Topic 2 - Molecular Biology Flashcards
Recognize common functional groups: AMINE.
A nitrogen atom bonded to two hydrogen atoms (-NH2)
Recognize common functional groups: CARBOXYL.
A carbon double bonded to an oxygen (=O) and a hydroxyl (-OH)
Recognize common functional groups: HYDROXYL.
Polar covalent bond between an oxygen and a hydrogen (-OH).
Recognize common functional groups: PHOSPHATE.
A central phosphorus bonded to four oxygen atoms (-PO₄). This functional group has a negative charge.
Outline the number and type of bond carbon can form with other atoms.
Carbon can form four covalent bonds with other atoms.
List the four major classes of carbon compounds used by living organisms.
Carbohydrates
monosaccharides
disaccharides
polysaccharides
Proteins
amino acids
dipeptides
polypeptides
Lipids
fatty acids
sterols
triglycerides
phospholipids
Nucleic Acids
nucleotides
DNA
RNA
Define metabolism.
The chemical processes that occur within a living organism in order to maintain life.
Define catalysis.
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.
Define anabolism.
Constructing larger molecules from smaller subunits.
Define monomer.
A small molecule that can bind with other molecules of the same type to form a large polymer.
Define polymer.
A large molecule composed of many repeating monomer subunits.
Describe condensation (dehydration synthesis) reactions.
A chemical reaction in which two molecules (monomers) combine to form a larger molecule with the formation of water.
Define catabolism.
Catabolism is the breaking down of large molecules into smaller subunits.
Describe hydrolysis reactions.
A chemical reaction in which a polymer breaks apart into smaller subunits; addition of water is used to break the bonds.
Draw the molecular structure of urea.
Describe how urea can be synthesized by living and artificial mechanisms.
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.
Draw the molecular diagram of ribose.
Draw the molecular diagram of alpha-glucose.
Draw the molecular diagram of a saturated fatty acid.
Identify the carboxyl and methyl groups on a fatty acid.
Carboxyl = COOH
Methyl = CH3
Draw the generalized structure of an amino acid.
Label the amine group, carboxyl group, alpha carbon and R group on an amino acid.
Identify a triglyceride from molecular drawings.
Identify a triglyceride from molecular drawings.
Identify a sterol from molecular drawings.
Identify cellulose from molecular drawings.
Polymer of beta-glucose with bonds between carbons 1 and 4 of adjacent molecules
Identify glycogen from molecular drawings.
Polymer of alpha-glucose with many branch points.
Identify amylose from molecular drawings.
Amylose starch is a polymer of apha-glucose with few or no branch points.
Identify amylopectin from molecular drawings.
Amylopectin is a polymer of apha-glucose with some branch points.
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.
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.
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.
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.
Define anion.
A negatively charged ion because it has gained electrons
Define cation.
A positively charged ion because it has lost electrons.
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.
Write the molecular formula for water.
Water is H2O
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.
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.
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.
Define adhesion.
Water molecules bonding to non-water molecules through hydrogen bonding or attraction to an ionic charge.
Define cohesion.
Water molecules attaching to other water molecules through hydrogen bonding.
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.
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.
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.
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.
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.
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.
List the types of molecules that water will dissolve.
Water will dissolve substances that are polar or ionically charged.
List types of molecules that are hydrophilic.
Water is a polar molecule that attracts other polar or ionic substances, making them hydrophilic.
List types of molecules that are hydrophobic.
Nonpolar or non-ionic molecules are hydrophobic.
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.
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).
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.
Define hydrophobic.
A molecule or substance that is NOT attracted to water.
Define hydrophilic.
A molecule or substance that is attracted to water.
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.
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)
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.
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.
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.
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.
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.
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.
State if the following molecule is hydrophobic or hydrophilic: sodium chloride.
Hydrophilic
The ions are able to dissolve in water.
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.
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.
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.
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.
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.
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.
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.
Define monosaccharide.
The simplest form of carbohydrate; “one sugar.”
Define disaccharide.
The sugar formed when two monosaccharides are joined; “two sugar.”
Define polysaccharide.
Long chains of bonded monosaccharides; “many sugars.”
List three examples of monosaccharides.
Glucose (C6H12O6)
Ribose (C5H10O5)
Deoxyribose (C5H10O4)
Fructose (C6H12O6)
Galactose (C6H12O6)
List three examples of disaccharides.
Maltose (glucose + glucose)
Sucrose (glucose + fructose)
Lactose (glucose + galactose)
List three examples of polysaccharides.
Starch: polymer of alpha-glucose (amylose and amylopectin)
Cellulose: polymer of beta-glucose
Glycogen: polymer of alpha-glucose
Draw the formation of maltose from two glucose monomers.
Carbon #1 of one glucose binds to carbon #4 of the other glucose
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.
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.
Define “isomer.”
Isomers are molecules that have the same molecular formula but a different arrangement of atoms.
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.
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
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.
State two functions of triglycerides.
-source of energy
-storage of chemical energy
-thermal insulation
-waterproofing
-protection
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”
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.
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.
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.
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.
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.
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
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
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?
Identify carbon, hydrogen and oxygen atoms by color in molecular visualization software.
Carbon = black
Hydrogen = white
Oxygen = red
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.
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.
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
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.
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.
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.
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.
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
Define dipeptide.
A molecule containing two amino acids joined by a single peptide bond
Define oligopeptide.
A molecule that contains a relatively small number (2-20) of amino-acids joined by peptide bonds.
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.
Draw the structure of a generalized amino acid.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
