The Cell 8e Student Resources

After cells are broken apart, the subcellular constituents are fractionated using different types of centrifugation.

The polymerization of sugars, amino acids, and nucleotides to form polysaccharides, polypeptides, and nucleic acids, respectively, occurs through covalent bonding.

In a chemical reaction, an enzyme lowers the amount of energy required to reach the transition state, allowing the reaction to proceed at an accelerated rate.

In this example, an enzyme brings two substrates together to facilitate their reaction with each other.

Molecules that cross a membrane in an energetically favorable direction do so by passive transport.

Glycolysis is the initial stage in the breakdown of glucose, resulting in two molecules of pyruvate and a net gain of two molecules of ATP.

The citric acid cycle is the central pathway in oxidative metabolism and completes the oxidation of glucose to six molecules of carbon dioxide.

During the light reactions of photosynthesis, energy absorbed from sunlight drives the synthesis of ATP and NADPH, coupled to the oxidation of H20 to 02.

In the Calvin cycle of photosynthesis, six molecules of carbon dioxide are used to generate a molecule of glucose.

A nonpathogenic strain of Pneumococcus can be transformed into a pathogenic strain by taking up DNA fragments from the pathogenic strain and incorporating them into its chromosome.

Through a series of experiments in 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty established that the transforming principle (genetic material) is DNA.

The central dogma of molecular biology, as first stated by Francis Crick, asserts that information flows from DNA to RNA, and then from RNA to protein.

A single base-pair mutation in the coding region of a gene can result in a prematurely terminated polypeptide or in a polypeptide with an incorrect amino acid in its amino acid chain, depending on the particular mutation.

As part of a replication cycle within a host cell, a retrovirus uses the enzyme reverse transcriptase to copy its RNA genome into DNA.

Restriction endonucleases cleave DNA at specific sequences, leaving staggered or blunt ends on the resulting DNA fragments.

A DNA fragment is cloned by being inserted into a vector that replicates in a host cell.

One method of DNA sequencing involves a modified DNA synthesis reaction using chainterminating fluorescent nucleotides, which can be identified by automated detection systems.

The polymerase chain reaction allows the production of millions of copies of a DNA fragment from just one starting DNA molecule.

At high temperatures, the complementary strands of DNA separate, and then when they are cooled, they reform double-stranded molecules as dictated by complementary base pairing.

DNA fragments are separated by size using gel electrophoresis, and then—as part of the Southern blotting technique—they are incubated with a labeled DNA probe to identify specific DNA fragments.

Monoclonal antibodies can be made by inoculating an animal (such as a mouse) with an antigen, providing the animal time to mount an immune response, collecting the B cells from the animal, and then fusing the B cells to long-lived myeloma cells—thereby creating hybridomas that can be tested for the production of useful antibodies.

In next-generation DNA sequencing, millions of templates are sequenced simultaneously, dramatically increasing the speed of sequencing.

DNA microarrays allow expression of tens of thousands of genes to be analyzed simultaneously.

In alternative splicing, the multiple exons of a gene can be joined in different combinations to produce distinct mRNAs and proteins from a single primary RNA transcript.

Helicase, primase, and two molecules of DNA polymerase III carry out the coordinated synthesis of both the leading and lagging strands of DNA at a replication fork.

During B cell development, site-specific recombination joins regions of the immunoglobulin light-chain genes, leading to the production of unique immunoglobulin light chains.

Site-specific recombination between three regions leads to the formation of immunoglobulin heavychain genes.

Transcription is DNA-directed RNA synthesis, catalyzed by the enzyme RNA polymerase.

Eukaryotic cells must process the RNA product of transcription to form a mature, translatable messenger RNA.

Translation is RNA-directed polypeptide synthesis.

By attaching a chain of ubiquitin molecules to a protein, a eukaryotic cell marks the protein for rapid degradation by a protease complex.

Proteins are targeted to or from the nucleus by virtue of having nuclear localization signals or nuclear export signals, respectively, allowing the proteins to be recognized by receptors that direct their transport through the nuclear pore complex.

In mammals, proteins enter the ER primarily by a cotranslational pathway, a process that requires a signal sequence on the newly forming protein.

The Golgi apparatus is composed of flattened membrane-enclosed sacs that receive proteins from the ER, process them, and sort them to their eventual destinations.

A proplastid with inner and outer membranes develops into a mature chloroplast with a third membrane system—the thylakoid membranes.

Actin monomers polymerize to form actin filaments, a process that is reversible and is regulated within the cell by actin-binding proteins.

The thin filaments of skeletal muscle consist of actin filaments decorated with tropomyosin–troponin complexes covering the myosin binding sites.

Tubulin dimers can polymerize as well as depolymerize to assemble or break down microtubules.

Kinesin is a motor protein that moves vesicles and organelles toward the plus ends of microtubules.

The arrival of a nerve impulse at the terminus of a neuron triggers synaptic vesicles to fuse with the plasma membrane, thereby releasing the neurotransmitter.

The sodium and potassium ion gradients across the plasma membrane are maintained by the Na+-K+ pump, which hydrolyzes ATP to fuel the transport of these ions against their electrochemical gradients.

In endocytosis, the plasma membrane pinches off small vesicles or large vesicles (phagocytosis) to take in extracellular materials.

Receptor molecules in the plasma membrane cluster in clathrin-coated pits, become bound to specific macromolecules from outside the cell, and then pinch off in the form of clathrin-coated vesicles.

Cell wall formation in plants requires the synthesis of cellulose chains by enzyme complexes in the plasma membrane.

In endocrine signaling, hormones act on distant target cells; in paracrine signaling, a molecule released from a cell acts on nearby targets; and in autocrine signaling, a cell produces a signaling molecule to which it also responds.

The largest family of cell surface receptors transmits signals inside the cell by activating G proteins, which bind GTP and then activate effector proteins.

In a signal transduction cascade, each enzyme activated at a stage in the cascade may activate numerous molecules of the next enzyme, quickly amplifying the response to the receptor-bound ligand.

The cell cycle of most eukaryotic cells is divided into four discrete phases: M, G1, S, and G2.

During early embryonic cell cycles, the cells do not grow, but instead divide into progressively smaller cells.

Several checkpoints function throughout the cell cycle to ensure that complete genomes are transmitted to daughter cells.

Maturation promoting factor (MPF)—consisting of cyclin B and Cdk1—regulates the transition from G2 to M phase of the cell cycle.

Mitosis is the division of the nucleus. It consists of four phases—prophase, metaphase, anaphase, and telophase—and is followed by the division of the cytoplasm, called cytokinesis.

During cell division, a plant cell divides its cytoplasm by depositing Golgi vesicles containing cell wall precursors at the former site of the metaphase plate, building a larger and larger disk-like structure that grows toward and fuses with the plasma membrane.

Programmed cell death is an active process that usually proceeds by a distinct series of cellular changes known as apoptosis.

Many forms of cell stress activate the intrinsic pathway of apoptosis—a pathway that leads to the release of cytochrome c from mitochondria, the activation of caspase-9, and the subsequent death of the cell.

A cancer begins when one altered cell gives rise to a proliferative cell population, forming a primary tumor from which cells can break away and form secondary tumors elsewhere in the body.

In culture, normal cells proliferate until they reach a certain cell density, but tumor cells continue to proliferate independent of cell density.

Paramecium caudatum feeds on bacteria and other small cells via a deep oral groove that contains compound oral cilia used to draw in food.

Super-resolution microscopy techniques allow the capture of images with a higher resolution than the diffraction limit of visible light.

All proteins are made out of the same twenty amino acids, combined and folded in different ways—this 3D structure is critical for protein function.

Cholesterol molecules in a cell membrane influence the arrangement of the phospholipids in the bilayer.

ATP synthase generates ATP from ADP and phosphate using a rotary mechanism that turns about 150 times every second.

RNA interference (RNAi) is an important process that regulates the activity of genes via small interfering RNAs (siRNAs) and microRNAs (miRNAs).

C. elegans is an important model organism used in the study of molecular and developmental biology.

In DNA replication, both strands of the double helix act as templates for the formation of new DNA molecules, using two different mechanisms.

In E. coli, mismatch repair is facilitated by the lack of methylation on the newly-synthesized DNA strands.

During transcription, DNA is read by RNA polymerase, which produces a complementary RNA strand.

The splicing process removes non-coding regions (introns) from the RNA transcript, leaving only protein-coding regions in the final mRNA.

Epigenetic regulation of gene expression includes a number of different types of modification to the chromatin.

In translation, mRNA is decoded by a ribosome to produce a specific amino acid sequence—a protein.

Computer simulations of the complexities of protein folding have provided important insights into the process.

Alzheimer's disease is characterized by the formation of beta amyloid plaques and neurofibrillary tangles, which impede neuronal communication.

The nuclear pore complex consists of an assembly of spokes attached to rings surrounding a central channel.

Proteins pass through the nuclear pore complex by a selective transport process.

Proteins are transported from the ER to the Golgi apparatus and from the Golgi to the plasma membrane.

Transport vesicles bud from the trans-Golgi network and deliver their secretory cargo to their destinations.

After processing in the Golgi apparatus, proteins are transported to the plasma membrane.

Transport vesicles move between the ER, Golgi, and cell membrane along cytoskeletal filaments.

In most cells, mitochondria exist as part of a large interconnected network.

Continual fusion and fission events remodel the mitochondrial network and modify morphology and function.

Chloroplasts are responsible for the photosynthetic conversion of CO₂ to carbohydrates.

Lamellipodia are sheetlike extensions at the leading edge of fibroblasts.

Cell movement across a surface involves extension of the leading edge, attachment, and retraction.

The formation of lamellipodia during cell movement is based on the assembly and disassembly of actin filaments.

Vesicles are transported through the cytoplasm along microtubules by kinesin and dynein.

Microtubules and associated motor proteins move mitochondria within the cell.

Cilia cover the surface of some protozoans and are responsible for cell motility and directing food particles into the oral cavity.

Flagella are used for locomotion by a variety of protozoans and by sperm.

In animals, the coordinated motion of cilia can move fluid or mucus over a surface.

The plasma membrane is composed of a fluid lipid bilayer.

Lipid rafts are small, transient, semisolid patches in the plasma membrane composed of cholesterol and sphingolipids.

A clathrin-coated pit first forms on the surface of the membrane, then buds and pinches off inside the cell, forming the vesicle.

Focal adhesions are large protein complexes through which mechanical force and regulatory signals are transmitted between the extracellular matrix and an interacting cell.

The dynamic assembly and disassembly of focal adhesions plays a central role in cell migration.

Cadherins are transmembrane proteins essential for cell–cell adhesion and are dependent on calcium ions to function.

Receptor tyrosine kinases bind many polypeptide growth factors, cytokines, and hormones to initiate signal transduction.

Mitosis and cytokinesis together define the mitotic phase of an animal cell cycle.

Fission yeast divide by medial fission to produce two daughter cells of equal sizes, which makes them a powerful tool in cell cycle research.

Mitosis is the most dramatic stage of the cell cycle, corresponding to the separation of daughter chromosomes and usually ending with cell division.

During mitosis, the chromosomes condense, the nuclear envelope breaks down, the cytoskeleton forms the mitotic spindle, and the chromosomes move to opposite poles.

The spindle assembly checkpoint monitors the alignment of chromosomes on the metaphase spindle.

During metaphase, the chromosomes align in the center of the spindle, and at anaphase, the sister chromatids separate and move to opposite poles of the spindle.

Cells differentiate into a wide range of cell types, including blood cells, epithelial cells, adipocytes, vascular smooth muscle cells, nerve cells, and even beating heart muscle cells.

Methods have been developed to direct the differentiation of both mouse and human embryonic stem cells into various types of neurons.

Somatic cell nuclear transfer is used to produce clones of cells with the same genetic background as the donor nucleus.

Programmed cell death is an active process which usually proceeds by a distinct series of cellular changes known as apoptosis.

The cell surface receptor Fas plays important roles in controlling cell death in the immune system.

Rather than responding appropriately to the signals that control normal cell behavior, cancer cells grow and divide in an uncontrolled manner.

Tumor cells migrate over one another and grow in a disordered, multilayered pattern.

The disruption of tumor suppressor gene expression causes the cancerous cell to divide when it should not.

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Animation 1.1 Subcellular Fractionation

Animation 2.1 Bond Formation

Animation 2.2 Catalysts and Activation Energy

Animation 2.3 Enzyme-Catalyzed Reactions

Animation 2.4 Passive Transport

Animation 3.1 Glycolysis

Animation 3.2 The Citric Acid Cycle

Animation 3.3 The Light Reactions

Animation 3.4 The Calvin Cycle

Animation 4.1 Bacterial Transformation

Animation 4.2 Avery, MacLeod, & McCarty

Animation 4.3 The “Central Dogma”

Animation 4.4 DNA Mutations

Animation 4.5 HIV Reproduction

Animation 4.6 Restriction Endonucleases

Animation 4.7 Recombinant DNA Molecules

Animation 4.8 Sequencing a DNA Strand