MCAT Biology Review

Chapter 1: The Cell

Conclusion

Our first chapter introduced the basis of all biology: the cell theory. All living things are made of prokaryotic or eukaryotic cells. Prokaryotes are simpler and do not contain membrane-bound organelles. Eukaryotes contain membrane-bound organelles with highly specialized functions. While eukaryotic organisms (especially humans!) will be the primary focus on Test Day, an understanding of prokaryotic structure and physiology is necessary to understand infection. Viruses are nonliving infectious particles that must invade cells in order to reproduce. Finally, we discussed the smallest infectious particles, prions and viroids.

Our discussions from here on out will focus primarily on eukaryotes, but you will spend significant time in your clinical career battling the pathogens we’ve presented in this chapter. Vaccines are available for a number of bacteria (Bacillus anthracis [anthrax], Corynebacterium diphtheriae[diphtheria], Haemophilus influenzae type B [many upper respiratory and ear infections], Neisseria meningitidis [some cases of bacterial meningitis], Streptoccocus pneumoniae [many cases of bacterial pneumonia], Clostridium tetani [tetanus], and Salmonella typhi [typhoid]) and viruses (varicella zoster virus [chicken pox and shingles], hepatitis A and B viruses, human papillomavirus [HPV], influenza, measles, mumps, pertussis, polio, rabies, rotavirus, rubella, and yellow fever). Those for which we do not have vaccines may be targeted with antibiotic and antiviral therapies; the appropriate pharmacotherapy is almost always predicated on an understanding of the bacterial or viral physiology one is targeting and the known resistance patterns in the local area. In other words, the principles presented in this chapter will show up in your everyday life as a physician; it is important not to just memorize but to understand the content in this chapter.

We’ve discussed one method of cellular reproduction—the division of a bacterial cell into two by binary fission. Eukaryotic cells also must replicate, but use a different process: mitosis. It is to this process, as well as meiosis and the human reproductive system, that we turn our attention in the next chapter.

Concept Summary

Cell Theory

·        The cell theory has four basic tenets:

o   All living things are composed of cells.

o   The cell is the basic functional unit of life.

o   Cells arise only from preexisting cells.

o   Cells carry genetic information in the form of DNA. This genetic material is passed on from parent to daughter cell.

·        Viruses are not considered living things because they are acellular, cannot reproduce without the assistance of a host cell, and may contain RNA as their genetic material.

Eukaryotic Cells

·        Eukaryotes have membrane-bound organelles, a nucleus, and may form multicellular organisms.

·        The cell membrane and membranes of organelles contain phospholipids, which organize to form hydrophilic interior and exterior surfaces with a hydrophobic core.

·        The cytosol suspends the organelles and allows diffusion of molecules through-out the cell.

·        The eukaryotic organelles each serve specific functions:

o   The nucleus contains DNA organized into chromosomes. It is surrounded by the nuclear membrane or envelope, a double membrane that contains nuclear pores for two-way exchange of materials between the nucleus and cytosol. DNA is organized into coding regions calledgenes.

o   The nucleolus is a subsection of the nucleus in which ribosomal RNA (rRNA) is synthesized.

o   Mitochondria contain an outer and inner membrane. The outer membrane forms a barrier with the cytosol; the inner membrane is folded into cristae and contains enzymes for the electron transport chain. Between the membranes is the intermembrane space; inside the inner mitochondrial membrane is the mitochondrial matrix. Mitochondria can divide independently of the nucleus via binary fission; they can trigger apoptosis by releasing mitochondrial enzymes into the cytoplasm.

o   Lysosomes contain hydrolytic enzymes that can break down substances ingested by endocytosis and cellular waste products. When these enzymes are released, autolysis of the cell can occur.

o   The endoplasmic reticulum (ER) is a series of interconnected membranes and is continuous with the nuclear envelope. The rough ER (RER) is studded with ribosomes, which permit translation of proteins destined for secretion. The smooth ER (SER) is used for lipid synthesis and detoxification.

o   The Golgi apparatus consists of stacked membrane-bound sacs in which cellular products can be modified, packaged, and directed to specific cellular locations.

o   Peroxisomes contain hydrogen peroxide and can break down very long chain fatty acids via β-oxidation. They also participate in phospholipid synthesis and the pentose phosphate pathway.

·        The cytoskeleton provides stability and rigidity to the overall structure of the cell, while also providing transport pathways for molecules within the cell.

o   Microfilaments are composed of actin. They provide structural protection from the cell and can cause muscle contraction through interactions with myosin. They also help form the cleavage furrow during cytokinesis in mitosis.

o   Microtubules are composed of tubulin. They create pathways for motor proteins like kinesin and dynein to carry vesicles. They also contribute to the structure of cilia and flagella, where they are organized into nine pairs of microtubules in a ring with two microtubules at the center (9 + 2 structure). Centrioles are found in centrosomes and are involved in microtubule organization in the mitotic spindle.

o   Intermediate filaments are involved in cell–cell adhesion or maintenance of the integrity of the cytoskeleton; they help anchor organelles. Common examples include keratin and desmin.

·        Epithelial tissues cover the body and line its cavities, protecting against pathogen invasion and desiccation. Some epithelial cells absorb or secrete substances, or participate in sensation.

o   In most organs, epithelial cells form the parenchyma, or the functional parts of the organ.

o   Epithelial cells may be polarized, with one side facing a lumen or the outside world, and the other side facing blood vessels and structural cells.

o   Epithelia can be classified by the number of layers they contain: simple epithelia have one layer, stratified epithelia have many layers, and pseudostratified epithelia appear to have multiple layers because of differences in cell heights, but actually have only one layer.

o   Epithelia can be classified by the shapes of the cells they contain: cuboidal cells are cube-shaped, columnar cells are long and narrow, and squamous cells are flat and scalelike.

·        Connective tissues support the body and provide a framework for epithelial cells.

o   In most organs, connective tissues form the stroma or support structure by secreting materials to form an extracellular matrix.

o   Bone, cartilage, tendons, ligaments, adipose tissue, and blood are all connective tissues.

Classification and Structure of Prokaryotic Cells

·        Prokaryotes do not contain membrane-bound organelles; they organize their genetic material in a single circular molecule of DNA concentrated in the nucleoid region.

·        There are three overarching domains of life; prokaryotes account for two of these:

o   Archaea are often extremophiles, living in harsh environments (high temperature, high salinity, no light) and often using alternative sources of energy, like chemosynthesis. They have similarities to both eukaryotes (start translation with methionine, similar RNA polymerases, histones) and bacteria (single circular chromosome, divide by binary fission or budding).

o   Bacteria have many similar structures to eukaryotes, and have complex relationships with humans, including symbiosis and pathogenesis.

o   Eukarya is the only non-prokaryotic domain.

·        Bacteria can be classified by shape:

o   Spherical bacteria are called cocci.

o   Rod-shaped bacteria are called bacilli.

o   Spiral-shaped bacteria are called spirilli.

·        Bacteria can be classified based on metabolic processes:

o   Obligate aerobes require oxygen for metabolism.

o   Obligate anaerobes cannot survive in oxygen-containing environments and can only carry out anaerobic metabolism.

o   Facultative anaerobes can survive in environments with or without oxygen and will toggle metabolic processes based on the environment.

o   Aerotolerant anaerobes cannot use oxygen for metabolism, but can survive in an oxygen-containing environment.

·        The cell wall and cell membrane of bacteria form the envelope. Together, they control the movement of solutes into and out of the cell.

o   Bacteria can be classified by the color their cell walls turn during Gram staining with a crystal violet stain, followed by a counterstain with safranin. Gram-positive bacteria turn purple, while gram-negative bacteria turn pink-red.

o   Gram-positive bacteria have a thick cell wall composed of peptidoglycan and lipoteichoic acid.

o   Gram-negative bacteria have a thin cell wall composed of peptidoglycan and an outer membrane containing phospholipids and lipopolysaccharides.

·        Bacteria may have one, two, or many flagella that generate propulsion to move the bacterium toward food or away from immune cells. Moving in response to chemical stimuli is called chemotaxis. Bacterial flagella contain a filament composed of flagellin, a basal body that anchors and rotates the flagellum, and a hook that connects the two.

·        Prokaryotes carry out the electron transport chain using the cell membrane.

·        Prokaryotic ribosomes are smaller than eukaryotic ribosomes (30S and 50S, rather than 40S and 60S).

Genetics and Growth of Prokaryotic Cells

·        Prokaryotes multiply through binary fission, in which the chromosome replicates while the cell grows in size, until the cell wall begins to grow inward along the midline of the cell and divides it into two identical daughter cells.

·        In addition to the single circular chromosome in prokaryotes, extrachromosomal material can be carried in plasmids. Plasmids may contain antibiotic resistance genes or virulence factors. Plasmids that can integrate into the genome are called episomes.

·        Bacterial genetic recombination increases bacterial diversity.

o   Transformation is the acquisition of genetic material from the environment, which can be integrated into the bacterial genome.

o   Conjugation is the transfer of genetic material from one bacterium to another across a conjugation bridge; a plasmid can be transferred from F+ cells to F cells, or a portion of the genome can be transferred from an Hfr cell to a recipient.

o   Transduction is the transfer of genetic material from one bacterium to another using a bacteriophage as a vector.

o   Transposons are genetic elements that can insert into or remove themselves from the genome.

·        Bacterial growth follows a predictable pattern:

o   The bacteria adapt to new local conditions during the lag phase.

o   Growth then increases exponentially during the exponential (logphase.

o   As resources are reduced, growth levels off during the stationary phase.

o   As resources become insufficient, bacteria undergo a death phase.

Viruses and Subviral Particles

·        Viruses contain genetic material, a protein coat (capsid), and sometimes a lipid-containing envelope.

·        Viruses are obligate intracellular parasites, meaning that they cannot survive and replicate outside of a host cell. Individual virus particles are called virions.

·        Bacteriophages are viruses that target bacteria. In addition to the other structures, they contain a tail sheath, which injects the genetic material into a bacterium, and tail fibers, which allow the bacteriophage to attach to the host cell.

·        Viral genomes may be made of various nucleic acids:

o   They may be composed of DNA or RNA and may be single- or double-stranded.

o   Single-stranded RNA viruses may be positive sense (can be translated by the host cell) or negative sense (a complementary strand must be synthesized using RNA replicase, which can then be translated).

o   Retroviruses contain a single-stranded RNA genome, to which a complementary DNA strand is made using reverse transcriptase. The DNA strand can then be integrated into the genome.

·        Viruses infect cells by attaching to specific receptors, and then either fusing with the plasma membrane, being brought in by endocytosis, or injecting their genome into the cell.

·        The virus reproduces by replicating and translating genetic material using the host cell’s ribosomes, tRNA, amino acids, and enzymes.

·        Viral progeny are released through cell death, lysis, or extrusion.

·        Bacteriophages have two specific life cycles:

o   In the lytic cycle, the bacteriophage produces massive numbers of new virions until the cell lyses. Bacteria in the lytic phase are termed virulent.

o   In the lysogenic cycle, the virus integrates into the host genome as a pro-virus or prophage, which can then reproduce along with the cell. The provirus then leaves the genome in response to a stimulus at some later time and enters the lytic cycle.

·        Prions are infectious proteins that trigger misfolding of other proteins, usually converting an α-helical structure to a β-pleated sheet. This decreases the solubility and degradability of the misfolded protein.

·        Viroids are plant pathogens that are small circles of complementary RNA that can turn off genes, resulting in metabolic and structural derangements of the cell and—potentially—cell death.

Answers to Concept Checks

·        1.1

1.    All living things are made of cells. The cell is the basic functional unit of life. All cells arise from other cells. Genetic information is carried in the form of deoxyribonucleic acid (DNA) and is passed from parent to daughter cell.

·        1.2

1.    The nucleus stores genetic information and is the site of transcription. The mitochondria are involved in ATP production and apoptosis. Lysosomes break down molecules ingested through endocytosis and cellular waste products, and can also be involved in apoptosis. The rough endoplasmic reticulum synthesizes proteins destined for secretion. The smooth endoplasmic reticulum is involved in lipid synthesis and detoxification. The Golgi apparatus packages, modifies, and distributes cellular products. Peroxisomes break down very long chain fatty acids, synthesize lipids, and contribute to the pentose phosphate pathway.

2.    Peroxisomes are dependent on hydrogen peroxide for their functions, so an enzyme deficiency that results in an inability to form hydrogen peroxide would likely result in an inability to digest very long chain fatty acids. These fatty acids would build up in peroxisomes until most of the cellular contents were displaced by oversized peroxisomes. This would ultimately result in cell death.

3.    Microfilaments are composed of actin. Microtubules are composed of tubulin. Intermediate filaments differ by cell type, but include keratin and desmin.

4.    Centrioles consist of nine triplets of microtubules around a hollow center, while flagella consist of nine doublets on the outside, with two microtubules on the inside.

5.    Endothelial cells and α-cells are epithelial cells. Fibroblasts, osteoblasts, and chondroblasts are connective tissue cells.

·        1.3

1.    Archaea are similar to bacteria in that both are single-celled organisms that lack a nucleus or membrane-bound organelles, contain a single circular chromosome, divide by binary fission or budding, and overall share a similar structure. They are similar to eukaryotes in that they start translation with methionine, contain similar RNA polymerases, and associate their DNA with histones.

2.    The three common shapes of bacteria are spherical (cocci), rod-shaped (bacilli), and spiral-shaped (spirilli).

3.     

 

Oxygen Present

Oxygen Absent

Type of Bacteria

Can survive

Can carry out aerobic metabolism

Can survive

Can carry out anaerobic metabolism

Obligate aerobe

Yes

Yes

No

No

Facultative anaerobe

Yes

Yes

Yes

Yes

Obligate anaerobe

No

No

Yes

Yes

Aerotolerant anaerobe

Yes

No

Yes

Yes

4.    Gram-positive bacteria have a thick layer of peptidoglycan and lipoteichoic acid, and contain no outer membrane. Gram-negative bacteria have a thin layer of peptidoglycan, but also have an outer membrane containing lipopolysaccharides and phospholipids.

5.    Eukaryotic flagella contain microtubules composed of tubulin, organized in a 9 + 2 arrangement. Bacterial flagella are made of flagellin and consist of a filament, a basal body, and a hook.

·        1.4

1.    Transformation is the acquisition of genetic material from the environment that can be integrated into the bacterial genome. Conjugation is the transfer of genetic material from one bacterium to another across a conjugation bridge; a plasmid can be transferred from F+ cells to F cells, or a portion of the genome can be transferred from an Hfr cell to a recipient. Transduction is the transfer of genetic material from one bacterium to another using a bacteriophage as a vector.

2.     

Phase

Features

Lag phase

Bacteria get used to environment; little growth during this time

Exponential phase

Bacteria use available resources to multiply at an exponential rate

Stationary phase

Bacterial multiplication ceases as resources are used up

Death phase

Bacteria die as resources become insufficient to support the colony

·        1.5

1.    Viruses do not contain organelles such as ribosomes; therefore, in order to reproduce and synthesize proteins, viruses must infect cells and hijack their cellular machinery.

2.    This description indicates that the virus contains an outer layer of phospholipids with an inner capsid. Within the capsid, there is single-stranded RNA that can be immediately translated to protein by the ribosomes of the host cell.

3.    The nucleic acid enters as single-stranded RNA, which undergoes reverse transcription (using reverse transcriptase) to form double-stranded DNA. This DNA can enter the host genome and replicate with the host cell. The DNA is transcribed to mRNA, which can be used to make structural proteins. This mRNA doubles as the viral genome for new virions. Once new virions are assembled from the structural proteins and mRNA (single-stranded RNA) genome, the virions can be released to infect other cells.

4.    In the lytic cycle, bacteriophages replicate in the host cell in extremely high numbers until the host cell lyses and releases the virions. In the lysogenic cycle, the bacteriophage genome enters the host genome and replicates with the host cell as a provirus. At some point (after exposure to a particular stimulus), the provirus leaves the host genome and can be used to synthesize new virions.

5.    Prions cause disease by triggering a change in the conformation of a protein from an α-helix to a β-pleated sheet. This change reduces solubility of the protein and makes it highly resistant to degradation.

Shared Concepts

·        Biochemistry Chapter 3

o   Nonenzymatic Protein Function and Protein Analysis

·        Biochemistry Chapter 8

o   Biological Membranes

·        Biochemistry Chapter 10

o   Carbohydrate Metabolism II

·        Biology Chapter 2

o   Reproduction

·        Biology Chapter 8

o   The Immune System

·        Biology Chapter 12

o   Genetics and Evolution