Hydrogen (H), oxygen (O), carbon (C), and nitrogen (N).

Carbon can form four, nitrogen three, oxygen two and hydrogen one.

Water has the structure:        (+)   (-)   (+)

                                             H —O— H

The bonds between oxygen and each of the two hydrogen atoms are polar, meaning that oxygen, with eight times as many protons as hydrogen, draws the shared electrons closer to its nucleus. Water molecules interact with each other through hydrogen bonds. 

What determines a molecule’s solubility or lack of solubility in water?

For a molecule to dissolve in water (i.e., be hydrophilic), it must be electrically attracted to water molecules. In other words, it must have a sufficient number of polar bonds and/or ionized groups. Nonpolar molecules do not dissolve in water, and are said to be hydrophobic.

What distinguishes a weak acid from a strong acid?

Name the four classes of organic molecules in the body.

What properties are characteristic of lipids?

Steroids: These are composed of four interconnected rings of carbon atoms bound to hydrogen atoms and each other, with a variety of chemical groups attached to different places in the rings.

Describe the linkages between amino acids that form polypeptide chains.

Describe the types of interactions that determine the conformation of a polypeptide chain.

The conformation of a polypeptide is its three-dimensional shape. It is determined by (1) hydrogen bonds between portions of the chain or with surrounding water molecules; (2) ionic bonds between polar and ionized regions along the chain; (3) van der Waals forces between hydrophobic regions of the chain and (4) covalent bonds, called disulfide bonds, between the side chains of the amino acid cysteine (not all polypeptides have disulfide bonds).Hydrogen bonds between the hydrogen linked to the nitrogen in one peptide bond and the oxygen in another occur at regular intervals along the chain and coil it into a helical shape (alpha helix). Hydrogen bonds between peptide bonds running parallel to each other can force a straight structure called a beta sheet.

                Some proteins, called multimeric proteins, consist of more than one polypeptide chain.

DNA and RNA are nucleic acids, deoxyribonucleic acid and ribonucleic acid, respectively. The subunits of both nucleic acids are called nucleotides, and consist of a phosphate group, a sugar (deoxyribose in DNA, ribose in RNA), and one of five possible carbon-nitrogen rings called purine or pyrimidine bases. Nucleotides are linked together by covalent bonds between the sugar and phosphate groups of adjacent subunits.

                The three-dimensional structure of DNA is a double helix, with the two strands held together by hydrogen bonds between a purine base on one chain and a pyrimidine base on the other. RNA consists of a single chain of nucleotides.

The bases in DNA are the purines adenine and guanine and the pyrimidines thymine and cytosine. Adenine binds only to thymine and guanine only to cytosine. 

                RNA can form base pairs with DNA, as above, except that RNA has the pyrimidine uracil instead of thymine. Uracil forms hydrogen bonds with adenine.

Identify the location of cytoplasm, cytosol, and intracellular fluid within a cell.

A eukaryotic cell comprises, within its plasma membrane, a nucleus and everything else—the cytoplasm. Cytoplasm includes cellular organelles other than the nucleus and the fluid cytosol. Intracellular fluid includes cytosol and the fluid within the organelles, including the nucleus.

Describe the orientation of the phospholipid molecules in a membrane.

Phospholipids are amphipathic molecules that align themselves in the membrane in a bimolecular layer such that their hydrophilic region is oriented toward the aqueous border (either the extracellular fluid or the cytosol in the case of the plasma membrane, or the intraorganelle fluid or cytosol in the case of organelle membranes), and their nonpolar fatty acid chains are oriented toward the middle of the membrane.

Desmosomes consist of disks on the cytoplasmic surface of the membrane from which protein fibers extend both into the cytoplasm to attach to the cytoskeleton, and through the membrane to the intercellular space, where they interlock with protein fibers extending from a desmosome in an adjacent cell. They function to “spot weld” cells firmly together, and are important in tissues that are subject to considerable stretching, such as skin.

are formed between cells whose plasma membranes are joined together so that there is no extracellular space between them. Cells bound together in this way (primarily epithelial cells) form barriers to the passage of polar molecules from one side of the tissue to the other. An example is the epithelium lining the small intestine.

are protein channels that pass through the plasma membrane of one cell and bind to similar proteins in an adjacent cell, forming pores that allow for the passage of small molecules and ions directly from one cell to another. These are important when groups of cells must act as a unit, such as cardiac (heart) muscle cells and some smooth muscles.

Describe the location and function of ribosomes.

Ribosomes are the sites for protein synthesis in cells. They are either bound to granular endoplasmic reticulum or free in cytoplasm. Proteins synthesized on free ribosomes are released into the cytosol of the cell. Proteins synthesized on ribosomes associated with endoplasmic reticulum are ultimately secreted by the cell or distributed to other organelles in it.

Contrast the structure and functions of the rough and smooth endoplasmic reticulum.

Endoplasmic reticulum (ER) consists of a network of membranes that enclose an extensive space inside the cell. Granular ER membranes are a network of flattened sacs that have ribosomes attached to their cytosolic surface. They package the proteins synthesized on their attached ribosomes, and direct the packages to the Golgi apparatus for further processing before secretion or distribution to other organelles. Agranular ER membranes are highly branched and tubular, and do not have attached ribosomes. These organelles contain enzymes for fatty acid and steroid synthesis and also store intracellular calcium ion.

What function does the Golgi apparatus perform?

Mitochondria are spherical or elongated, rod-like structures that have both an inner and an outer membrane. The outer membrane is smooth but the inner membrane is folded into sheets called cristae that extend into the inner mitochondrial compartment, the matrix. These organelles are the site of most of the energy production, in the form of adenosine triphosphate (ATP), in the cell.

What functions do lysosomes and peroxisomes perform?

Lysosomes contain acidic fluid and enzymes that can digest bacteria and cell debris that have been engulfed by the cell, or damaged cell organelles. 

Peroxisomes use molecular oxygen to remove hydrogen atoms from various organic molecules and they destroy the toxic hydrogen peroxide formed.

List the three types of filaments associated with the cytoskeleton. Identify the structures in cells that are

       composed of microtubules.

Describe how the genetic code in DNA specifies the amino acid sequence in a protein.

DNA contains four bases—adenine (A), cytosine (C), guanine (G), and thymine (T). The structure of DNA is such that each gene has double chains of thousands of these bases. The code is the sequence of a triplet of bases, with 64 possible triplets. Each triplet codes for an amino acid (except for three “stop” signals). The sequence of such a triplet codes for the primary structure of the protein to be synthesized.

List the four nucleotides found in mRNA.

Adenine ribonucleotide (A), cytosine ribonucleotide (C), guanine ribonucleotide (G), and uracil ribonucleotide (U).

Describe the main events in the transcription of genetic information in DNA into RNA.

An enzyme, RNA polymerase, binds to the promoter region of a gene and separates the two strands of the DNA double helix in the region of the gene to be transcribed. Free ribonucleotide triphosphates base-pair with the deoxyribonucleotides in the template strand of DNA (uracil ribonucleotide pairs with adenine deoxyribonucleotide). The ribonucleotides paired with the strand of DNA are linked by RNA polymerase to form a primary RNA transcript containing a sequence of bases complementary to the template strand of the DNA base sequence.

Exons are regions of primary RNA transcript that code for amino acid sequences. Introns are regions between the exons that do not code for amino acids, and must be spliced out of the primary RNA. This splicing forms a molecule of messenger (m)RNA.

Describe the role of tRNA in protein assembly.

A transfer (t)RNA molecule binds to a specific amino acid and also has an anticodon region that complements a specific codon on mRNA, to which it bonds. Thus, tRNA acts as a link between the amino acid and mRNA.

Describe the events of protein translation that occur on the surface of a ribosome.

After mRNA passes from the nucleus to the cytoplasm, one end of the mRNA binds to the small subunit of a ribosome. Proteins called initiation factors establish an initiation complex, which positions the corresponding tRNA opposite the mRNA codon that signals the start site at which assembly is to begin. Following the initiation process (the slowest step in protein assembly), the protein chain is elongated by the successive addition of amino acids. A ribosome has two binding sites for tRNA. One holds the tRNA that is attached to the first amino acid, and the other holds the tRNA containing the next amino acid to be added to the growing polypeptide chain. Ribosomal enzymes catalyze the formation of a peptide bond between these two amino acids. Following the formation of the peptide bond, the tRNA at the first binding site is released from the ribosome, and the tRNA at the second site is transferred to the first binding site. The ribosome then moves one codon step along the mRNA, and the process described above is repeated until the ribosome reaches a "stop" codon, when the completed protein/peptide is released from the ribosome.

Protein transcription factors activate or repress the transcription of specific genes by binding to regions of DNA that interact with the promoter region of a gene.

Describe the pathway that leads to the secretion of proteins from cells.

After the signal sequence directs the ribosome, mRNA, and emerging protein to the RER, synthesis of the protein is completed. Modifications, such as removal of the signal sequence and the addition of carbohydrates, are made to the protein in the lumen of the ER. The protein is then transported to the Golgi apparatus in a vesicle that buds off of the ER. Further modification and sorting of the protein takes place in the Golgi apparatus. A secretory vesicle containing the protein then buds off and travels to the plasma membrane where exocytosis occurs.

List the three general types of effects that a mutation can have on a cell's function.

The effect of a mutation on cell function depends largely upon the degree to which the protein's function is changed and the role of that protein in the cell. (1) It is possible that the mutation will have no effect on cell function. (2) The mutation may alter cell function slightly, but the cell is still capable of growth and replication. (3) The cell may die

What two factors determine the percent saturation of a binding site?

Allosteric (other shape) proteins have two ligand-binding sites—a functional or active site that, when bound to a functional ligand, carries out that protein’s function, and a regulatory site. Binding of a ligand (called a modulator molecule) to the regulatory site changes the shape of the functional site, thus affecting (increasing or decreasing) its affinity for the functional ligand.

How do molecules acquire the activation energy required for a chemical reaction?

Activation energy is acquired when reactants collide. Increasing the temperature increases the likelihood of reaching activation energy because it increases the speed of molecular movement and thus the energy of impact. Catalysts reduce the activation energy of a reaction.

List five characteristics of enzymes.

An enzyme undergoes no net chemical change as a result of catalyzing a reaction.

1.       The binding of substrate to an enzyme’s active site has all the

characteristics—chemical specificity, affinity, competition, and saturation—of a ligand binding to a protein.

2.       An enzyme increases the rate of a chemical reaction but does not cause a reaction to occur that would not occur in its absence.

3.       An enzyme increases both the forward and the reverse rates of a chemical reaction, and thus does not change the chemical equilibrium that is finally reached. It only increases the rate at which equilibrium is achieved.

4.       An enzyme lowers the activation energy of a reaction but does not alter the net amount of energy that is added to or released by the reactants in the course of a reaction.

38.    What is the difference between a cofactor and a coenzyme?

A cofactor is a modulator molecule that binds to the regulatory site of allosteric enzymes. Cofactors are often trace metals. A coenzyme is an organic molecule that acts as a cofactor except that it participates in the reaction being catalyzed and accepts or donates a few atoms to the substrate. In a subsequent reaction, the atoms are returned to or taken away from the coenzyme so that it is restored to its original form.

From which class of nutrients are coenzymes derived?

Vitamins.

What are the end products of glycolysis under aerobic and anaerobic conditions?

Under aerobic conditions (per molecule of glucose):

2 pyruvate + 2 ATP + 2 NADH+H⁺ + 2 H₂O

Under anaerobic conditions (per molecule of glucose): 2 lactate + 2 ATP + 2 H₂O

Substrates: Acetyl coenzyme A, (amino acid intermediates – mentioned in class but not studied in detail)

        Products: 2 CO₂ per molecule of coenzyme A, some intermediates used to synthesize amino acids and other organic molecules.

Why does the Kreb’s cycle operate only under aerobic conditions even though molecular oxygen is not used in any of its reactions?

44.    Identify the molecules that enter the oxidative phosphorylation pathway and the products that form.

44.    Where are the enzymes for the Krebs cycle located? The enzymes for oxidative phosphorylation? The enzymes for glycolysis?

Krebs cycle: the mitochondrial matrix

Oxidative phosphorylation: inner mitochondrial membrane

Glycolysis: the cytosol

Under aerobic conditions: 38 ATP (ACTUALLY 36 due to the energy required to get the NADHs produced in Glycolysis into the Mitochondria)

                Under anaerobic conditions: 2 ATP

What determines the direction in which net diffusion of a nonpolar molecule will occur?

The net diffusion of nonpolar molecules is dependent only upon their concentration difference across a membrane. The molecule will diffuse from its region of higher concentration to its region of lower concentration.

In what ways can the net solute flux between two compartments separated by a permeable membrane be increased?

By increasing the concentration difference across the membrane, the surface area of the membrane, and/or the membrane permeability constant.

Why are membranes more permeable to nonpolar molecules than to most polar and ionized molecules?

                Nonpolar molecules are soluble in the lipids of membranes and thus diffuse through the lipid portions of the membranes.

Ions diffuse across cell membranes by what pathway?

Ions diffuse across membranes by passing through specific ion channels formed by integral membrane proteins. 

When considering the diffusion of ions across a membrane, what driving force, in addition to the ion concentration gradient, must be considered? 

The (resting) membrane potential. The combination of the ion concentration gradient and the membrane potential is the electrochemical gradient that governs ion diffusion.

The magnitude of flux across a mediated-transport system depends upon the degree of transporter saturation, the number of transporters in the membrane, and the rate at which the conformational change in the transporter occurs.

What characteristics distinguish diffusion from facilitated diffusion? 

Unlike diffusion, facilitated diffusion is a mediated-transport process, i.e., it requires a transporter. Like diffusion, it moves molecules from higher to lower concentration until the two concentrations become equal.

What characteristics distinguish facilitated diffusion from active transport? 

How can the concentration of water in a solution be decreased? 

What change in cell volume will occur when a cell is placed in a hypotonic solution? In a hypertonic solution? 

Hypertonic = a solution with a high concentration of solute particles.

                Hypotonic = a solution with a low concentration of solute particles.

                Isotonic = a solution with an equal concentration of solute particles (in equilibrium)

                * Remember these are relative to cells and tissues or other solutions.