its activity it is called a protein.
Some proteins are composed of multiple polypeptides linked together.
114
Outline the structure and function of an example protein composed of two or more polypeptides linked together.
Hemoglobin is a protein found in red blood cells that transports oxygen from the lungs to the tissues and facilitates the return transport of carbon dioxide.
Hemoglobin is a protein composed of four subunits, each having one polypeptide chain and one heme group.
115
Outline how the amino acid sequence determines the 3D shape of a protein.
Each type of protein has a unique sequence of amino acids. As a result of chemical interactions between the amino acids, each type of protein has a particular three-dimensional structure, which is determined by the order of the amino acids in its chain.
116
Explain how the polar R groups on amino acids affect the 3D shape of the protein.
Amino acids with polar R groups tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules. When polar amino acids are buried within the protein, they are usually hydrogen-bonded to other polar amino acids or to the polypeptide backbone.
117
Explain how the nonpolar R groups on amino acids affect the 3D shape of the protein.
Amino acids with nonpolar R groups nonpolar (hydrophobic) side chains in a protein—belonging to such amino acids as phenylalanine, leucine, valine, and tryptophan—tend to cluster in the interior of the molecule. This enables them to avoid contact with the water that surrounds them inside a cell.
118
Explain how the ionically charged R groups on amino acids affect the 3D shape of the protein.
Amino acids with ionically charged R groups tend to arrange themselves near the outside of the molecule, where they can form hydrogen bonds with water and with other polar molecules. When charged amino acids are buried within the protein, they are usually ionically-bonded to other charged amino acids.
119
Define "globular protein".
In globular proteins the polypeptide chain folds up into a compact shape like a ball with an irregular surface. Enzymes tend to be globular proteins: even though many are large and complicated, with multiple subunits, most have an overall rounded shape
120
Define "fibrous protein".
Fibrous proteins generally have a relatively simple, elongated three-dimensional structure and have roles in the cell requiring each individual protein molecule to span a large distance.
121
Summarize the function of enzyme proteins.
Enzymes are proteins that are often referred to as biological catalysts because they speed up chemical reactions.
For example, lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food.
122
Summarize the function of hormone proteins.
Hormonal proteins are messenger proteins that are transported by the circulatory system to target distant organs to regulate physiology and behaviour. Examples include insulin and oxytocin.
123
Summarize the function of immunoglobin proteins.
Immunoglobulins are antibodies, specialized proteins involved in defending the body from antigens (foreign invaders). They can travel through the bloodstream and are utilized by the immune system to identify and defend against bacteria, viruses, and other foreign intruders.
124
Summarize the function of pigment proteins.
Pigment proteins selectively absorb certain wavelengths of light while reflecting others. Chlorophyll is the primary pigment in plants.
125
Summarize the function of structural proteins.
Structural proteins are fibrous and stringy and because of this formation, they provide support for various body parts. Examples include keratin, collagen, and elastin.
126
Summarize the function of receptor proteins.
Receptor proteins work as monitors, changing their shape and activity in response to metabolic signals or messages from outside the cell.
127
Summarize the function of contractile proteins.
Contractile proteins are responsible for muscle contraction and movement. Examples of these proteins include actin and myosin.
128
Summarize the function of storage proteins.
Storage proteins store amino acids for the body to use later. Examples include albumin, which is found in egg whites, and casein, a milk-based protein.
129
Summarize the function of transport proteins.
Transport proteins are carrier proteins which move molecules from one place to another. Hemoglobin is one of these and is responsible for transporting oxygen through the blood via red blood cells. Cytochromes are another that operate in the electron transport chain as electron carrier proteins.
130
List functions of proteins.
Proteins are responsible for nearly every task of cellular life, including cell shape and inner organization, product manufacture and waste cleanup, and routine maintenance. Proteins also receive signals from outside the cell and mobilize intracellular response.
1. Contraction/movement
2. Enzyme
3. Hormone
4. Immune defense
5. Pigment
6. Receptor
7. Storage
8. Structure
9. Transport
131
Define "proteome."
The proteome is the entire set of proteins that can be made by a cell, tissue, or organism.
132
Outline why each individual of a species will have a unique proteome.
The proteome of any given individual will be unique, as protein expression patterns are determined by an individual's genes and each individual has a (at least slightly) unique genome.
133
Outline why each cells of a organism will have a unique proteome.
The genome is the same in all the cells of an organism however the proteome will vary between cells. Cells with different functions will produce different proteins as different genes are expressed in different cells.
134
State the function of rubisco.
Rubisco is an enzyme present in plant chloroplasts, involved in the light independent reactions of photosynthesis.
135
State the function of insulin.
Insulin is a hormone protein produced in the pancreas that regulates the amount of glucose in the blood.
136
State the function of rhodopsin.
Rhodopsin is a pigment protein found in the rod cells of the retina. Rhodopsin is extremely sensitive to light, and thus enables vision in low-light conditions.
137
State the function of collagen.
Collagen is the main structural protein in the extracellular space in the various connective tissues in animal bodies. As the main component of connective tissue, it is the most abundant protein in mammals.
138
State the function of spider silk.
Spider silk is a structural protein spun by spiders and uses to make webs or other structures.
139
Define "denaturation."
Denaturation is the alteration of a protein shape through some form of external stress (for example, by applying heat or acid), in such a way that it will no longer be able to carry out its cellular function.
140
Outline the effect of heat on protein structure.
Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions within proteins.
This occurs because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted.
This can lead to altered protein recognition or an enzyme might become inactive.
141
Outline the effect of pH on protein structure.
pH changes can affect the state of ionization of acidic or basic amino acids.
If the state of ionization of amino acids in a protein is altered then the ionic bonds that help to determine the 3D shape of the protein can be altered.
This can lead to altered protein recognition or an enzyme might become inactive.
142
Draw peptide bond formation in a condensation reaction.
143
Define "universal" in relation to the genetic code and amino acids.
The genetic code is the universal (applicable to all cases) language that relates base triplets in DNA to amino acids in proteins. All known organisms use the same triplet-amino acid equivalences and the same amino acids to assemble proteins.
144
Outline a discrepancy in the trend of all organisms using the same amino acids to assemble polypeptides.
Most species use 20 amino acids for assembly of polypeptides. However, a few species use up to 22 amino acids. The additional two amino acids (selenocysteine and pyrrolysine) require alternative mechanisms for their incorporation to proteins.
145
Define "enzyme."
Enzymes are proteins that act as a catalyst to bring about a specific biochemical reaction.
146
Define "substrate."
The substrate is the substance on which an enzyme acts.
147
Define "active site" of the enzyme.
The active site is the region on the surface of the enzyme which binds to the substrate molecule.
148
State the relationship between enzyme substrate and enzyme active site.
Since the substrate must fit into the active site of the enzyme before catalysis can occur, only properly shaped molecules can serve as substrates for a given enzyme. The shape of the substrate is specific to the enzyme (and visa versa).
149
Define "specificity."
Enzymes are specific to the reactions they catalyze because they can only fit a certain substrate(s) into the active site. A few enzymes exhibit absolute specificity; that is, they will catalyze only one particular reaction. Other enzymes will be specific for a particular type of chemical bond or functional group.
150
Define "collision" in relation to enzyme function.
For two molecules to react they must collide (hit with force when moving) with one another. They must collide in the right direction (orientation) and with sufficient energy.
151
Outline the relationship between the rate of molecular motion and the collision of substrates with the enzyme active site.
As the rate of molecular motion increases, so does the rate of chemical reaction. This is because motion causes more collisions, with more energy, between the enzyme molecules and their substrate molecules.
152
Summarize the process of enzyme catalysis.
1. Substrate binds to active site.
2. Conformational change in the enzyme (induced fit) stresses bonds in the substrate, increasing reactivity.
3. Substrates change into different chemical substances (products)
4. Products separate from active site, leaving it available for the next reaction.
153
Describe the 'lock and key' model of enzyme action.
The lock-and-key model states that the substrate acts as a 'key' to the 'lock' of the enzyme active site. The active site and substrate are exact matches for each other. In this model, only a single substrate is the precise match for the enzyme. Once the enzyme finds its exact counterpart, the chemical reaction can begin.
154
Describe the induced fit model of enzyme action.
The induced-fit model maintains that enzymes are rather flexible structures in which the active site is reshaped by its interactions with the substrate until the time the substrate is completely bound to it (which is also the point at which the final form and shape of the enzyme is determined).
Induced fit explains how enzymes may exhibit broad specificity (e.g. lipase can bind to a variety of lipids).
155
Explain how temperature affects the rate of enzyme activity.
Like most chemical reactions, the rate of an enzyme-catalyzed reaction increases as the temperature is raised.
The reaction rate increases with temperature to a optimum level, then abruptly declines with further increase of temperature. The decline is because most enzymes rapidly become denatured at higher temperatures.
156
Draw a graph of depicting the effect of temperature on the rate of enzyme activity.
The graph shows the typical change in an enzyme's activity with increasing temperature. The enzyme activity gradually increases with temperature (up to around 37ºC, or body temperature for human enzymes). Then, as the temperature continues to rise, the rate of reaction falls rapidly as heat energy denatures the enzyme.
157
Explain how pH affects the rate of enzyme activity.
Extremely high or low pH values generally result in complete loss of activity for most enzymes. pH is a factor in the chemical stability of enzyme structure.
158
Draw a graph of depicting the effect of pH on the rate of enzyme activity.
The graph shows the typical change in an enzyme's activity with changing pH. The enzyme activity increases around an optimum pH. Then, as the pH continues to change, the rate of reaction falls rapidly as the chemical interactions between the enzyme and the solution denatures the enzyme.
159
Identify the optimum temperature or pH for enzyme activity on a graph.
Different enzymes work best at different pH values and temperatures. The optimum pH and temperature for an enzyme depends on where it normally works. For example, intestinal enzymes have an optimum pH of about 7.5. Enzymes in the stomach have an optimum pH of about 2.
The optimum is the pH or temperature at which enzyme activity is greatest.
160
Explain how substrate concentration affects the rate of enzyme activity.
One single enzyme molecule can react over and over, however it is only capable of combining with a certain maximum number of substrate molecules per minute.
At low concentration of substrate, there is a steep increase in the rate of reaction with increasing substrate concentration. The active site of the enzyme is empty, waiting for substrate to bind, for much of the time, and the rate at which product can be formed is limited by the concentration of substrate which is available.
As the concentration of substrate increases, the enzyme becomes saturated with substrate. As soon as the active site is empty, more substrate is available to bind and undergo reaction. The rate of formation of product now depends on the activity of the enzyme itself, and adding more substrate will not affect the rate of the reaction to any significant effect.
161
Draw a graph of depicting the effect of substrate concentration on the rate of enzyme activity.
The graph shows the typical change in an enzyme's activity with increasing substrate. The enzyme activity initially increases with substrate. Then, as the substrate concentration continues to rise, the rate of reaction levels off as the enzyme active sites become saturated with substrate.
162
Define "denature."
To denature means to destroy the characteristic properties of a protein (or other biological macromolecule) by heat, acidity, or other effects that disrupt its molecular shape.
163
State the effect of denaturation on enzyme structure and function.
Both high temperatures and extremes of pH change the bonds between amino acids in the enzyme, so changing its shape. If the shape of the active site is altered, the enzyme will no longer be able to bind its substrate and enzyme function will be lost.
164
List examples of industries in which enzymes are used.
Enzymes have wide range of commercial applications. These include their use in food production, food processing and preservation, washing powders, textile manufacture, leather industry, paper industry, medical applications, and improvement of environment and in scientific research.
165
Explain how and why industrial enzymes are often immobilized.
An immobilized enzyme is an enzyme attached to an inert, insoluble material. It lets enzymes be held in place throughout a reaction after which they can be easily separated from the products and used again. Immobilized enzymes are widely used in industry for enzyme catalysed reactions.
166
State the source of the lactase enzyme used in food processing.
The lactase used to produce lactose free dairy products is obtained from a yeast. The yeast is cultured and then the lactase is extracted and purified.
167
State the reaction catalyzed by lactase.
The enzyme lactase converts the disaccharide sugar in milk (lactose) into two monosaccharides (galactose and glucose).
168
Summarize what it means to be "lactose intolerant."
Lactose intolerance is usually caused from a deficiency in lactase — the body produces no enzyme or too little enzyme. When the body does not have enough lactase enzyme, the undigested and unabsorbed lactose sugar is moved into the colon (lower part of your digestive
system), where it becomes fermented by intestinal bacteria. The fermentation process produces a lot of gas and causes the unpleasant discomfort of gas bloating, cramps, and diarrhea. The amount of reaction and discomfort differs among individuals.
169
Outline reasons for using lactase in food processing.
1. Forming lactose free milk for people who are lactose intolerant.
2. Sweetening of dairy products: galactose and glucose are sweeter than lactose so less sugar needs to be added to sweeten dairy products.
3. Lactose free milk produces smoother ice cream: lactose tends to crystallize during production of ice cream. However because galactose and glucose are more soluble than lactose, they remain dissolved during the formation of ice cream, leaving a smoother texture.
170
Explain the need to control variables in experimental design.
Controlled variables are what is kept the same between experimental groups throughout the experiment. Any change in a control variable in an experiment would invalidate a relationship between the manipulated variable and the responding, thus skewing the results.
171
Define "manipulated (independent) variable."
The manipulated (independent) variable is the variable that is changed in a scientific experiment to test the effects on the responding (dependent) variable.
172
List potential manipulated (independent) variables for experiments testing the activity of enzymes.
Possible manipulated variables include:
Substrate concentration
Enzyme concentration
Temperature
Source of enzyme
pH
Inhibitor presence
Inhibitor type
173
Define "responding (dependent) variable."
The responding (dependent) variable is the variable being measured to test the effect of the manipulated variable in a scientific experiment.
174
List potential responding (dependent) variables for experiments testing the activity of enzymes.
Possible responding variables include:
Enzyme reaction time (s)
Enzyme reaction rate (s^-1)
Amount of product
Amount of substrate
175
Describe three techniques for measuring the activity of an example enzyme.
Catalase is an enzyme that converts hydrogen peroxide (H2O2) to water (H2O) and oxygen gas (O2, which bubbles out of solution).
The activity of catalase can be measured by measuring the amount of O2 formed in a set amount of time via one of the following methods:
- time to float an enzyme saturated filter disc
- H2O displacement in by formation of O2 gas
- O2 gas bubble volume
- change in pressure due to O2 gas
- change in O2 levels with sensor
176
Define "quantitative."
Quantitative data is information that can be measured and recorded with numbers.
177
Define "qualitative."
Qualitative data are types of information that have aspects that are unable to be measured. Qualitative data is a expressed not in terms of numbers, but rather by means of a natural language description.
178
Describe how uncertainty of a measurement tool is determined.
To determine uncertainty:
1. Find the smallest increment of measurement on your measurement device
2. Divide it by two
3. Round up to one significant digit
For example, the ruler has smallest increment of 1 mm. Half of that is 0.5 mm. So the uncertainty of the ruler is +/- 0.5 mm.
179
Explain the need for repeated measurements (multiple trials) in experimental design.
Repeated measurements (multiple trials) are done for a couple of reasons:
1. To minimize the impacts of errors done in any one trial by averaging multiple trials together.
2. To minimize random effects and the effects of uncontrolled variables by averaging multiple trials together.
180
Outline why measurements have "uncertainties."
All measurements have a degree of uncertainty caused by two factors:
1. the precision f the measuring instrument
2. the skill of the experimenter making the measurements.
Scientists usually specify a range of values that they expect a "true value" to fall within. The most common way to show the range of values is:
measurement =
best estimate ± uncertainty
181
State the two types of nucleic acid.
DNA: deoxyribonucleic acid
RNA: ribonucleic acid
182
Outline the parts of a nucleotide.
A nucleotide is the monomer subunit of the nucleic acids. A nucleotide has three component parts:
1. a nitrogenous base
2. A 5-carbon sugar (ribose or deoxyribose)
3. A phosphate group
183
Identify and label carbons by number (for example, C1, C2, C3) on a nucleotide drawing.
The carbons of the sugar component of the nucleotide are numbers clockwise, starting from the oxygen in the ring at the top and the phosphate group to the left.
184
Explain how nucleotides can connect to form a nucleic acid polymer.
Nucleotides connect by creating covalent bonds between the sugar of one nucleotide and the phosphate group of another nucleotide in a condensation reaction.
185
State the names of the nitrogenous bases found in DNA and RNA.
Cytosine (DNA and RNA)
Thymine (DNA only)
Guanine (DNA and RNA)
Adenine (DNA and RNA)
Uracil (RNA only)
186
Identify nitrogenous bases as either a pyrimidine or purine.
Pyrimidine: single ring nitrogenous bases
Cytosine
Thymine
Uracil
Purine: double ring nitrogenous bases
Guanine
Adenine
187
State the complementary base pairing rules.
A purine complementary base pairs to a pyrimidine.
In DNA and RNA, guanine bonds with
cytosine
In DNA, adenine bonds with thymine
In RNA, adenine bonds with uracil
188
Compare the structure of DNA and RNA.
RNA
ribose
single stranded
A, G, C, U
DNA
deoxyribose
double stranded
A, G, C, T
189
Define "antiparallel" in relation to DNA structure.
Adjacent molecules are oriented parallel to each other but oriented in opposite directions.
In DNA, one strand runs 5' to 3' and the complementary strand unds 3' to 5'
190
Outline the formation of a DNA double helix by hydrogen bonding between nitrogenous bases.
Complementary DNA nucleotides form hydrogen bonds between the nitrogenous bases, forming two strands ("double") that wind around each other ("helix")
191
Identify the four bases of DNA based on the numbers of rings (purines or pyrimidines) and the number of hydrogen bonds it can form.
Purines have two rings. If it can form 2 H-bonds it is adenine and if it can form 3 H-bonds it is guanine.
Pyrimidines have one ring. If it can form 2 H-bonds it is thymine and if it can form 3 H-bonds it is cytosine.
192
State the number of nitrogenous bases per complete turn of the DNA double helix.
A complete turn is when one strand circles back on itself. There are 10 base pairs per turn of the helix.
193
Outline the role of Chargaff in the discovery of DNA structure.
Chargaff determined that there are equal numbers of A and T bases and G and C bases in a DNA sample.
194
Outline the role of Watson and Crick in the discovery of DNA structure.
Watson figured out how the nitrogenous base pairs could fit within a DNA double helix while maintaining a constant helix diameter.
Crick suggested that the DNA backbone was anti-parallel.
195
Outline the role of Franklin in the discovery of DNA structure.
Franklin took clear, detailed x-ray diffraction photos that provided clues to DNA structure.
196
Explain how Watson and Crick used model building to determine the structure of DNA.
Watson and Crick used model building to narrow down the possibilities for DNA structure and to eventually create an accurate representation of DNA that fit within the experimental evidence collected by Franklin and others.
197
Draw the basic structure of a single nucleotide (using circle, pentagon and rectangle).
198
Draw a simple diagram of the structure of RNA.
199
Draw a simple diagram of the structure of DNA.
200
Identify and label the 5' and 3' ends on a DNA or RNA diagram.
The 5' and 3' ends of a nucleic acid refer to the direction of the chain. In DNA, one strand will run from 5' to 3' and the complementary strand will run anti-parallel, from 3' to 5'.
The 5' end is identified by the presence of the phosphate group and the 3' end is identified as ending in the pentose sugar (ribose or deoxyribose).
201
List types of models used in science.
Mathematical Models
Use of math to describe and/or predict the behavior of a system
Computer Models
Computer programs that attempt to simulate the behavior of a system
Physical Models
Models of structures that can be carried, touched or held
Images
Diagrams used to represent a structure or process
Analogy
Comparisons for the purpose of explanation or clarification
202
State a common feature of models in science.
A model is a representation of a phenomenon, object or idea. Models are used to explain difficult concepts or to have tangible visualizations of structures. Models can be used to make and test predictions and to understand processes that are not easily observed.
203
List ways in which models are different from the structure or process they represent.
All models have limitations.
-variations in size
-simplification of complexity
-may be static representations of moving structures/processes
-do not represent all dimensions or variables
204
Describe the meaning of "semi-conservative" in relation to DNA replication.
Semi-conservative means the products of DNA replication each contain one of the original DNA strands and one new strand.
205
Explain the role of complementary base pairing in DNA replication.
Complementary base pairing (A-T, C-G) ensures that the DNA sequence remains consistent after DNA replication. This ensures that the genetic code remains intact between generations.
206
State why DNA strands must be separated prior to replication.
The two strands of the parent DNA molecule must separate so that each can serve as a template for the new DNA strands that are being built.
207
Outline the function of helicase.
Helicase is an enzyme that attaches to the DNA and moves along the molecule separating unwinding the helix and separating the two strands by breaking hydrogen bonds.
208
State the role of the origin of replication in DNA replication.
The origin of replication is the sequence of DNA nucleotides at which replication is initiated.
209
Contrast the number of origins in prokaryotic cells to the number in eukaryotic cells.
Prokaryotic cells have 1 origin of replication (therefor one replication bubble with two replication forks)
Eukaryotic cells have many origins of replication (therefor multiple replication bubbles that eventually fuse)
210
Describe the movement of DNA polymerase along the DNA template strand.
DNA polymerase moves along the parent DNA strand from the 3' end to the 5' end of the parent strand. The parent/template is read from 3' to 5'.
DNA polymerase builds a complementary strand of DNA from the parent/template strand. The daughter strand is built from 5' to 3'.
211
Describe the action of DNA polymerase III in DNA replication.
DNA polymerase "reads" a parent/template DNA strand and adds complementary nucleotides to build a new strand of DNA.
DNA polymerase can only add new nucleotides to the 3' end of the growing daughter strand.
212
Define "transcription."
During transcription, a section of the cell's DNA serves as a template for creation of an RNA molecule.
In some cases, the newly created RNA molecule is itself a finished product, and it serves an important function within the cell. In other cases, the RNA molecule carries messages from the DNA to other parts of the cell for processing. Most often, the RNA is used to manufacture proteins (during translation).
213
Outline the role of RNA polymerase in transcription.
RNA polymerase is an enzyme that is responsible for transcribing a DNA sequence into an RNA sequence.
214
Summarize the steps of transcription.
Initiation
RNA polymerase, together with one or more general transcription factors, binds to a sequence of DNA called the "promoter".
RNA polymerase separates the two strands of the DNA helix by breaking the hydrogen bonds between complementary DNA nucleotides.
Elongation
RNA polymerase adds RNA nucleotides (which are complementary to the nucleotides of one DNA strand).
RNA polymerase catalyzes the formation of the RNA sugar-phosphate backbone to form an RNA strand.
Termination
At a DNA sequence called the "terminator", RNA polymerase breaks the hydrogen bonds of the RNA-DNA helix, freeing the newly synthesized RNA strand.
215
Outline the base pairing in transcription.
A complementary strand of RNA may be constructed from a DNA template sequence following the base pairing rules: A=U and G≡C.
216
Define "sense" and "antisense" in relation to DNA transcription.
Two strands of complementary sequence are referred to as sense and antisense. The DNA sense strand has the same sequence as the mRNA being transcribed (substituting U for T) however the DNA sense strand is itself is not transcribed.
The DNA antisense strand, with bases complementary to the DNA sense strand, is used as a template for the RNA during transcription.
217
Identify the sense and antisense strands of DNA given a diagram of translation.
On a diagram of transcription, the DNA strand that is serving as the template for making RNA is the antisense strand. The strand of DNA that not being transcribed is the sense strand.
218
Define "translation"
Translation is the process in which ribosomes in the cytoplasm or ER synthesize a specific amino acid chain, or polypeptide, based on the mRNA sequence (that had been transcribed from DNA).
219
State the location of translation in a prokaryotic cell.
Because there is no nucleus to separate the processes of transcription and translation, when bacterial genes are transcribed, their transcripts can immediately be translated by a ribosome in the cytoplasm.
220
State the location of translation in a eukaryotic cell.
Transcription and translation are spatially and temporally separated in eukaryotic cells; transcription occurs in the nucleus to produce a mRNA which exits the nucleus and is translated in the cytoplasm on a free ribosome or at the endoplasmic reticulum (ER) on a bound ribosome.
221
Summarize the steps of translation.
Initiation
The ribosome subunits binds to mRNA at a specific area (called the start codon).
Elongation
The ribosome repeatedly matches tRNA anticodon sequences to the mRNA codon sequence. Each time a new tRNA comes into the ribosome, the amino acid that it was carrying gets added to the elongating polypeptide chain.
Termination
The ribosome hits a stop sequence of mRNA (called the stop codon), then it releases the polypeptide and the mRNA.
222
Define "genetic code."
The genetic code is the rules used by all cells to translate information encoded within genetic material (DNA) into proteins. The code defines how sequences of three mRNA nucleotides, called codons, specify which amino acid will be added next during protein synthesis.
223
Outline the role of messenger RNA (mRNA) in translation.
Messenger RNA (mRNA) carries the genetic information transcribed from DNA in the form of a series of three-nucleotide code ("codon"), each of which specifies a particular amino acid.
224
Outline the role of transfer RNA (tRNA) in translation.
Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next codon of mRNA calls for it. The correct tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a three-base sequence ("anticodon") that can base-pair with its complementary code on the mRNA.
225
Outline the role of ribosomal RNA (rRNA) in translation.
Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into polypeptide chains.
226
Define "codon" as related to translation.
A codon is a three-base sequence (three nitrogenous bases in a row) on mRNA. It codes for a specific amino acid to be brought to the growing polypeptide during translation.
227
Define "redundant" as related to the genetic code.
The genetic code is redundant, meaning more than one codon may specify a particular amino acid. For example, the codons CCC and CCG both code for the same amino acid, proline.
228
Explain how using a 4 letters nucleic acid "language" can code for a "language" of 20 amino acid letters in proteins.
There are 64 possible permutations, or combinations, of three-letter nucleotide sequences that can be made from the four nucleotides. Although each codon is specific for only one amino acid (or one stop signal), the genetic code is described as redundant, because a single amino acid may be coded for by more than one codon.
229
Define "anticodon" as related to translation.
An anticodon is a three-base sequence on tRNA that is complementary to the mRNA codon to which it forms hydrogen bonds.
230
Outline the role of complementary base pairing between mRNA and tRNA in translation.
The incorporation of the correct amino acid into the polypeptide chain depends on a tRNA bringing the correct amino acid to the ribosome.
In order to ensure the correct amino acid, the mRNA codons are recognized by the tRNA anticodon which binds to the appropriate codon by complementary base pairing via hydrogen bonds. Each time a new tRNA comes into the ribosome, the amino acid that it was carrying gets added to the elongating polypeptide chain by the ribosome.
231
State the purpose of PCR.
Polymerase chain reaction (PCR) is a technique used to amplify, or make many copies of, a specific target region of DNA in a test tube.
232
Outline the process of the PCR.
Denaturation
Heat is used to denature a sequence of DNA
Annealing
The temperature is lowered and a primer sequence is added to the reaction mixture. The primer is a short sequence of nucleotides that binds ("anneals") to the DNA and provides a starting point for DNA synthesis.
Extension
Raise the reaction temperatures again so that Taq polymerase can synthesize new strands of DNA, starting from the primer.
This cycle repeats multiple times to create many copies of the original DNA strand.
233
Explain the use of Taq DNA polymerase in the PCR.
Taq DNA polymerase is an enzyme that makes new strands of DNA, using existing strands as templates. It is named after the heat-tolerant bacterium from which it was isolated (Termus aquaticus) which lives in hot springs and hydrothermal vents. Taq polymerase is very heat-stable, meaning it can withstand the high temperatures used in the PCR.
234
Outline uses of the PCR.
The goal of PCR is to make enough copies of the target DNA sequence that it can be analyzed or used in some other way. For instance, DNA amplified by PCR may be sent for sequencing, visualized by gel electrophoresis, or cloned into a plasmid for further experiments. PCR is used in many areas of biology, forensics and medicine.
235
Outline the benefits of using gene transfer technology in the production of pharmaceutical insulin.
Prior to widespread use of gene transfer technology, insulin for diabetes was isolated from pig pancreases. Some benefits of using gene transfer technology to produce insulin are:
Biotechnologically produced insulin is indistinguishable from human insulin produced in the pancreas and is therefore less likely to cause allergic reactions in diabetics.
Large quantities of insulin can be produced at the same time.
The ethical issues for diabetics who could not use pig's insulin because of religious beliefs or vegetarianism are overcome.
This form of insulin is absorbed more rapidly than animal derived insulin thus showing its effectiveness in a shorter duration.
236
Define "universal" as related to the genetic code.
With minor exceptions, all life uses the same genetic code.
237
Summarize the process for production of human insulin in bacteria.
Recombinant DNA technology has made it possible to insert a human gene into the DNA of a common bacterium. This "recombinant" bacteria will produce the protein encoded by the human gene because the genetic code is universal.
Scientists build the human insulin gene in the laboratory. Then they remove a plasmid from the bacteria insert the human insulin gene into the plasmid.
The "recombinant" plasmid is returned to the bacteria. The "recombinant" bacteria are put in large fermentation tanks where they repeatedly divides and use the insulin gene to begin producing human insulin.
The insulin is then harvested from the bacteria, purified and used as a medicine for people.
238
Use a genetic code table to deduce the mRNA codon(s) given the name of an amino acid.
If given the amino acid name and asked to find the mRNA codon(s) by which it is coded:
Find the amino acid name in the genetic code table and the corresponding mRNA codons.
For example: the amino acid PHE is coded for by UUU and UUC.
239
Use a genetic code table to deduce amino acid given an mRNA codon sequence.
If given the mRNA codon and asked to find the amino acid for which it codes:
Find the mRNA codon in the genetic code table and the corresponding amino acid.
For example: The mRNA codon CCG codes for the amino acid PRO.
240
Use a genetic code table to deduce amino acid given an tRNA anticodon sequence.
If given the tRNA anticodon, first determine the complementary mRNA codon and then find the mRNA codon in the genetic code table and the corresponding amino acid. Unless otherwise noted, the genetic code table uses mRNA codons!
For example: The tRNA anticodon CCG is the complement to the mRNA codon GGC which codes for the amino acid GLY.
241
Use a genetic code table to deduce amino acid given an DNA antisense sequence.
The antisense DNA is complementary to the mRNA. So if given the antisense sequence, first determine the complementary mRNA codon and then find the mRNA codon in the genetic code table and the corresponding amino acid. Unless otherwise noted, the genetic code table uses mRNA codons!
For example: The antisense DNA TTT is the complement to the mRNA codon AAA which codes for the amino acid LYS.
242
Use a genetic code table to deduce amino acid given an DNA sense sequence.
The sense DNA is the same code as the mRNA, substituting T and U. So if given the sense sequence, determine the mRNA codon and then find the mRNA codon in the genetic code table and the corresponding amino acid. Unless otherwise noted, the genetic code table uses mRNA codons!
For example: The if the sense DNA is ATG then the mRNA codon is AUG which codes for the amino acid MET.
243
Compare dispersive, conservative and semi-conservative replication.
Semi-conservative model
Two parental strands separate and each makes a copy of itself. After one round of replication, the two daughter molecules each comprises one old and one new strand.
Conservative model
The parental molecule directs synthesis of an entirely new double-stranded molecule, such that after one round of replication, one molecule is conserved as two old strands.
Dispersive model
Material in the two parental strands is distributed more or less randomly between two daughter molecules.
244
Outline the method used in the Meselson and Stahl experiment.
1. Grow bacteria in a medium with "heavy" nitrogen (N15) so all the DNA contains heavy nitrogen to start.
2. Transfer some bacteria to "light" nitrogen (N14), bacterial growth continues and with each cell division cycle the light nitrogen incorporates into the DNA.
3. Take samples of bacteria after each round of replication (about 20 minutes).
4. Centrifuge the samples. The DNA with heavy and/or light nitrogen separate into different bands within the tube.
245
Explain how the Meselson and Stahl experiments suggested DNA replication was semiconservative.
After two generations of replication, half of the DNA was of intermediate density and have of the DNA was light only. There was no heavy-only DNA.
This pattern could only have been observed if each DNA molecule contains a template strand from the parental DNA; thus DNA replication is semiconservative.
246
Define "cell respiration."
Cellular respiration is a series of metabolic reactions that convert biochemical energy from organic molecules into adenosine triphosphate (ATP), and then release waste products.
247
State the reaction for cellular respiration.
Cellular respiration is the chemical reaction in which glucose and oxygen are turned into water, carbon dioxide, and ATP energy. In the reaction, glucose and oxygen are reactants, while water, carbon dioxide, and energy (ATP) are products.
248
State the types of organic compounds used in cellular respiration by animals and plants.
The main organic compound used for cellular respiration is the carbohydrate glucose, although lipids and proteins can also be used if glucose is not readily available to the cell.
249
State three example uses of ATP in the cell.
ATP is an energy-rich molecule that can be used throughout the cell to *power active transport, synthesize polymers , and move structures within the cell. In addition, many enzymes require ATP to catalyze reactions within the cell that would otherwise proceed very slowly.
250
Outline energy transfer in the formation and use of ATP.
Energy is released when a phosphate group is removed from ATP in a hydrolysis reaction.
The reverse reaction (which is what happens in cellular respiration) regenerates ATP and requires energy input.
251
Outline the role of NADH in cellular respiration.
The NADH molecule is an electron carrier. In cellular respiration, electrons are removed from glucose and transferred to other molecules.
252
State reasons why cellular respiration must be continuously performed by all cells.
1. ATP can not be stored for later use.
2. ATP can not be transferred from cell to cell.
3. When ATP is used in cells heat energy is released. This heat energy can not be reused and will be lost to the environment.
253
Outline how the structure of ATP relates to its function.
ATP is an RNA nucleotide with three phosphates. Ribose is attached to the nitrogenous base adenine and to the chain of three phosphates.
ATP is made unstable by the three adjacent negative charges in the phosphates, which "want" to get away from each other. Energy is released when one of these bonds is broken in a hydrolysis reaction.
254
Define "anaerobic respiration."
Anaerobic respiration is a type of cellular respiration that does not use oxygen.
255
List situations in which anaerobic respiration is useful.
Anaerobic respiration can act as a backup when cellular oxygen is depleted. For example, when muscle cells use up oxygen faster than it can be replenished, the cells start to perform anaerobic respiration in order to keep muscles moving.
Anaerobic respiration is used when ATP is needed quick, because anaerobic respiration is more rapid than aerobic respiration.
Anaerobic metabolism allows microbes to inhabit low-oxygen or oxygen-free environments which allows them to exploit an otherwise empty habitat.
256
Outline the anaerobic respiration reaction performed by yeasts.
First, in glycolysis, glucose is broken down to pyruvate and NADH and ATP are created.
Then, in alcohol fermentation, pyruvate is converted to ethanol. Carbon dioxide is released and NADH is recycled into NAD+.
The reaction nets two molecules of ATP.
257
Outline the anaerobic respiration reaction performed by humans.
First, in glycolysis, glucose is broken down to pyruvate and NADH and ATP are created.
Then, in lactic acid fermentation, pyruvate is converted to lactic acid. NADH is recycled into NAD+.
The reaction nets two molecules of ATP.
258
State the location of anaerobic respiration in the cell.
Anaerobic respiration occurs in the cell cytoplasm.
259
Compare the total amount of ATP made from anaerobic and aerobic respiration.
Anaerobic respiration produces a net of 2 ATPs per molecule of glucose.
Aerobic respiration produces up to 38 ATPs per molecule of glucose.
260
State the location of aerobic respiration in the cell.
Aerobic respiration occurs in the cell mitochondria.
261
Outline how anaerobic respiration in yeast is used in baking and brewing.
Anaerobic respiration in yeast is used during brewing and bread-making:
glucose → ethanol + carbon dioxide
Ethanol is the alcohol found in alcoholic drinks like beer and wine. In bread-making, bubbles of carbon dioxide gas expand the dough and help the bread rise.
262
Outline how anaerobic respiration in yeast is used to make ethanol bio-fuel.
Bioethanol is a fuel produced by yeast alcohol fermentation of sugarcane or corn in large scale fermentors.
Enzymes are used to break down starch and cellulose into glucose and then yeast carry out anaerobic respiration using the glucose; producing ethanol.
263
State the condition in which humans would perform anaerobic respiration.
When exercising at high intensity, cell demand will exceed available supplies of O2. Muscle cells will start breaking down glucose anaerobically to supply ATP rapidly for a short period of time.
Red blood cells do not have mitochondria, so anaerobic respiration always happens.
264
Outline production of lactate in humans during anaerobic respiration.
In lactic acid fermentation NADH produced in glycolysis transfers its electrons directly to pyruvate, generating lactate as a byproduct.
265
Define "respirometer."
A respirometer is any measuring tool used to determine the cellular respiration rate of an organism by measuring the rate use of O2 or production of CO2.
266
Outline the use of a respirometer to measure cellular respiration rate.
The living specimen (i.e. germinating seeds or invertebrate) is enclosed in a sealed container.
Oxygen use or carbon dioxide production can be measured directly with a data logger.
Alternatively, changes in pressure can be measured. If KOH is included in the sealed container, the CO2 that is produced during cellular respiration will combine with it to form a solid precipitate (K2CO3), removing CO2 gas from the container. Since O2 is being used up and CO2 gas is precipitating, there is less gas in the system and the pressure will decrease. The change in pressure can be measured with a data logger or U-tube manometer.
267
State how changes in CO2 and/or O2 levels can be measurements of cellular respiration.
Increasing carbon dioxide levels indicates an increase in respiration (CO2 is a product of aerobic respiration and alcohol fermentation).
Decreasing oxygen levels indicate an increase in respiration (O2 is a requirement for aerobic respiration).
268
List ethical questions that must be considered before using animals in experiments.
One of the important issues in scientific research is to consider ethics in animal experimentation. Regulations and guidelines govern the use of animals, including:.
1. The purpose of the experiment must have some benefit.
2. Overall use of animals should be minimized. Alternative methods should be used if available.
3. Pain and distress must be minimized.
269
Define "photosynthesis."
Photosynthesis is the process by which photoautotrophic organisms convert light energy (usually from the Sun) into chemical energy (glucose).
The photosynthetic process uses light energy to produce glucose from water and carbon dioxide, releasing oxygen gas as a byproduct.
270
State the chemical equation for photosynthesis.
Six molecules of water plus six molecules of carbon dioxide produce one molecule of glucose plus six molecules of oxygen.
271
Define "visible light."
Visible light is the portion of the electromagnetic spectrum that is visible to the human eye.
272
State the relationship between wavelength and energy.
Shorter wavelengths have more energy and longer wavelengths have less energy.
273
State the range of wavelengths that fall within the visible spectrum.
A typical human eye will respond to wavelengths from about 390 to 700 nanometers.
The order of colors in light, arranged from shortest wavelength to longest:
Violet
Blue
Green
Yellow
Organge
Red
274
Define "pigment."
Biological pigments are protein molecules that selectively absorb certain wavelengths of light while reflecting others.
275
State the name and role of the primary pigment used in photosynthesis.
The primary pigment is the most important/predominant pigment in the process of photosynthesis.
The primary pigment found in the chloroplast of photosynthetic cells in plants is Chlorophyll a which absorb blue and red wavelengths of light.
276
State the name and roles of accessory pigments used in photosynthesis.
Pigments used in addition to chlorophyll a are known as accessory pigments. Different pigments respond to different wavelengths of visible light. The use of accessory pigments allows a broader range of wavelengths to be absorbed, and thus, more energy to be captured from sunlight.
Accessory pigment include:
Chlorophyll b - absorbs blue and some yellow-orange light
Carotenoids - absorb violet and blue-green light
277
Explain why plants are green.
Plants look green because of chlorophyll. Chlorophyll absorbs the red, blue, and other wavelengths of light, and it reflects the green back to your eyes, so that is what you see.
278
Outline the role of "photolysis" in photosynthesis.
Photolysis means water splitting. During photosynthesis, light energy is used to split water molecules as represented by the following equation:
2H2O → 4H+ + 4e- + O2
Oxygen (O2) is released as a waste product in this process. The H+ and e- continue on in the photosynthesis light reactions.
279
State that the oxygen produced in photolysis is a waste product of photosynthesis.
In photolysis, water is split, creating oxygen gas as a byproduct.
2H2O → 4H+ + 4e- + O2
The oxygen (O2) is released as a waste product in this process.
280
Summarize the energy conversions that occur during photosynthesis.
In photosynthesis, light energy is converted into chemical energy stored in carbohydrate molecules.
During the light dependent reactions light energy is used to split water. The 4H+ + 4e- formed as a result of the photolysis are used to fuel the formation of two molecules needed for the next stage of photosynthesis: ATP and the electron carrier NADPH.
In the light independent reactions, carbon atoms from CO2 are used to build carbohydrates. This process relies on ATP and NADPH from the light dependent reactions.
281
Explain why the photosynthesis reactions are endothermic.
Photosynthesis is endothermic because an input of energy is required to carry out the process of converting carbon dioxide and water into carbohydrates. The energy for photosynthesis comes from light.
282
Define "limiting factor."
A limiting factor is a variable of a system that can limit the rate of a reaction.
Either the amount of light, temperature or CO2 concentration will limit the rate of photosynthesis. Whichever of the three is furthest from its optimal will be the limiting factor.
283
Explain how temperature can limit the rate of photosynthesis.
Photosynthesis is an enzyme-catalyzed reaction, and like with other enzyme reactions, photosynthesis rate will increase as the temperature is raised until an optimal temperature is reached.
After the optimum, the rate of photosynthesis abruptly declines with further increase of temperature. The decline is because most enzymes involved in photosynthesis rapidly denature at higher temperatures.
284
Explain how light intensity can limit the rate of photosynthesis.
Without enough light, a plant cannot perform photosynthesis because light energy is required in the light dependent reactions.
Increasing the light intensity will increase the rate of photosynthesis. However, at a certain point the photosynthetic rate will plateau. The leveling off is because all available chlorophyll pigments are being used.
285
Explain how CO2 concentration can limit the rate of photosynthesis.
Without carbon dioxide, a plant cannot perform photosynthesis because CO2 is required in the light independent reactions.
Increasing carbon dioxide concentration will increases the rate of photosynthesis.
However, at a certain point the photosynthetic rate will plateau. The leveling off is because all enzymes used in the reactions are being used.
286
State the major groups of organisms that carry out photosynthesis.
Plants, some prokaryotes and algae are capable of performing photosynthesis.
287
Define the "Great Oxidation Event."
The Great Oxygenation Event is defined as the appearance and rise of oxygen gas (O2) in the earth's atmosphere beginning about 2.4 billion years ago. The oxygen is thought to be a result of photosynthesis by prokaryotes called cyanobacteria.
288
Outline evidence for the "Great Oxidation Event."
Banded Iron Formations are layers found in sedimentary rock. The hypothesis is that the banded iron layers were formed as the result of oxygen released by photosynthetic cyanobacteria. The oxygen combined with dissolved iron in Earth's oceans to form insoluble iron oxides, which precipitated out, forming layers on the ocean floor.
289
Describe the "action spectrum" in relation to photosynthesis.
The action spectrum shows is the rate of a photosynthesis plotted against wavelength of light. It shows that blue and red wavelengths of light are most effectively used for photosynthesis.
290
Describe the "absorption spectrum" in relation to photosynthesis.
An absorption spectrum shows the wavelengths of light absorbed by a pigment. Chlorophyll, the most prevalent pigment used in photosynthesis, has a peak absorption between 400 and 500 nm (blue light) and another (smaller) peak between 600 and 700 nm (red light). There is no absorption around 600 nm (green light) as most of this light is reflected.
291
Explain the relationship between the photosynthesis absorption spectrum and action spectrum.
The peaks in the action spectrum showing the rate of photosynthesis correspond to the peak light energy wavelengths that are able to be absorbed by chlorophyll. Since chlorophyll is most effective at absorbing blue and red light, the rate of photosynthesis is also higher with blue and red light.
Differences between the chlorophyll absorption spectrum and the action spectrum are due to absorption by accessory (ie carotene).
Chlorophyll does not absorb green light, so the there is less photosynthesis within the green light wavelengths. This is shown as a dip in the action spectrum.
292
List techniques for measuring the rate of photosynthesis.
There are a few key methods to calculate the rate of photosynthesis. These include:
Measuring the uptake of CO2
-immobilized algae in hydrogen carbonate indicator solution
-monitor the CO2 concentration using a CO2 sensor
Measuring the production of O2
-counting bubbles formed
-measuring water displacement by O2 gas formed
-floating leaf disk
Measuring the increase in dry mass
-harvest plants and record how much mass they have accumulated as a proxy measure for carbohydrate formation
293
Outline the process of paper chromatography.
Paper chromatography is a technique used to separate substances in a mixture based on the
movement of the different substances up a piece of paper by capillary action.
294
Explain why pigments separate during chromatography.
The pigment molecules migrate, or move up the paper, at different rates because of differences in solubility, molecular mass, and variable hydrogen bonding with the chromatography paper.
295
Calculate the Rf value for pigments using pigment chromatography.
The ratio of the distance moved by a pigment to the distance moved by the solvent is a constant,
Rf. Each type of molecule has its own Rf value.
Rf = distance traveled by pigment / distance traveled by solvent
296
Outline why chromatography is used in the study of plant pigments.
Pigments extracted
from plant cells contain a variety of molecules, such as chlorophyll, beta carotene, and
xanthophyll, that can be separated using paper chromatography.
297
Outline the movement of the major plant pigments in chromatography.
Beta carotene is carried the furthest because it is highly soluble in the solvent and because it forms no hydrogen
bonds with the chromatography paper fibers. Xanthophyll contains oxygen and does not travel quite as far with the solvent because it is less soluble than beta carotene and forms some hydrogen bonds with the paper. Chlorophylls are bound more tightly to the paper than the other two, so they travel the shortest distance.
298
Explain the need to control variables in experimental design.
Controlled variables are what is kept the same between experimental groups throughout the experiment. Any change in a control variable in an experiment would invalidate a relationship between the manipulated variable and the responding, thus skewing the results.
299
Define "manipulated (independent) variable."
The manipulated (independent) variable is the variable that is changed in a scientific experiment to test the effects on the responding (dependent) variable.
300
List potential manipulated (independent) variables for experiments about photosynthesis.
Possible manipulated variables include:
-light intensity
-light wavelength
-temperature
-CO2 availability
301
Define "responding (dependent) variable."
The responding (dependent) variable is the variable being measured to test the effect of the manipulated variable in a scientific experiment.
302
List potential responding (dependent) variables for experiments about photosynthesis.
Possible responding variables in a photosynthesis experiment include:
-uptake of CO2
-production of O2
-biomass production
