Cell biology chapter 1: a preview of cell biology

Null hypothesis

A statement or idea that can be falsified, or proved wrong.

Model organisms

Study cellular processes directly in living cells and organisms.

Telomeres

Normal cells can only divide about 50 times before undergoing cell death because the ends of their chromosomes.

Myc protein

Normally controls cell growth, overexpression of myc is associated with uncontrolled cell division and cancer.

Cellula

"Little room".

Cell capacity

1.) Grow. 2.) Reproduce. 3.) Specialized.

Cell theory

1.) All organisms consist of one or more cells. 2.) The cell is the basic unit of structure for all organisms. 3.) All cells arise only from preexisting cells.

M. musculus

1.) Mammalian organism with many similarities to humans. 2.) Numerous strains with genetic "knockouts". 3.) Widely used as models for human disease.

Wild-type D. melanogaster

1.) Multicellular eukaryotic organism with a short generation time. 2.) Many mutant strains available with well characterized genetic defects. 3.) Widely used for studies of embryogenesis and development.

C. elegans

1.) Multicellular eukaryotic organism with a short life cycle. 2.) Nearly transparent with cell fates mapped out. 3.) Widely used for cell differentiation and development studies.

Lack's family's raises ethical considerations

1.) Once a blood or tissue sample is removed from your body, is it still yours? Many people believe donated tissue should be used in medical research for the common good. 2.) If the donated tissue is used to develop a commercial product, should the donor be granted a share of the profits? 3.) When a group of scientists published the DNA sequence of HeLa cells without the family's knowledge or permission.

A. thaliana

1.) Rapid life cycle and one of the smallest plant genomes. 2.) Easily mutagenized with thousands of mutant lines available. 3.) Widely used for studies of plant-specific processes.

Factors restricting further understanding the nature of cells in the 1600s

1.) The microscopes of the day had limited resolution. 2.) The descriptive nature of seventeenth-century biology. It was an age of observation, with little thought given to explaining the intriguing architectural details being discovered in biological materials.

E. coli colonies

1.) Unicellular bacterium with short generation time. 2.) Easily mutagenized and transformed to study gene function. 3.) Widely used for gene cloning and protein function.

S. cerevisiae cells

1.) Unicellular eukaryotic cells that are easy to grow in the lab. 2.) Thousands of mutant lines available to study gene function. 3.) Widely used to study the cell cycle and protein-protein interactions.

Cell biology timeline

1600 - Van Leeuwenhoek improves lenses. Hooke described cells in cork slices. 1825 - Wohler synthesized urea in the laboratory. Brown describes nuclei. 1850 - Pasteur links living organisms to specific processes. Development of dyes and strains. Mendel formulated his fundamental laws of genetics. Virchow (every cell comes from a cell). Schleiden and Schwann formulate cell theory. 1875 - Roux and Weissman (chromosomes carry genetic information). Invention of the microtome. Flemming identifies chromosomes. Miescher discovered DNA. 1900 - Buchner and Buchner (demonstrate fermentation with cell extracts). Golgi complex described. Chromosomal theory of heredity is formulated. Rediscovery of Mendel's laws by Correns, von Tschermak, and de Vries. 1925 - Embden and Meyerhof describe the glycolytic pathway. Feulgen develops strain for DNA. Morgan and colleagues develop genetics of Drosophila. Levene postulates DNA as a repeating tetranucleotide structure. 1950 - Avery, MacLeod, and McCarty show DNA to be the agent of genetic transformation. Hershey and Chase establish DNA as the genetic material. Claude isolates first mitochondrial fractions. Krebs elucidates the citric acid cycle. Invention of the electron microscope by Knoll and Ruska. Svedberg develops the ultracentrifuge. 1975 - DNA sequencing methods developed. Heuser, Reese, and colleagues develop deep-etching technique. Berg, Boyer, and Cohen develop DNA cloning techniques. Genetic code elucidated. Palade, Sjostrand, and Porter develop techniques for electron microscopy. Kornberg discovered DNA polymerase. Watson and Crick propose double helix model for DNA. 2000 - Green fluorescent protein used to detect functional proteins in living cells. Allen and Inoue perfect video-enhanced contrast light microscopy. Dolly the sheep cloned. First transgenic animals produced. 2010 - Nanotechnology allows rapid sequencing of entire genomes to become routine. Fluorescence resonance energy transfer (FRET) microscopy used to study molecular interactions. Mass spectrometry used to study proteomes. Human genome sequenced. Motion of myosin molecule "walking" down actin microfilament captured on video. Advanced light microscopes begin to surpass the theoretical limit of resolution. Quantum dots used to improve fluorescent imaging. Yeast two-hybrid systems used to analyze protein-protein interactions. Bioinformatics developed to analyze sequence data. Stereoelectron microscopy used for three-dimensional imaging.

Human papillomavirus (HPV)

A cause of cervical cancer. HeLa cells contain a copy of HPV inserted into the chromosome near the myc gene, causing it to be overexpressed.

Biochemical

A compound made by living organisms could be synthesized in a laboratory just like any other chemical, Wohler helped to dispel the notion that biochemical processes were somehow exempt from the laws of chemistry and physics.

Human Genome Project

A cooperative international effort that began in 1990, involved hundreds of scientists, and established the complete sequence of the human genome by 2003.

Centrifugation

A means of separating and isolating subcellular structures and macromolecules based on their size, shape, and/or density.

Fluorescence microscopy

A powerful method that enables researchers to detect specific proteins, DNA sequences, or other molecules that are made fluorescent by coupling them to a fluorescent dye or binding them to a fluorescently.

DNA cloning

A process used to generate many copies of specific DNA sequence for detailed study and further manipulation and DNA transformation, the process of introducing DNA into cells.

Antibody

A protein molecule produced by the immune system that binds one particular target molecule, known as antigen.

Model organism

A species that is widely studied, well characterized, and easy to manipulate, and has particular advantages, making it useful for experimental studies.

Resolving power

Ability to see fine details of structure, of the microscope. A better microscope might have a resolution of 200 nm, meaning that objects only 200 nm apart can be distinguished from each other.

Peer-reviewed

After scientists have conducted their research and submitted a written article to a journal, the article was examined in detail by several experts in the particular field and found to be sound in methodology, experimental design, and analysis of results.

Proteomic studies

Aim to understand the structure and properties of every protein produced by a genome and to learn how these proteins interact with each other in biological networks to regulate cellular functions.

Genome

All the DNA in one cell of an organism.

Differential interference contrast

Also uses optical modifications to exaggerate differences in refractive index.

Telomerase

An enzyme that allows telomeres to be synthesized anew with each round of cell division.

Microtome

An instrument developed for rapid and efficient preparation of very thin (several um) tissue slices of biological samples.

Compound microscope

An instrument in which one lens (the eyepiece) magnifies the image created by a second lens (the objective). This allowed both higher magnification and better resolution.

Wild type

An organism with unaltered DNA. E.coli, yeast, a mouse, or other model organism.

Theoretical limit of resolution

Approximately half of the size of the wavelength of light used for illumination, allowing maximum magnifications of about 1000-1400X.

S. cerevisiae

Baker's and brewer's - offer several similar experimental advantages. They are unicellular, as well as easy to grow and mutagenize, and well-characterized mutant are available.

Mutagenesis

By chemicals or radiation, scientists have learned much about how eukaryotic cells function.

Omnis cellula e cellula

Cells arose only by the division of other, preexisting cells.

HeLa

Comes from the name of the women from whom the cells were taken.

Mass spectrometry

Commonly used to determine the size and composition of individual proteins. This technique allows researchers to determine the identity and characteristics of individual proteins.

Proteins

Composed of 20 different amino acids.

DNA

Composed of only four different nucleotides

Cytology

Concerned primarily with cellular structure. Cyto- or the suffix -cyte, both of which mean "hollow vessel" and refer to cells.

Central dogma of molecular biology

DNA-transcription-RNA-translation-protein.

Chromatography

Describes a variety of techniques by which a mixture of molecules in solution is separated into individual components. Techniques separate molecules based on their size, charge, or affinity for specific molecules or funcional group.

Ultracentrifuge

Developed by Swedish chemist Theodor Svedberg in the late 1920s. Capable of very high speeds - more than 100,000 revolutions per minute - and can thereby subject samples to forces exceeding 500,000 times the force of gravity.

Phase contrast

Enhances contrast in unstained cells by amplifying variations in refractive index within specimen; especially useful for examining living, unpigmented cells.

Krebs cycle

For energy production.

Glycolysis

For glucose breakdown.

Double helix model

For the DNA structure, which immediately suggested how replication during cell division could occur by precise base pairing between complementary strands.

Green fluorescent protein (GFP)

From the bioluminescent jellyfish Aequorea victoria has become an invaluable tool for studying the temporal and spatial distribution of particular proteins in a cell.

Enzymes

From zyme, a Greek word meaning "yeast". Biological catalyst; protein molecule that acts on one or more specific substrates, converting them to products with different molecular structures.

Recombinant DNA technology

Group of laboratory techniques for joining DNA fragments from multiple sources using the techniques of molecular biology to produce a DNA molecule not found in an organism.

Biochemistry

Helps our understanding of cellular structure and function.

Adenosine triphosphate (ATP)

High-energy compound is the principal energy storage compound in most cells.

Mutant strain

Identical to the wild type except that it lacks one particular gene's function.

Electron microscope

In place of visible light and optical lenses, the electron microscope uses a beam of electrons that is deflected and focused by an electromagnetic field. The wavelength of electrons is so much shorter than the wavelengths of visible light, the practical limit of resolution for the electron microscope is much better - generally about 100 times better than a light microscope, or 2 nm. As a result, the useful magnification of the electron microscope is also much higher - up to 100,000x.

Spiral sickenings

In the cell walls of plant xylem tissue give strength to these water-conducting vessels in wood, and the highly branched cells of a human neuron allow it to interact with numerous other neurons.

Light microscope

Instrument consisting of a source of visible light and a system of glass lenses that allows an enlarged image of a specimen to be viewed. Allowed cytologists to identify membrane-bounded structures such as nuclei, mitochondria, and chloroplasts within a variety of cell types.

Translation

Involves a language change - from the nucleotide sequence of an RNA molecule to the amino acid sequence of a polypeptide chain. A ribosome synthesizes the specific protein encoded by the mRNA.

Genetics

It encodes the tremendous variety of proteins and RNA (ribonucleic acid) molecules responsible for most of the functional and structural features of cells.

Superresolution

Light microscopy methods have been developed that use imaging and computational methods so advanced that they can see beyond the theoretical limit of resolution.

Phase-contrast and differential interference contrast microscopy

Make it possible to see living cells clearly. Both techniques enhance and amplify slight changes in the phase of transmitted light as it passes through a structure having a different density than the surrounding medium.

Independent variable

Many individual conditions can be varied, such as length of treatment or temperature, but it is best to vary, or perturb, only one condition and hold all others constant.

Cell cultures

Many types of cells can be grown in the laboratory outside their tissue of origin - such as skin cells, muscle cells, and cancer cells.

Transfer RNA (tRNA)

Molecules serve as intermediaries that recognize the coded base sequence of an mRNA and bring the appropriate amino acids to the ribosome for protein synthesis.

Brightfield (unstained speecimen)

Passes light directly through specimen; unless cell is naturally pigmented or artificially stained, image has little contrast.

Cloning

Production of genetically identical organisms.

Chromosome theory of heredity

Proposed that the hereditary factors responsible for Mendelian inheritance are located on the chromosomes within the nucleus.

Transcriptomics

RNA sequencing allow us to determine the complete set of genes transcribed in a cell.

Messenger RNA (mRNA)

RNA that is translated into protein because if carries a genetic message from DNA to macromolecular complexes known as ribosomes, where protein synthesis actually takes place. mRNas exit through nuclear pores and bind to cytoplasmic ribosomes.

Transcription

Refers to RNA synthesis using DNA as a template to emphasize that this phase of gene expression is simply a transfer of information from one nucleic acid to another so the basic "language" remains the same. Nuclear DNA directs the synthesis of specific mRNA molecules.

Limit of resolution

Refers to how far apart adjacent objects must be to appear as separate entities. If the limit of resolution of a microscope is 400 nm, objects must be 400 nm apart to be recognizable as separate entities.

Electrophoresis

Refers to several related techniques that use an electrical field to separate macromolecules based on their mobility through a semisolid gel. Different molecules move at different rates depending on their size and charge.

Proteomics

Researchers are attempting to understand the functions and interactions of all of the proteins present in a particular cell.

Resolution (microscopes)

Resolving power. The ability to see fine details of structure. Even van Leeuwenhoek's superior instruments could push this limit only so far.

Scanning electron microscope (SEM)

Scans the surface of the specimen and forms an image by detecting electrons that are deflected from its outer surface.

Fluorescence

Shows the locations of specific molecules in the cell. Fluorescent substances absorb ultraviolet radiation and emit visible light. The fluorescing molecules may occur naturally in the specimen but more often are made by tagging the molecules of interest with fluorescent dyes or antibodies.

Brightfield (stained specimen)

Staining with various dyes enhances contrast, but most staining procedures require that cells be fixed (preserved).

Transmission electron microscope (TEM)

TEM forms an image from electrons that are transmitted through the specimen.

Subcellular fractionation

Technique for isolating organelles from homogenates using various types of centrifugation. Process helps us to study specific parts of the cell, such as the nucleus or specific proteins.

DNA sequencing

Technology used to determine the linear order of bases in DNA molecules or fragments.

Hypothesis

Tentative explanation that can be tested experimentally or via further observation.

Specialized cells

The ability to respond to stimuli and adapt to changes in the environment.

Metabolomics

The analysis of all metabolic reactions happening at a given time in a cell.

Cell

The basic unit of biology. Every organism either consists of cells or is itself a single cell.

Ionomics

The global study of all the ions in a cell.

Chlamydomonas

The green chlorophyll, cell shows that these algae carry out photosynthesis.

Calvin cycle

The most common pathway for photosynthetic carbon metabolism.

Dependent variable

The outcome of the change that is measured (which depends on the independent variable).

Limitation of brightfield microscopy

The specimens must be chemically fixed (preserved), dehydrated, embedded in paraffin or plastic for slicing into thin sections, and stained to highlight otherwise transparent features. Fixed and stained specimens are no longer alive, and therefore features observed by this method could be distortions caused by slide preparation processes that are not typical of the living cells.

Genomics

The study of all the genes of an organism, is providing remarkable insights into cell biology and human health.

Lipidomics

The study of all the lipids in a cell.

Proteome

The total protein content of a cell.

Limitation of fluorescence microscopy

The viewer can focus on only a single plane of the specimen at a time, yet fluorescent light is emitted throughout the specimen, blurring the image.

Chromosomes

Threadlike bodies seen in dividing cells.

Deep-sea thermal vents

Thriving communities of organisms that live around them, none of which depends on solar energy. These organisms depend on energy derived from hydrogen sulfide (H2S) by bacteria, which use this energy to synthesize organic compounds from carbon dioxide.

Angstrom

Used in cell biology when measuring dimensions within proteins and DNA molecules. Equals 0.1 nm, which is about the size of a hydrogen atom.

Confocal

Uses lasers and special optics to focus illuminating beam on a single plane within the specimen. Only those regions within a narrow depth of focus are imaged. Regions above and below the selected plane of view appear black rather than blurry.

Bioinformatics

Using computers to analyze the vast amounts of data generated by sequencing and expression studies on genomes and proteomes.

Cell shapes

Vary is shapes and sizes, ranging from filamentous fungal cells to spiral-shaped Treponema bacteria. Other shapes are diatom and the protozoan.

Visible light

Wavelengths of 400-700 nm, the limit of resolution would be about 200-350 nm.

Reverse transcription

Whereby the viral RNA is used as a template for DNA synthesis - a "backward" flow of genetic information.

Two-hybrid system

Which allows researchers to determine whether and how specific proteins interact within a living cell, has contributed greatly to our understanding of the complex molecular interactions involved in cellular function.

Restriction enzymes

Which have the ability to cleave DNA molecules at specific sequences so that scientists can create recombinant DNA molecules containing DNA sequences from two different sources.

Confocal microscopy

Which uses a laser beam to illuminate just one plane of the specimen at a time.

Digital video microscopy

Which uses video cameras to collect digital images for computer storage.

Brightfield microscopy

White light is passed directly through a specimen that is either stained or unstained and the background (the field) is illuminated.

HeLa cells

Would become the first immortal human cell line and 60 years later are still one of the most widely used human cell lines. Have made an enormous contribution to science; they have been cited in more than 70,000 scientific papers, and they have been instrumental in research on viruses, cancer, and AIDS.

Gene

"Hereditary factor" that specifies an inherited trait; consists of a DNA base sequence that codes for the amino acid sequence of one or more polypeptide chains, or alternatively, for one of several types of RNA that perform functions other than coding for polypeptide chains.

Nanometer

(nm) Is the unit of choice for molecules and subcellular structures that are too small to be seen using the light microscope. A nanometer is one-billionth of a meter (10^-9 m), so it takes 1000 nanometers to equal 1 micrometer. A ribosome has a diameter of about 25 to 30 nm.

Micrometer

(um) Is the most useful unit for expressing the size of cells and organelles. One micrometer is one-millionth of a meter (10^-6 m). One inch equals approximately 25,000 um. Bacterial cells are a few micrometers in diameter, and the cells of plants and animals are 10 to 20 times larger. Organelles such as mitochondria and chloroplasts tend to be a few micrometers in size and are thus comparable in size to whole bacterial cells.

Mitosis

Division process, from the Greek word for "thread".

Ribosomal RNA (rRNA)

Molecules are integral components of the ribosome itself.

Nucleus

Term derived from the Latin word for "kernel".