Biology Exam 2 Focus Questions

What is a polymer? What is a monomer? How are biological polymers synthesized? How are they degraded?

A polymer is a molecule that covalently combines multiple simpler subunits. Monomers are the subunits. Biological polymers are synthesized by condensation reactions (also called dehydration synthesis). These reactions release a water molecule from the atoms of the subunits as they are joined. The polymers are degraded by hydrolysis, where a water molecule is added as the subunits are separated.

.What is the structure of a simple sugar? What are some of the familiar simple sugars?

A simple sugar is a carbohydrate, which has a general formula of (CH2O)n. The simple sugar ribose with n=5 is a component of the nucleotides that make RNA (in pure ribose form) and DNA (in modified deoxyribose form). The familiar food sugars glucose, fructose and galactose all have n=6. Several common carbohydrates in foods are disaccharides with two units of n=6. These include sucrose (table sugar) and lactose (milk sugar).

What kinds of atoms are affected by van der Waals bonding? What are the two components of van der Waals bonding? What is the net effect of van der Waals bonding?

All atoms are affected by van der Waals bonding. The two components of van der Waals bonding are an attractive and a repulsive component. The net effect of the two components of van der Waals bonding is to help keep atoms at a most favorable distance. They're not fixed at that distance, but they tend to stay there.

What are example organic acids and bases? How are they affected by changes in pH?

An example organic acid is compounds containing the carboxylic acid functional group (COOH). This group is the neutral COOH at acidic pH and becomes the negativelycharged COO- at basic pH. An example organic base is compounds containing the amine functional group (NH2). This group is the neutral NH2 at basic pH and becomes the positively-charged NH3+ group at acidic pH.

What types of bonds do hydrogen, carbon, nitrogen and oxygen form in biological molecules? How many covalent bonds can each of these elements form?

Carbon, hydrogen, oxygen and nitrogen form covalent bonds. Covalent bonds are the mechanisms that these elements use to form complex biological molecules. The number of covalent bonds each of these elements can make is related to the number of electrons that they need to gain to complete their electron shell. Hydrogen can make one covalent bond, carbon four, nitrogen three, and oxygen two.

What are the health consequences of consuming the various kinds of fatty acids?

Cis unsaturated fatty acids are the healthiest kind. Saturated fatty acids are less healthy. Excess consumption of saturated fatty acids is associated with increased risk for diabetes and heart disease, although more recent evidence suggest they're not so bad if consumption is coupled with a vigorous enough life style that most of the fatty acids are oxidized for energy by your body. Trans unsaturated fatty acids are quite unhealthy. Consumption of trans unsaturated fatty acids ("trans fats") is thought to be responsible for half the heart attacks in the U.S.

What distinguishes the structure and function of DNA versus RNA?

DNA is used to store the genetic information. RNA is used to express it. DNA is usually double-stranded with two strands; each strand is made of one covalently connected polymer, but the two strands are not covalently connected to each other. Instead, the two strands of DNA are held together by hydrogen bonding between the complementary base pairs (AT and CG). RNA can be single-stranded or double-stranded.

How is this basic architectural principle expressed in different types of eukaryotic organisms eukaryotic organisms?

Different types of eukaryotic organisms have generally different types of cells. While there is lots of variation between organisms (and within one organism, see the next question), there a generic cell types for fungi, protists, plants and animals. We examined a generic plant and animal cell in lecture and discussed some of the properties of cells from protists and fungi in the Diversity I lab.

What are the fatty acids and glycerol components of triglycerides?

Fatty acids are components of the triglycerides and phospholipids; fatty acids include a carboxylic acid group at one end, connected to a long chain of methylene (CH2) groups, with a methyl (CH3) group at the other end. Glycerol is a short carbohydrate with 3 carbon atoms and 3 hydroxyl groups.

What are formal charges, oxidation state and partial (or fractional charges)? What is the difference between them? Which overestimates the true charges? Which underestimates it? Which is most accurate?

Formal charges, oxidation sate and partial charges are all ways of understanding the distribution of electrons and charge in a molecule. Formal charges are calculated assuming that the electrons in a covalent bond are evenly split between the two atoms. This results in an underestimate (less extreme values) of the charge on an atom. Oxidation state is calculated assuming that both electrons in a covalent bond go with the more electronegative atom. This results in an overestimate (more extreme values) of the charge on an atom. Partial charges are calculated by formulas that try to estimate the true charge on an atom considering the differences in electronegativity. This results in the most accurate estimate

What are functional groups and how are they useful? What distinguishes a polar from nonpolar functional group?

Functional groups are groups of 2-6 atoms that form modules in making organic molecules. The properties of complex organic molecules can be deduced from the properties of the component modules, the functional groups. A nonpolar functional group has only C and H atoms, while a polar functional group has C or H bonded to N or O.

How does hydrogen bonding arise? How is electronegativity related to hydrogen bonds?

Hydrogen bonding arises when a hydrogen is covalently bonded to a more electronegative atom. This gives the hydrogen a partial positive charge which attracts the partial negative charge on another electronegative atom. This attraction forms a hydrogen bond. The other electronegative atom can be a different molecule or even the same molecule. Electronegativity polarizes the covalent bonds to create regions of partial positive and negative charge, which can then attract each other.

How does hydrogen bonding affect the properties of water?

Hydrogen bonding help gives cohesion to water and helps give it a high boiling point. The fact the hydrogen bonds are reversible allows water to still be a liquid, and not solidify into ice.

If you have a series of organic compounds how can you tell which are more reduced and which are more oxidized?

In a series of organic compounds, the more reduced ones have more hydrogen atoms and fewer (or no) oxygen atoms. These hydrogen atoms are covalently and stably bound to carbon atoms; they cannot be released to make a solution more acidic. The more oxidized organic compounds have fewer (or no) hydrogen atoms and more oxygen atoms.

What is the difference between ionic bonds and covalent bonds?

Ionic bonds involve the complete transfer of one or more electrons to another atom to create stable positive and negatively charged ions. These oppositely charged ions then interact via electrostatic attraction. On the other hand covalent bonds involve the sharing of electrons between two atoms. The electrons are not fully transferred between atoms in a covalent bond, but are shared by both.

What is the relationship between ionic, covalent and noncovalent bonding? How are they related in terms of the energy? What kinds of interactions does noncovalent bonding make? What are the two kinds of noncovalent bonding?

Ionic, covalent and noncovalent bonding represent three different types of bonding. (Noncovalent bonding is not the same as ionic bonding, nor the same as "not covalent".) Noncovalent bonding is much weaker than ionic or covalent bonding. Noncovalent bonding creates effective, but reversible, interactions. The two kinds of noncovalent bonding are van der Waals and hydrogen (or H-) bonding.

What are the characteristics that define life?

Life is defined by a set of characteristics. Life shows complexity and organization, responds to external environment, maintains internal environment (homeostasis), carries out metabolism and growth (particularly an energy metabolism based on ATP), reproduces and maintains heredity, and adapts to environment and evolves. To count as living a cell must do all of these things.

What are lipids?

Lipids are biological nonpolar molecules of several different kinds. Lipids include triglycerides (3 fatty acids attached to a glycerol), phospholipids (2 fatty acids and a phosphate/ modified phosphate attached to a glycerol), and steroids (lipid molecules with 4 rings of C and H atoms and different attachments off the rings).

What is the size range of cells? What are the factors that limit cell size and how do they operate?

Most cover a 1000-fold range in size from 1µm to 1mm. Cells can't be too small or else they won't have enough of essential materials. Cells can't be too large or they won't have enough cell surface to import nutrients and export wastes.

How is this basic architectural principle extended in multicellular eukaryotic organisms?

Multicellular eukaryotic organisms also have specialized cell types within one organism. Different cell types have different functions within an organism and as a result have a different composition and arrangement of compartments (organelles) in each, although the differences between cells here are less dramatic than those between cells in different types of organisms (say, between plant and animal cells).

What distinguishes polar from nonpolar covalent bonds? How is the polarity of bonds related to electronegativity?

Nonpolar covalent bonds involve equal (or nearly equal) sharing of electrons. Polar covalent bonds involve an unequal sharing of electrons. The polarity of bonds can be determined by the electronegativities of the atoms involved. For the purposes of this course an electronegativity difference of < 0.5 makes a bond nonpolar, and an electronegativity difference of > or = 0.5 makes a bond polar.

Organic molecules are characterized by which element and exploit what property of that element? What are the names given to small and large biological molecules? How are the large molecules usually made?

Organic molecules are compounds that include the atom carbon and employ carbon's ability to make 4 covalent bonds to achieve a great variety of molecules. Small biological molecules are called metabolites. Large biological molecules are called macromolecules. Macromolecules are made as polymers of simpler subunits.

What other structures (not envelope, not pores) are found in the nucleus and what do they do (Note: functions for some of them may not have been described in lecture)?

Other structures in the nucleus include: (i) the chromosomes, the long linear molecules of DNA that contain the genetic information (the chromosomes are combined with protein and RNA in a mixture called chromatin); (ii) the nucleolus, the site of rRNA transcription and ribosome formation; (iii) the nuclear lamina, a mesh of proteins that lies immediately underneath the inner bilayer of the nuclear envelope; and (iv) the nuclear matrix, a second mesh of proteins, this one extending throughout the volume of the nucleus.

What are our foods made of? And what determines their properties?

Our foods are mostly made of cells and since cells are mostly made of macromolecules, our food is mostly macromolecules. Thus the properties of the foods are determined by the properties of the macromolecules, including their sequences and how they are digested (hydrolyzed).

What are phospholipids and what is their function? How is their structure related to their function?

Phospholipids are molecules containing 2 fatty acids and a phosphate/modified phosphate attached to a glycerol. Phospholipids are used as the major component of cellular membranes, which are aggregates (irregular associations) of lipids. A phospholipid has a polar head and two nonpolar tails. The phospholipids associate in water to form a bilayer, with the polar head facing water and the nonpolar tails associating together in the center of the bilayer.

What are the structures and function(s) of complex carbohydrates? What distinguishes the different polymers of glucose? Are each of the polymers found in both plants and animals?

Polymers of the simple sugar glucose with n=6 form more complex carbohydrates. The different polymers of glucose are distinguished by different chemical connections between the glucose molecules and whether the polymer is unbranched (cellulose) or branched (starch and glycogen) and the extent of branching (some branching, starch; more branching, glycogen). The functions of complex carbohydrates are structural (cellulose) and energy storage (glycogen and starch). Cellulose and starch are found in plants (cellulose is the most common biological molecule on earth), while glycogen is found in animals. Starch is used for energy storage in plants, such as the starch that supplies energy to the seeds in a potato, while glycogen provides short term energy storage in animals, such as when we sleep.

What are the major categories of biological macromolecules and what monomers are they made of?

Polypeptides (one or more polypeptides are called proteins) are made of amino acids. Nucleic acids are made of nucleotides. Triglycerides (and phospholipids) are made of fatty acids linked to glycerol (with a phosphate group in a phospholipid). Complex carbohydrates are made of (simple) sugars.

How is the plant cell wall different from the prokaryotic cell wall and the fungal cell wall?

Prokaryotic cells have a cell wall of peptidoglycan (a combination of carbohydrate polymers and short polypeptides), while plant cell walls are made of cellulose, a polymer of glucose. Fungal cell walls are made of chitin.

Describe the basic structure of a prokaryotic cell. What organelles are found in prokaryotic cells?

Prokaryotic cells have a cell wall of peptidoglycan outside of a plasma membrane. Inside the membrane there is a cytoplasm and a loosely organized nucleoid that contains the DNA. Prokaryotic cells do not have any membrane-bound organelles, but they do have ribosomes that are the site of protein synthesis. The ribosomes of prokaryotic and eukaryotic cells are similar, but not identical.

What is the diversity of prokaryotic cells? How are prokaryotic cells the dominant forms of life on earth?

Prokaryotic cells include 2 of the 3 domains of life, bacteria and archaea. Prokaryotic cells have the greatest number of cells and the greatest biomass. Prokaryotic cells grow in the greatest diversity of environments. Prokaryotic cells also have a dominant effect on the overall biosphere, producing oxygen for the atmosphere and fixing nitrogen and carbon dioxide from the atmosphere, incorporating them into other molecules. Prokaryotes thus provide the base for all other forms of life.

What is the difference between proton transfer (acid-base) reactions and electron transfer (redox) reactions?

Proton transfer (acid-base) reactions transfer protons (also known as hydrogen ions, H+) between molecules. These are happening all the time (very rapidly) inside cells (they have a very low activation energy barrier, more on that later), but especially with changes in pH. Electron transfer (redox) reactions result from the transfer of electrons between molecules. These reactions happen much less readily and more slowly (larger activation energy barrier), generally involve the making or breaking of covalent bonds, and usually require either biological catalysts (enzymes) or special sets of molecules (electron transport chains, more on them later also).

What is reduction and what is oxidation? How is reduction always coupled to oxidation?

Reduction is the gain of electrons, while oxidation is the loss of electrons. Since electrons are conserved (they're not usually created or destroyed), if one atom is oxidized and loses an electron, then another atom must gain that electron and become reduced.

.What is the difference between fats that are solid at room temperature and oils that are liquid at room temperature?

Saturated fatty acids have only single bonds between carbon atoms. They are fully saturated for hydrogen atoms; no more hydrogens can be added to these molecules. Triglycerides with mostly saturated fatty acids are solid at room temperature, and usually called fats. Triglycerides that are liquid at room temperature have mostly unsaturated fatty acids. These molecules are called fats or oils. Unsaturated fatty acids have some double bonds between carbon atoms. They are not fully saturated for hydrogen atoms; more hydrogen atoms could be added to them.

What is the self-ionization of water? How is self-ionization related to acids and bases?

Self-ionization is the formation of H+ and OH- ions from neutral water molecules. It goes on spontaneously, but only a small portion of the molecules are ionized at any given time. The product of the concentration of H+ ions and OH- ions is always fixed at 10-14, [H+][OH-]=10-14. Acids and bases are solutes in water that alter the amounts of H+ and OH- ions. However, the 10-14 product stays fixed. Whenever an acid increases the concentration of H+ ions, the concentration of OH- ions goes down by a proportionate amount.

What is the basic architectural principle seen in eukaryotic cells?

The basic architectural principle of eukaryotic cells is compartmentalization and specialization. Eukaryotic cells have a number of different compartments (organelles, usually membrane-bound) for performing specialized functions. The membrane-bound compartments help to isolate specific conditions for the functions of each compartment, but they also create a need for transporting materials between compartments.

What is the structure of the basic monomer used to make polypeptides/proteins? How many different monomers are used to make polypeptides? How are the different monomers organized into a few basic types?

The basic monomer used to make polypeptides/proteins is the amino acid. The amino acid has a constant backbone and a variable side chain. The backbone consists of an amino group on one end, a carboxylic acid group on the other end, with a central carbon atom (alpha carbon) in the middle. The variable side chain is attached to the central carbon atom. There are 20 different amino acids and each has a distinct side chain. The different side chains include nonpolar, polar and uncharged, polar and charged and special types. Polar and charged can be acidic or basic

How do the two statements that define the cell theory explain the characteristics that define life?

The cell theory states that all living organisms are made of cells and all cells (except the first one or ones) come from pre-existing cells. Cells carry out all the functions that define life, and the fact that cells come from pre-existing cells explains reproduction, heredity, adaptation and evolution.

What is the donor and the acceptor in hydrogen bonding? How do the donor, the hydrogen and the acceptor have to be arranged for a hydrogen bond to form?

The donor is the electronegative atom covalently bonded to the hydrogen. It (and the hydrogen) are said to donate a hydrogen bond to the acceptor, which is the other electronegative atom. The donor, the hydrogen (which is covalently bonded to the donor) and the acceptor all have to be in an approximately straight line to form a hydrogen bond.

What two kinds of bonds are there in unsaturated fatty acids?

The double bond in unsaturated fatty acids can be either cis or trans. The double bonds from natural triglycerides are all cis. Trans fatty acids are made artificially by "partial hydrogenation" of cis fatty acids. During this reaction hydrogen is added to some of the natural cis double bonds while other of the natural cis double bonds are converted to trans.

How does the hydrophobic effect arise?

The hydrophobic effect arises because nonpolar molecules do not associate favorably with polar water. Therefore, the nonpolar molecules associate with each other as much as possible and as little as possible with water. This creates effects like droplets of chicken fat in chicken soup and many important phenomena in biology.

What happens to the linear polypeptide polymer after synthesis? What force drives this process and how are the amino acids arranged afterwards?

The linear polypeptide folds into a more compact 3D form after synthesis. This folding is driven by the hydrophobic effect, the tendency of nonpolar molecules to associate with each, away from water. After folding the nonpolar side chains are located inside the folded protein and the polar side chains on the outside.

What is the name of the basic monomer used to make nucleic acids and what is its structure? How many different monomers are there? Which monomers are found in DNA and which are found in RNA? How are the different monomers organized into two kinds and how do the two kinds differ?

The monomer used to make nucleic acids is called a nucleotide. A nucleotide is made of a ribose (or deoxyribose) sugar, a phosphate and a nitrogenous base. There are 5 different monomers. Four of the monomers (A, T, G, and C) with deoxyribose are used to make DNA. Four monomers (A, U, G, and C) with ribose are used to make RNA. The two kinds of monomers are the smaller (1 ring of atoms) pyrimidines and the larger (2 rings of atoms) purines. A and G are purines. T, U, and C are pyrimidines. Remember, "Big AGgies are pure, but small TeChies are pyrates".

What kinds of bonds hold together the monomers in a polypeptide? What are the two ends of the polypeptide called?

The monomers (amino acids) in a polypeptide are held together by amide bonds (that are called peptide bonds). The two ends of the polypeptide are the amino and carboxyl ends that contain the amino and carboxylic acid groups, respectively.

What is the structure of the nuclear envelope? What structures are located in the nuclear envelope and how are they located within it? How does material travel between nucleus and cytoplasm?

The nuclear envelope consists of two membranes, each of which is a lipid bilayer. The envelope is pierced by nuclear pores, which extend through both membranes. The nuclear pores provide a regulated pathway for material to travel between nucleus and cytoplasm.

How are the nucleotides in RNA and DNA assembled into a linear polymer? What are the two ends of the polymer called?

The nucleotides in RNA and DNA are assembled into a linear polymer, a polynucleotide strand, through a backbone of phosphates and sugars, connected by covalent phosphodiester bonds. The two ends of a polynucleotide strand are called 5' and 3'. They have either the 5' carbon or the 3' carbon of a ribose (or deoxyribose) sticking out that end.

What's the importance of the sequence of bases in DNA and RNA?

The sequence of bases, usually written in the 5' to 3' direction, contains the important genetic information that determines heredity, that makes us like are parents, but also distinguishes us from each other and from other species. This information that determines heritable traits is the basis for Evolution by Natural Selection

How many different basic cell architectures are there? How are the two architectures distinguished?

The two different basic cell architectures are prokaryotic and eukaryotic cells. Eukaryotic cells have a distinct nucleus and a series of internal membranes; prokaryotic cells do not. Interestingly, there are no cells that are partway between prokaryotic and eukaryotic.

What are triglycerides and what are their functions?

Triglycerides are 3 fatty acids attached to a glycerol. Triglycerides are used as a dense store of energy, storing much energy in a relatively small mass.

How is pH defined? What is neutral pH and how do acids and bases affect pH?

pH is defined as the -log[H+]. The logarithm is helpful in converting scientific notation with exponents into small numbers, while the - sign, makes the pH scale all positive numbers. Neutral pH is 7; at pH 7 there are an equal number of H+ and OH- ions. Acids increase the proton concentration and thus decrease the pH, while bases decrease the proton concentration and increase the pH.