Deck 1: The Facts of Life: Chemistry Is the Logic of Biological Phenomena

Question 1

What Are the Distinctive Properties of Living Systems?

Answer 1

Living systems consist of complex arrangements of molecules that, when organized correctly, can undergo the process of growth, perform metabolism, reproduce (asexually or sexually), and respond to stimuli. Their immense diversity stems from the various possible organizations of these molecules that are capable of performing the tasks mentioned above.
As organisms become more complex, their structures generally undergo further and further specialization to have ideal functionality in performing the certain tasks that each cell and structure is assigned. Organelles are an example of a living system organizing molecules into macromolecules and then combining and arranging these macromolecules into a larger structure with a specified function.
Living systems must acquire energy from an external source in order to sustain life, whether it is from the sun (via photosynthesis) or consuming organic matter.
Reproduction is how an organism propagates its DNA, which is the genetic material.

Question 2

The Principle of Molecular Recognition Through Structural Complementarity
Biomolecules interact with one another through molecular surfaces that are structurally complementary. How can various proteins interact with molecules as different as simple ions, hydrophobic lipids, polar but uncharged carbohydrates, and even nucleic acids?

Answer 2

Proteins interact with other biomolecules through weak chemical forces or non-covalent bonds. The properties of the amino acid side chains that are present in a protein, influence other kinds of molecules, a protein can interact with.
Proteins can interact with simple ions through ionic interactions. Ionic interactions occur between molecules that are oppositely charged, such as if the protein had a negative charge and the ion had a positive charge. Proteins often interact with metal ions through ionic interactions.
Proteins can interact with hydrophobic lipids through hydrophobic interactions and Van der Waals forces. Hydrophobic interactions occur because water tends to exclude hydrophobic segments, such as those containing long carbon-hydrogen chains. These hydrophobic segments clump together away from the water. Van der Waals forces occur between all molecules but are stronger between larger molecules such as proteins and lipids.
Proteins can interact with polar but uncharged carbohydrates through hydrogen bonding. Both carbohydrates and many amino acid side chains contain hydrogen bound to oxygen. These two types of molecules have many potential hydrogen donor and acceptor groups.
Proteins can interact with nucleic acids by any of the above interactions. These interactions provide the protein with structural complementarity to the nucleic acid molecule. The protein recognizes the nucleic acid strand because of the many separate interactions that occur between the protein and the nucleic acid.

Question 3

What Kinds of Molecules Are Biomolecules?

Answer 3

Biomolecules are carbon (C) compounds that predominantly also contain hydrogen (H), oxygen (O), nitrogen (N), and to a lesser degree phosphorus (P) and sulfur (S). All biomolecules contain carbon due to its incredibly diverse ability to form stable covalent bonds with itself and other atoms (H, O, and N especially since atoms with lower atomic weights can form stronger covalent bonds).
The second reason that all biomolecules contain carbon is that, carbon atoms form a tetrahedral structure (capable of a variety of structures) when forming four single bonds to fill its octet. This tetrahedral structure, along with bonds to H, O, and N, allows carbon molecules to form a diverse number of structures.

Question 4

The Properties of Informational Macromolecules
What structural features allow biological polymers to be informational macromolecules? Is it possible for polysaccharides to be informational macromolecules?

Question 5

What Is the Structural Organization of Complex Biomolecules?

Question 6

The Importance of Weak Forces in Biomolecular Recognition
Why is it important that weak forces, not strong forces, mediate biomolecular recognition?

Question 7

How Do the Properties of Biomolecules Reflect Their Fitness to the Living Condition?

Question 8

Interatomic Distances in Weak Forces versus Chemical Bonds
What is the distance between the centers of two carbon atoms (their limit of approach) that are interacting through van der Waals forces? What is the distance between the centers of two carbon atoms joined in a covalent bond? (See Table 1.4)

Question 9

What Is the Organization and Structure of Cells?

Question 10

The Strength of Weak Forces Determines the Environmental Sensitivity of Living Cells
Why does the central role of weak forces in biomolecular interactions restrict living systems to a narrow range of environmental conditions?

Question 11

What Are Viruses?

Question 12

Cells As Steady-State Systems
Describe what is meant by the phrase "cells are steady-state systems".

Question 13

The Biosynthetic Capacity of Cells
The nutritional requirements of Escherichia coli cells are far simpler than those of humans, yet the macromolecules found in bacteria are about as complex as those of animals. Because bacteria can make all their essential biomolecules while subsisting on a simpler diet, do you think bacteria may have more biosynthetic capacity and hence more metabolic complexity than animals? Organize your thoughts on this question, pro and con, into a rational argument.

Question 14

Cell Structure
Without consulting figures in this chapter, sketch the characteristic prokaryotic and eukaryotic cell types and label their pertinent organelle and membrane systems.

Question 15

The Dimensions of Prokaryotic Cells and Their Constituents
Escherichia coli cells are about 2 µm (microns) long and 0.8 µm in diameter.
a. How many E. coli cells laid end to end would fit across the diameter of a pinhead? (Assume a pinhead diameter of 0.5 mm.)
b. What is the volume of an E. coli cell? (Assume it is a cylinder, with the volume of a cylinder given by V= ?r 2 h, where ? = 3.14.)
c. What is the surface area of an E. coli cell? What is the surface-to-volume ratio of an E. coli cell?
d. Glucose, a major energy-yielding nutrient, is present in bacterial cells at a concentration of about 1 mM. What is the concentration of glucose, expressed as mg/ml? How many glucose molecules are contained in a typical E. coli cell? (Recall that Avogadro's number = 6.023 x 10 23.)
e. A number of regulatory proteins are present in E. coli at only one or two molecules per cell. If we assume that an E. coli contains just one molecule of a particular protein, what is the molar concentration of this protein in the cell? If the molecular weight of this protein is 40 kD, what is its concentration, expressed as mg/ml?
f. An E. coli cell contains about 15,000 ribosomes, which carry out protein synthesis. Assuming ribosomes are spherical and have a diameter of 20 nm (nanometers), what fraction of the E. coli cell volume is occupied by ribosomes?
g. The E. coli chromosome is a single DNA molecule whose mass is about 3.0 x 10 9 daltons. This macromolecule is actually a circular array of nucleotide pairs. The average molecular weight of a nucleotide pair is 660 and each pair imparts 0.34 nm to the length of the DNA molecule. What is the total length of the E. coli chromosome? How does this length compare with the overall dimensions of an E. coli cell? How many nucleotide pairs does this DNA contain? The average E. coli protein is a linear chain of 360 amino acids. If three nucleotide pairs in a gene encode one amino acid in a protein, how many different proteins can the E. coli chromosome encode? (The answer to this question is a reasonable approximation of the maximum number of different kinds of proteins that can be expected in bacteria.)

Question 16

The Dimensions of Mitochondria and Their Constituents
Assume that mitochondria are cylinders 1.5 µm in length and 0.6 µm in diameter.
a. What is the volume of a single mitochondrion?
b. Oxaloacetate is an intermediate in the citric acid cycle, an important metabolic pathway localized in the mitochondria of eukaryotic cells. The concentration of oxaloacetate in mitochondria is about 0.03 µM. How many molecules of oxaloacetate are in a single mitochondrion?

Question 17

The Dimensions of Eukaryotic Cells and Their Constituents
Assume that liver cells are cuboidal in shape, 20 µm on a side.
a. How many liver cells laid end to end would fit across the diameter of a pinhead? (Assume a pinhead diameter of 0.5 mm.)
b. What is the volume of a liver cell? (Assume it is a cube.)
c. What is the surface area of a liver cell? What is the surface-to-volume ratio of a liver cell? How does this compare to the surface-to-volume ratio of an E. coli cell? (Compare this answer to that of problem 3c.) What problems must cells with low surface-to-volume ratios confront that do not occur in cells with high surface-to-volume ratios ?
d. A human liver cell contains two sets of 23 chromosomes, each set being roughly equivalent in information content. The total mass of DNA contained in these 46 enormous DNA molecules is 4 x 10 12 daltons. Because each nucleotide pair contributes 660 daltons to the mass of DNA and 0.34 nm to the length of DNA, what is the total number of nucleotide pairs and the complete length of the DNA in a liver cell? How does this length compare with the overall dimensions of a liver cell?
The maximal information in each set of liver cell chromosomes should be related to the number of nucleotide pairs in the chromosome set's DNA. This number can be obtained by dividing the total number of nucleotide pairs calculated above by 2. What is this value?
If this information is expressed in proteins that average 400 amino acids in length and three nucleotide pairs encode one amino acid in a protein, how many different kinds of proteins might a liver cell be able to produce? (In reality livers cells express at most about 30,000 different proteins. Thus, a large discrepancy exists between the theoretical information content of DNA in liver cells and the amount of information actually expressed.)

Question 18

A Simple Genome and Its Protein-Encoding Capacity
The genome of the Mycoplasma genitalium consists of 523 genes, encoding 484 proteins, in just 580,074 base pairs (Table 1.6). What fraction of the M. genitalium genes encodes proteins? What do you think the other genes encode? If the fraction of base pairs devoted to protein-coding genes is the same as the fraction of the total genes that they represent, what is the average number of base pairs per protein-coding gene? If it takes 3 base pairs to specify an amino acid in a protein, how many amino acids are found in the average M. genitalium protein? If each amino acid contributes on average 120 daltons to the mass of a protein, what is the mass of an average M. genitalium protein?

Question 19

An Estimation of Minimal Genome Size for a Living Cell
Studies of existing cells to determine the minimum number of genes for a living cell have suggested that 206 genes are sufficient. If the ratio of protein-coding genes to non-protein-coding genes is the same in this minimal organism as the genes of Mycoplasma genitalium , how many proteins are represented in these 206 genes?
How many base pairs would be required to form the genome of this minimal organism if the genes are the same size as M. genitalium genes?

Question 20

An Estimation of the Number of Genes in a Virus
Virus genomes range in size from approximately 3500 nucleotides to approximately 280,000 base pairs. If viral genes are about the same size as M. genitalium genes, what is the minimum and maximum number of genes in viruses?

Question 21

Intracellular Transport of Proteins
The endoplasmic reticulum (ER) is a site of protein synthesis. Proteins made by ribosomes associated with the ER may pass into the ER membrane or enter the lumen of the ER. Devise a pathway by which:
a. a plasma membrane protein may reach the plasma membrane.
b. a secreted protein may be deposited outside the cell.

Question 22

Biological molecules often interact via weak forces (H bonds, van der Waals interactions, etc.).
What would be the effect of an increase in kinetic energy on such interactions?

Question 23

Proteins and nucleic acids are informational macromolecules. What are the two minimal criteria for a linear informational polymer?