Biology Articles

Cheat Sheet / Updated 03-25-2022

Biology is the study of life, from tiny bacteria to giant redwood trees to human beings. Understanding biology begins with knowing some of the basics, such as eukaryotic cell structure and common Latin and Greek roots that will help you decipher the sometimes-tough vocabulary.

Cheat Sheet / Updated 02-25-2022

Biology is the study of the living world. All living things share certain common properties: They are made of cells that contain DNA; they maintain order inside their cells and bodies; they regulate their systems; they respond to signals in the environment; they transfer energy between themselves and their environment; they grow and develop; they reproduce; they have traits that have evolved over time.

Cheat Sheet / Updated 02-24-2022

Studying molecular and cell biology can be challenging, but it’s necessary if you want to pursue microbiology, biotechnology, or genetics. Understanding molecular and cell biology entails knowing the four groups of macromolecules; the processes of central dogma and cellular respiration; and essential components of eukaryotic cells.

Cheat Sheet / Updated 02-23-2022

To estimate sample size in biostatistics, you must state the effect size of importance, or the effect size worth knowing about. If the true effect size is less than the “important” size, you don’t care if the test comes out nonsignificant. With a few shortcuts, you can pick an important effect size and find out how many subjects you need, based on that effect size, for several common statistical tests. All the graphs, tables, and rules of thumb here are for 80 percent power and 0.05 alpha (that is, the sample size you need in order to have an 80 percent chance of getting a p value that’s less than or equal to 0.05). If you want sample sizes for other values of power and alpha, use these simple scale-up rules: For 90 percent power instead of 80 percent: Increase N by a third (multiply N by 1.33). For α = 0.01 instead of 0.05: Increase N by a half (multiply N by 1.5). For 90 percent power and α = 0.01: Double N (multiply N by 2).

Cheat Sheet / Updated 02-18-2022

When you're studying microbiology, you need to know the key differences between the three domains of life, how scientists name and classify organisms, and how scientists identify microorganisms.

Article / Updated 04-10-2020

The eukaryotic cells of animals, plants, fungi, and microscopic creatures called protists have many similarities in structure and function. They have the structures common to all cells: a plasma membrane, cytoplasm, and ribosomes. All eukaryotic organisms contain cells that have a nucleus, organelles, and many internal membranes. With all the wonderful diversity of life on Earth, however, you’re probably not surprised to discover that eukaryotic cells have many differences. By comparing the structure of a typical animal cell with that of a typical plant cell, you can see some of the differences among eukaryotic cells. Cell walls, additional reinforcing layers outside the plasma membrane, are present in the cells of plants, fungi, and some protists, but not in animal cells. Chloroplasts, which are needed for photosynthesis, are found in the cells of plants and algae, but not animals. Large, central vacuoles, which contain fluid and are separated from the cytoplasm with a membrane, are found in the cells of plants and algae, but not animals. Centrioles, small protein structures that appear during cell division, are found in the cells of animals, but not plants. Home office: The nucleus The nucleus houses and protects the cell’s DNA, which contains all of the instructions necessary for the cell to function. The DNA is like a set of blueprints for the cell, so you can think of the nucleus as the office where the blueprints are kept. If information from the blueprints is required, the information is copied into RNA molecules and moved out of the nucleus. The DNA plans stay safely locked away. The boundary of the nucleus is the nuclear envelope, which is made of two phospholipid bilayers similar to those that make up the plasma membrane. The phospholipids bilayers of the nuclear envelope are supported by a scaffold of protein cables, called the nuclear lamina, on the inner surface of the nucleus. The nuclear envelope separates the contents of the nucleus from the cytoplasm. The structures within the nucleus are DNA in the form of chromosomes or chromatin: When a cell is about to divide to make a copy of itself, it copies its DNA and bundles the DNA up tightly so that the cell can move the DNA around more easily. The tightly bundled DNA molecules are visible through a microscope as little structures in the nucleus called Most of the time, however, when a cell is just functioning and not about to divide, the DNA is very loose within the nucleus, like a bunch of long, very thin spaghetti noodles. When the DNA is in this form, it is called chromatin. Nucleoli where ribosomal subunits are made: Information in the DNA needs to be read in order to make the small and large subunits needed to build ribosomes. The cell builds the ribosomal subunits in areas of the nucleus called nucleoli. Then, the cell ships the subunits out of the nucleus to the cytoplasm, where they join together for protein synthesis. When you stain cells and look at them under the microscope, nucleoli look like large spots within the nucleus. The DNA plans for the cell are kept in the nucleus, but most of the activity of the cell occurs in the cytoplasm. Because the DNA is separate from the rest of the cell, a lot of traffic crosses back and forth between the nucleus and the cytoplasm. Molecules enter and exit the nucleus through small holes, called nuclear pores, that pass through the nuclear membrane. Groups of proteins organize into little rings that penetrate through the nuclear envelope to form the nuclear pores. The traffic in and out of the nuclear pores include the following: RNA molecules and ribosomal subunits made in the nucleus must exit to the cytoplasm. Proteins made in the cytoplasm but needed for certain processes, such as copying the DNA, must cross into the nucleus. Nucleotides, building blocks for DNA and RNA, must cross into the nucleus so that the cell can make new DNA and RNA molecules. ATP molecules that provide energy for processes inside the nucleus like assembly of DNA molecules. Traffic through the nuclear pores is controlled by proteins called importins and exportins. Proteins that are to be moved into or out of the nucleus have specific chemical tags on them that act like zip codes, telling the importins and exportins which way to move the protein with the tag. The movement of molecules into and out of the cell requires the input of energy from the cell in the form of adenosine triphosphate (ATP). Post office: The endomembrane system The endomembrane system, shown in the following figure, of the eukaryotic cell constructs proteins and lipids and then ships them where they need to go. Because this system is like a large package-shipping company, you can think of it as the post office of the cell. The endomembrane system has several components: The endoplasmic reticulum is a set of folded membranes that begins at the nucleus and extends into the cytoplasm. It begins with the outer membrane of the nuclear envelope and then twists back and forth like switchbacks on a steep mountain trail. The endoplasmic reticulum comes in two types: Rough endoplasmic reticulum (RER) is called rough because it’s studded with ribosomes. Ribosomes that begin to make a protein that has a special destination, such as a particular organelle or membrane, will attach themselves to the rough endoplasmic reticulum while they make the protein. As the protein is made, it’s pushed into the middle of the rough ER, which is called the Once inside the lumen, the protein is folded and tagged with carbohydrates. It will then get pushed into a little membrane bubble, called a transport vesicle, to travel to the Golgi apparatus for further processing. Smooth endoplasmic reticulum (SER) doesn’t have attached ribosomes. It makes lipids — for example, phospholipids for cell membranes. Lipids from the SER may also travel to the Golgi apparatus. The Golgi apparatus looks a little bit like a stack of pancakes because it’s made of a stack of flattened membrane sacs, called cisternae. The side of the stack closest to the nucleus is called the cis face of the Golgi, whereas the side farthest from the nucleus is called the trans Molecules arrive at the cis face of the Golgi and incorporate into the nearest cisterna. Lipids become part of the membrane itself, while proteins get pushed into the middle, or lumen, of the cisterna. The Golgi apparatus constantly changes as new cisternae form at the cis face, and old cisternae are removed from the trans face. As molecules make their journey through this flowing system, they’re modified and marked with chemical tags, so that they’ll get shipped to their proper destination. Vesicles are little bubbles of membrane in the cell and come in several types: Transport vesicles carry molecules around the cell. They’re like the large envelopes that you put your letters in. Transport vesicles travel from the ER to the Golgi and then to the plasma membrane to bring molecules where they need to go. They travel by gliding along protein cables that are part of the cytoskeleton. Lysosomes are the garbage disposals of the cell. They contain digestive enzymes that can break down large molecules, organelles, and even bacterial cells. Secretory vesicles bring materials to the plasma membrane so that the cell can release, or secrete, the materials. Peroxisomes are small organelles encircled by a single membrane. Often, they help break down lipids, such as fatty acids. Also, depending on the type of cell they are in, peroxisomes may be specialists in breaking down particular molecules. For example, peroxisomes in liver cells break down toxins, such as the ethanol from alcoholic beverages. In plants cells, glyoxisomes, a special kind of peroxisome, help convert stored oils into molecules that plants can easily use for energy. Altogether, the endomembrane system works as a sophisticated manufacturing, processing, and shipping plant. This system is particularly important in specialized cells that make lots of a particular protein and then ship them out to other cells. These types of cells actually have more endoplasmic reticulum than other cells so that they can efficiently produce and export large amounts of protein. As an example of how the endomembrane system functions, follow the pathway of synthesis and transport for an exported protein: A ribosome begins to build a protein, such as insulin, that will be exported from the cell. At the beginning of the protein is a recognizable marker that causes the ribosome to dock at the surface of the rough endoplasmic reticulum. The ribosome continues to make the protein, and the protein is pushed into the lumen of the RER. Inside the lumen, the protein folds up, and carbohydrates are attached to it. The protein is pushed into the membrane of the RER, which pinches around and seals to form a vesicle, and the vesicle carries the protein from the RER to the Golgi. The vesicle fuses with the cis face of the Golgi apparatus, and the protein is delivered to the lumen of the Golgi, where the protein is modified. The protein eventually leaves in a vesicle formed at the trans face, which travels to the plasma membrane, fuses with the membrane, and releases the protein to the outside of the cell. The fireplace: Mitochondria The mitochondrion (see the following figure) is the organelle where eukaryotes extract energy from their food by cellular respiration. Mitochondria are like the power plants of the cell because they transfer energy from food to ATP. ATP is an easy form of energy for cells to use, so mitochondria help cells get usable energy. Part of the process that extracts the energy from food requires a membrane, so mitochondria have lots of internal folded membrane to give them more area to run this process. Mitochondria actually have two membranes, the outer membrane and the inner membrane. The inner membrane is the one that is folded back and forth to create more area for energy extraction; the folds of this membrane are called cristae. The outer membrane separates the interior of the mitochondrion from the cytoplasm of the cell. The two membranes of the mitochondrion create different compartments within the mitochondrion: The space between the two membranes of the mitochondrion is the intermembrane space. The inside of the mitochondrion is the Mitochondria also contain ribosomes for protein synthesis and a small, circular piece of DNA that contains the code for some mitochondrial proteins. The ribosomes and DNA of mitochondria resemble those found in bacterial cells. In the kitchen: Chloroplasts Chloroplasts, shown in the following figure, are the place where eukaryotes make food molecules by the process of photosynthesis. Chloroplasts are found in the cells of plants and algae. Like mitochondria, chloroplasts have two membranes, an inner membrane and an outer membrane. In addition, they have little sacs of membranes called thylakoids stacked up in towers called grana. The multiple membranes of the chloroplast divide it into several different spaces: The intermembrane space is between the inner and outer membranes. The central, fluid-filled part of the chloroplast is called the The interior of the thylakoid is another fluid-filled space. Like mitochondria, chloroplasts contain their own ribosomes for protein synthesis and a small, circular piece of DNA that contains the code for some chloroplast proteins. Scaffolding and railroad tracks: The cytoskeleton The structure and function of cells are supported by a network of protein cables called the cytoskeleton, shown in the following figure. These proteins underlie membranes, giving them shape and support, much like scaffolding can support a building. Cytoskeletal proteins run like tracks through cells, enabling the movement of vesicles and organelles like trains on a railroad track. When cells swim by flicking whip-like extensions called cilia and eukaryotic flagella, they’re using cytoskeletal proteins. In fact, you use cytoskeletal proteins literally every time you move a muscle. Cytoskeletal proteins come in three main types, with each one playing a different role in cells: Microfilaments are made of the protein Microfilaments are the proteins that make muscle cells contract, help pinch animal cells in two during cell division, allow cells like amoebae to crawl, and act as railroad tracks for organelles in some types of cells. Microtubules are made of the protein tubulin. Microtubules are the proteins inside of cilia and flagella. They move chromosomes during cell division and act as railroad tracks for the movement of vesicles and some organelles. Intermediate filaments are made of various proteins. They often act as reinforcing proteins. For example, the protein lamin that strengthens the nuclear membrane is an intermediate filament. Likewise, the keratin that strengthens your skin cells and makes them resistant to damage is an intermediate filament. You can easily mix up the words “microtubules” and “microfilaments.” Remember that “microtubules” are made of “tubul-in,” and they’re found in the “tube-shaped” cilia and flagella. (Okay, I’m stretching it on that last bit, but if it helps to remember it. . . .) Motor proteins Actin microfilaments and microtubules are long, cable-like proteins. They partner with motor proteins, proteins that use ATP to “walk” along the cables by repeatedly binding, changing shape, and releasing. Thus, the motor proteins use chemical energy to do cellular work in the form of movement. Several motor proteins work with microfilaments and microtubules: Myosin often acts as a partner to actin. For example, when myosin walks along actin microfilaments in muscle cells, it causes the actin microfilament to slide. The sliding of actin microfilaments is what causes muscle contraction. Myosin also attaches to cellular components, such as chloroplasts in plant cells, and then walks along microfilaments. The movement of the motor proteins causes the cellular components to flow around the cell in a process called cytoplasmic streaming. Dynein partners with microtubules inside of cilia and eukaryotic flagella. When dynein walks along microtubules on one side of a cilium or flagellum, it causes the microtubules to bend. The bending of different parts of cilia and flagella makes them flick back and forth like little whips. Kinesin is another partner with microtubules. One end of the kinesin molecule attaches to vesicles, while the other end walks along the microtubules. The movement of kinesin causes the vesicles to slide along the microtubules like freight cars on a railroad track. Cilia and flagella Cilia and flagella are essentially the same structure, but cilia are typically shorter and more numerous on the surface of the cell whereas flagella are typically longer in length and fewer in number. Cilia are found on cells that make up the surfaces of tissues, such as cells in the respiratory and genital tracts of humans, where the cilia beat to move fluid and materials along the surface. For example, in the human respiratory tract, the beating of cilia moves mucus upward where you can cough it out of the body. Some cells, such as microscopic protists and sperm cells, swim using cilia and flagella. The internal structure of cilia and flagella is distinctive. If you cut a cilium or a flagellum crosswise and look at the circular end with an electron microscope, you’ll see the same pattern of microtubules in in both cilia and flagella, shown in the following figure. The microtubules are grouped in pairs, called doublets, that are similar to two drinking straws laid tightly together side by side. The microtubules appear in a 9+2 arrangement, where nine pairs of microtubules (nine doublets) are arranged around the outside of the circle, while one pair of microtubules is in the center of the circle. Rebar and concrete: Cell walls and extracellular matrices The plasma membrane is the selective boundary for all cells that chooses what enters and exits the cell. However, most cells have additional layers outside of the plasma membrane. These extracellular layers provide additional strength to cells and may attach cells to neighboring cells in multicellular organisms. Typically, these layers are composed of long cables of carbohydrates or proteins embedded in a sticky matrix. The long, cable-like molecules work like rebar in concrete to create a strong substance. Two main types of extracellular layers support eukaryotic cells: Cell walls are extra reinforcing layers that help protect the cell from bursting. Among eukaryotes, cell walls appear around the cells of plants, fungi, and many protists. The primary cell walls of plants and algae are made of cellulose. If the plant is a woody plant, lignin is also present. (Lignin is a complex molecule that hardens the cell walls of plants.) Fungal cell walls are made of chitin. The layer around animal cells is the extracellular matrix (ECM), shown in the following figure. This layer is made of long proteins, such as collagen, embedded in a polysaccharide gel. The ECM supports animal cells and helps bind them together. Animal cells actually attach themselves to the ECM via proteins, called integrins, that are embedded in the plasma membrane. The integrins bind to the actin microfilaments inside the cell and to ECM proteins called fibronectins that are outside the cell.

Article / Updated 04-10-2020

DNA is so small that you can barely see it with an electron microscope — and yet, people have figured out how to read it, copy it, cut it into pieces, sort it, and put it back together in new combinations. When DNA from two different sources is combined together, the patchwork DNA molecule is called recombinant DNA. For example, scientists have combined human genes and DNA from E. coli and then placed the recombinant DNA into E. coli so that the bacterium makes human proteins. Doctors can use these proteins, such as insulin, to treat human diseases. The tools that let scientists manipulate DNA in these amazing ways are called recombinant DNA technology. Cutting DNA with restriction enzymes Bacteria make enzymes called restriction endonucleases, or more commonly, restriction enzymes, that cut strands of DNA into smaller pieces. Bacteria use restriction enzymes to fight off attacking viruses, chopping up the viral DNA so that the virus can’t destroy the bacterial cell. Scientists use restriction enzymes in the lab to cut DNA into smaller pieces so that they can analyze and manipulate DNA more easily. Each restriction enzyme recognizes and cuts DNA at a specific sequence called a restriction site. The restriction enzyme called EcoR1 cuts DNA at the sequence 5'GAATTC3'. If you mix DNA and a restriction enzyme, the enzyme will find all the restriction sites it recognizes and cut the DNA at those locations. Restriction enzymes make cutting and combining pieces of DNA easy. For example, if you wanted to put a human gene into a bacterial plasmid, you’d follow these steps: Choose a restriction enzymes that forms sticky ends when it cuts DNA. Sticky ends are pieces of single-stranded DNA that are complementary and can form hydrogen bonds. Restriction enzymes that form sticky ends cut the DNA backbone asymmetrically so that a piece of single-stranded DNA hangs off each end. For example, the sticky ends shown in the figure have the sequences 5'AATT3' and 3'TTAA5'. A and T are complementary base pairs, so these ends could form hydrogen bonds and thus stick to each other. Cut the human DNA and bacterial plasmids with the restriction enzyme. If you cut a plasmid DNA and human DNA with the same restriction enzyme, all the DNA fragments will have the same sticky ends. Combine human DNA and bacterial plasmids. The two types of DNA have the same sticky ends, so some pieces of plasmid DNA and human DNA will stick together. Thus, some plasmids will end up with a human gene inserted into the plasmid. Use DNA ligase to seal the backbone of the DNA. DNA ligase will form covalent bonds at the cut sites in the DNA, sealing together any pieces of DNA that combined together. Any plasmids that contain human DNA are recombinant. These plasmids could now be inserted into bacterial cells. cDNA with reverse transcriptase Scientists use recombinant DNA technology to combine eukaryotic DNA with that of bacteria and then introduce eukaryotic genes into bacterial cells. However, bacteria can’t use eukaryotic genes to make proteins unless the introns are removed from the eukaryotic genes. Scientists get around this problem by creating intron-free eukaryotic genes in the form of complementary DNA (cDNA). cDNA is made from eukaryotic mRNA that has already been spliced to remove the introns. The following figure shows the steps for making cDNA: Isolate mRNA for the protein you’re interested in. Use the enzyme reverse transcriptase to make a single-stranded DNA molecule that is complementary to the mRNA. Reverse transcriptase is a viral enzyme that uses RNA as a template to make DNA. Use reverse transcriptase or DNA polymerase to make a partner strand for the DNA molecule, creating a finished double-stranded molecule of cDNA. Cloning genes into a library Scientists store the DNA they’re working with in DNA libraries, recombinant DNA molecules that contain the gene of interest. Once a gene is put into a DNA library, DNA cloning makes many identical copies of the gene. To clone a gene into a library, you first need to put the gene into a vector. A vector, such as a plasmid or virus, helps carry DNA into a cell. The following figure illustrates the process for introducing a gene into a vector and then cloning the gene into a library. Using the same restriction enzyme, cut the vector and the DNA containing the gene to be cloned. That way, the vector and the DNA to be cloned will have the same sticky ends. Mix the vector and DNA to be cloned together and add DNA ligase. Some vectors will pick up the genes to be cloned. DNA ligase will form covalent bonds, sealing the genes into the vectors. The vectors that pick up genes are recombinant. Introduce the vector into a population of cells. The vector will be reproduced inside the cells. Once the vector is reproduced, the gene has been cloned. Cloning a gene isn’t the same thing as cloning an organism. Cloning a gene means making many copies of a gene, while cloning an organism means making an organism that is identical to another one (like the sheep Dolly). So, when someone talks about cloning, make sure that you know which version they mean! DNA libraries are recombinant vectors that store genes and keep them handy for scientists. DNA libraries make it easier for scientists to work with DNA they’re interested in, such as DNA from a particular type of cell or organism. Scientists use several types of DNA libraries: DNA libraries contain fragments of DNA inserted into a vector. cDNA libraries contain fragments of cDNA inserted into vectors. Genomic libraries contain DNA fragments that represent the entire genome of an organism. Finding a gene with DNA probes After genes are cloned into a library, scientists use DNA probes to find the vectors that contain specific genes of interest. Probes are pieces of single-stranded DNA that are used to locate a particular DNA sequence (see the following figure). Probes are made with a sequence that’s complementary to the sequence you’re looking for. Using a probe is like going fishing — you use the right bait (a complementary sequence) to catch something you want (a certain gene). Probes will attach with hydrogen bonds to their complementary sequence. For example, if you were looking for a gene that contained the sequence 5'TAGGCT3', you’d make a probe with the sequence 3'ATCCGA5'. Probes are also labeled with a fluorescent or radioactive marker so that you can locate them in a DNA sample. To use a probe to locate DNA, complete the following steps: Prepare a DNA sample to be probed for the gene of interest. You can look at DNA in many different forms — DNA in a gel, DNA attached to a microscope slide, and even DNA in colonies on a plate. To prepare any of these samples to be probed, you must treat the DNA with heat or chemicals to make it single-stranded and ready to pair with another strand of DNA. Wash your DNA probe over the surface of your DNA sample. The probe will attach to its complementary sequence in the sample. Locate your probe to find the gene of interest. A certain wavelength of light activates fluorescent probes. Radioactive probes are located by using the treated DNA to expose photographic film.

Article / Updated 04-10-2020

Recombinant DNA technology can be controversial. People, including scientists, worry about the ethical, legal, and environmental consequences of altering the DNA code of organisms: Genetically modified organisms (GMOs) that contain genes from a different organism are currently used in agriculture, but some people are concerned about the following potential impacts on wild organisms and on small farms: Genetically modified plants may interbreed with wild species, transferring genes for pesticide resistance to weeds. Crop plants that are engineered to make toxins intended to kill agricultural pests can also impact populations of other insects. Small farmers may not be able to afford genetically modified crop plants, putting them at a disadvantage to larger corporate farms. Genetic testing of fetuses allows the early detection of genetic disease, but some people worry that genetic testing will be taken to extremes, leading to a society where only “perfect” people are allowed to survive. Genetic testing of adults allows people to learn whether they have inherited diseases that run in their family, but some people worry that one day insurance companies will use genetic profiles of people to make decisions about who to insure. Parents of children with life-threatening diseases that can be treated with bone marrow transplants are using genetic testing to conceive children that can provide stem cells for their sick siblings. The umbilical cord is an excellent source of these stem cells, so the new babies aren’t harmed, but people worry that this may lead to an extreme future scenario where babies are born to serve as bone marrow or organ donors for existing people. Human hormones like insulin and human growth hormone are produced by bacteria through recombinant DNA technology and used to treat diseases like diabetes and pituitary dwarfism. However, some people seek hormones like human growth hormone for cosmetic reasons (for example, so that their children can be a little taller). People question whether it’s ethical for parents to make these choices for their children and whether too much emphasis is being placed on certain physical traits in society. Making useful proteins through genetic engineering Scientists use the bacterium E. coli as a little cellular factory to produce human proteins for treatment of diseases. To get E. coli to produce human proteins, cDNA copies of human genes are put into plasmid vectors and then the vectors are introduced into E. coli. The bacterium transcribes and translates the human gene, producing a human protein that is identical to the protein made by healthy human cells. Several human proteins are currently produced by this method, including the following: Human insulin for treatment of diabetes Human growth hormone for treatment of pituitary dwarfism Tumor necrosis factor, taxol, and interleukin-2 for treatment of cancer Epidermal growth factor for treatment of burns and ulcers Searching for disease genes Some people carry the potential for future disease in their genes. Genetic screening allows people to discover whether they’re carrying recessive alleles for genetic diseases, allowing them to choose whether or not to have children. Also, diseases that show up later in life, such as Alzheimer’s and Huntington’s disease, can be detected early, to seek the earliest possible treatment. In order to screen for a particular genetic disease, scientists must first discover the gene that causes the disease and study the normal and disease-causing sequences. Scientists have identified the genes for several genetic diseases, including cystic fibrosis, sickle-cell anemia, Huntington’s disease, an inherited form of Alzheimer’s, and an inherited form of breast cancer. Once the gene for a genetic disease has been identified, doctors can screen people to determine whether they have normal or disease-causing alleles. In order to screen a person for a particular gene, scientists amplify the genes linked to the disease using PCR. Then, scientists screen the genes for disease alleles: Scientists can copy and sequence a specific gene. If you have risk for a genetic disease, perhaps because people in your family suffer from the disease, scientists can use PCR to make amplify your copies of the gene associated with that disease. They use DNA sequencing to read the code of your genes, then compare your code to known codes for normal and disease-causing alleles of the gene. You might find out that you don’t have any disease-causing alleles, or that you’re a carrier who has one disease and one normal allele, or that you have two copies of the disease-causing form. Scientists can sequence your genome. If a specific gene isn’t identified as causing a problem, a doctor may order genome sequencing. A sample of all of your DNA will be cut into pieces, then sequenced using next-generation sequencing methods. The code from your DNA will be compared to reference human genomes to look for variations in your code that might be associated with disease. Building a “better” plant with genetic engineering Many important crop plants contain recombinant genes. These transgenic plants, which are a type of genetically modified organism (GMO), provide labor-saving advantages to farmers who can afford them: Transgenic plants that contain genes for herbicide resistance require less physical weed control. Farmers can spray crop plants that are resistant to a particular herbicide with that herbicide to control weeds. Weed plants will be killed, but the modified crop plants will not. Transgenic plants that contain genes for insect toxins will be less damaged by grazing insects. The crop plants use the introduced gene to produce insect toxins that kill insects that graze on the plants. Scientists often use the bacterium Agrobacterium tumefaciens to modify plant genomes. In nature, this soil bacterium slips a piece of its DNA into plant cells, resulting in crown gall disease. Scientists studying this disease discovered that Agrobacterium tumefaciens contains a small circle of DNA they named the Ti plasmid (Ti for tumor-inducing), which contains the genes necessary for the bacterium to transfer a section of its DNA into plant cells. When this bacterium receives the right signals, it takes a piece of DNA from the Ti plasmid and sends it into plant cells where it integrates into the plant genome. In the case of crown gall disease, the bacterial DNA causes production of plant hormones that produce a tumor-like growth (see the following figure). In the case of genetic engineering, scientists replace the disease-causing genes with the genes they want to introduce into the plant. Another potential benefit of transgenic plants is that certain crop plants may be altered to become more nutritious. For example, scientists are currently working on developing a strain of golden rice that may help combat Vitamin A deficiency in people around the world. Vitamin A deficiency can cause blindness and increase susceptibility to infectious diseases. Golden rice is being engineered to contain the genes necessary for the rice plants to produce beta-carotene. When people eat golden rice, their bodies will use beta-carotene to make Vitamin A. Rice is a staple food for half of the world’s people, so golden rice has great potential for fighting Vitamin A deficiency! Fixing a broken gene with gene therapy The ultimate cure for a genetic disease would be if scientists could replace the defective genes. As soon as recombinant DNA technology became available, scientists started wondering if they could use this technology to create cures for genetic diseases. After all, if scientists can transfer genes successfully into bacteria and plants, perhaps they can also transfer them into people that have defective disease-causing alleles (see the following figure). By introducing a copy of the normal allele into affected cells, the cells could be made to function normally, eliminating the effects of the disease. The introduction of a gene in order to cure a genetic disease is called gene therapy. Gene therapy for humans is being studied, and clinical trials have occurred for some diseases, but this type of treatment is far from being perfected. Many barriers to successful human gene therapy still need to be overcome: Scientists must discover safe vectors that can transfer genes into human cells. One possible vector is viruses that naturally attack human cells and introduce their DNA. Viral DNA is removed and replaced with therapeutic genes that contain the normal allele sequence. The viruses are allowed to infect human cells, thus introducing the therapeutic genes. Following are several safety issues associated with the use of viruses as vectors in gene therapy: Viruses that have been altered may recombine with existing viruses to recreate a disease-causing strain. Viruses that have been altered so that they can’t directly cause disease may still cause a severe allergic reaction that is potentially life threatening. Viruses that introduce genes into human cells may interrupt the function of normal genes. Scientists must develop methods for introducing therapeutic genes into populations of target cells. Humans are multicellular and have complex tissues. Genetic diseases can affect entire populations of cells. If gene therapy is to cure these diseases, the therapeutic genes must be introduced into all of the affected cells. Stem cells that produce target populations of cells need to be identified. If therapeutic genes are introduced into cells that have a limited lifespan in the body, then gene therapy will need to be repeated at regular intervals to maintain populations of healthy cells. On the other hand, if stem cells could be repaired with normal alleles, then they would continuously produce new populations of healthy cells, and the cure would be permanent. Because of the challenges of successfully treating people with genes delivered with vectors, many scientists are turning their attention to the newer technology of genome editing.

Article / Updated 04-10-2020

Scientists first discovered the basic principles of gene regulation by studying how gene expression works in bacteria. Bacteria regulate their gene expression in order to respond to an ever-changing environment. For example, the availability of food and water changes constantly, and bacteria must be able to take advantage of their current situation in order to survive. Bacteria respond to environmental changes by turning on genes for proteins that will help them survive. Genes are turned on and off by DNA-binding proteins that bind to DNA and control transcription. The basic steps of gene regulation in bacteria are as follows: The cell receives an environmental signal. The environmental signal either activates or inactivates a DNA-binding protein. DNA-binding proteins either bind to or let go of regulatory sequences in the DNA. Transcription is turned on or off by the DNA-binding proteins. Organizing bacterial genes Bacteria organize multiple genes under the control of one promoter. The set of genes plus promoter is called an operon. Typically, the genes in one operon contain the blueprints for proteins that work together in a single process. That way, transcription and translation of the operon make all the proteins needed for the process at the same time. Following are the important elements of a bacterial operon: The promoter marks the beginning of the operon. RNA polymerase binds to the operator to begin transcription. Structural genes are genes for proteins within the operon. One operon contains several structural genes. The operator is a regulatory sequence of DNA located between the promoter and the structural genes. DNA-binding proteins bind to the operator to control transcription of the operon. Taking E. coli to dinner Escherichia coli, better known as E. coli, is best known to most people as the bringer of gastrointestinal distress. However, your view of E. coli is probably skewed from the bad rap the bacterium gets in the news media. Basically, a few strains of E. coli run around causing very dangerous diseases and give the whole species a bad name. Many nicer strains of E. coli exist, some of them happily living in your intestines right now. Others are excellent bacterial lab rats, helping scientists learn about cells and how they function. In particular, scientists have discovered a lot about the structure and function of DNA, including gene regulation, from studying E. coli. Like you, E. coli uses enzymes to break down food molecules. E. coli has hundreds of genes for all the different enzymes it makes. Some genes are constitutively expressed. In other words, E. coli makes them all the time. Other genes are regulated — E. coli turns them on when it needs them and turns them off when it doesn’t. For example, the sugar glucose is usually available to E. coli, so E. coli always makes the enzymes it needs to break down glucose. Other food sources are more unpredictable, so E. coli turns on the enzymes to break down these food sources only when they become available. Looking at lac Lactose, the sugar found in milk, is occasionally available to E. coli. The genes for the enzymes to break down lactose are located within the lactose operon, or lac operon (see the following figure). The lac operon has three components: The lac promoter is the binding site for RNA polymerase. The lac operator is the binding site for a DNA-binding protein called the lac repressor protein. Three structural genes contain the blueprints for the two proteins needed to breakdown lactose plus a blueprint for a protective enzyme. The lacZ gene is the blueprint for the enzyme beta-galactosidase (β-galactosidase). Beta-galactosidase catalyzes the splitting of the disaccharide lactose into two monosaccharides, glucose and galactose, and then glycolysis breaks it down. The lacY gene is the blueprint for the membrane protein galactosidase permease, which brings lactose into the cell. The lacA gene is the blueprint for transacetylase, a protective enzyme that allows certain sugars to be removed from the cell when the sugars are too plentiful. Feeling repressed The DNA-binding protein that controls transcription of the lac operon is called the lac repressor protein. The lac repressor is a DNA-binding protein that regulates the lac operon. When the lac repressor is active, it binds to the operator, and transcription is blocked. The lac repressor has two binding sites that are critical to its function: A DNA-binding site that binds to the operator sequence of the lac operon An allosteric site that binds to an isomer of lactose (called allolactose) The allosteric site of the lac repressor controls its activity. When the allosteric site is empty, the lac repressor is active. When lactose is available, an isomer of lactose binds to the allosteric site, inactivating the lac repressor. The operator of the lac operon is right next to the promoter, so when the lac repressor is active, it gets in the way of RNA polymerase (refer to the preceding figure). If RNA polymerase can’t bind to the promoter, then transcription can’t occur. The blueprint for the lac repressor is contained in the I gene, which isn’t part of the lac operon. The I gene is constitutively expressed, so the lac repressor is always available in the cell. When the lac repressor is active, it shuts down the lac operon. Because the active repressor shuts down the operon, regulation of the lac operon by the lac repressor is called negative control. Game on: Inducing the lac operon Lactose is the inducer of the lac operon: When lactose is available, it turns the lac operon on so that E. coli can make the enzymes needed to break down lactose. Lactose regulates the lac operon by induction. Induction, or turning on, of the lac operon allows E. coli to use the lactose as a food source, which makes sense if you think about things from the perspective of E. coli; when lactose is available, E. coli “wants” to eat it. The tricky part about understanding gene regulation is to think about how lactose turns on the lac operon. After all, E. coli can’t really think about what it wants; it’s only a bacterium after all, so how does it “know” when lactose is available? The answer is the lac repressor. When lactose is available, an isomer of lactose (allolactose) binds to the lac repressor and inactivates it. The lac repressor lets go of the operator, and RNA polymerase can bind to the promoter. Transcription of the lac operon can occur and the enzymes to break down lactose are made. Game over: Repressing the lac operon The beauty of the regulation of the lac operon is its efficiency: when lactose is available, lactose turns on the lac operon. E. coli makes the enzymes to break down lactose and uses the lactose as a food source. As E. coli uses up the lactose, the allolactose isn’t available to bind to the repressor protein. The repressor protein becomes active again, and binds to the operator. So, when the lactose is gone, the lac operon is turned off again. Again, this process makes sense from the perspective of E. coli — if it doesn’t have any lactose, why make the enzymes to break it down? The tricky part is remembering how this process works: No lactose means no isomer (allolactose) bound to the allosteric site of the lac repressor, which means that the repressor protein binds to the operator and blocks transcription. To help you remember the regulation of the lac operon, think like E. coli. If lactose is available, would you want to make the enzymes to break it down? Of course! So, when lactose is available, the lac operon is on. If lactose isn’t available, do you want to make the enzymes to break it down? Why bother? So, when lactose isn’t available, the lac operon is off. Advancing to the next level: Catabolite repression of the lac operon Lactose isn’t the only sugar that has an effect on the regulation of the lac operon; glucose is a player in the game, too. E. coli always makes the enzymes to break down glucose so that the bacterium is always ready to use glucose when glucose is available. In fact, if glucose is available, E. coli won’t even bother making the effort to break down other sugars like lactose. How can a simple bacterium make these kinds of choices? The answer is through the regulatory DNA-binding protein catabolite activator protein (CAP), which responds to the levels of glucose available to the cell. CAP is an activator protein, which means it turns on transcription of genes (as compared to repressor proteins that turn off transcription). When CAP is active, it turns on transcription of catabolic operons like the lac operon that produce enzymes to break down different food sources (other than glucose). When glucose is available, CAP is inactive, so coli doesn’t make new enzymes and doesn’t bother breaking down food molecules other than glucose. When glucose runs out, CAP becomes active and turns on catabolic operons, which allows coli to make enzymes for food sources other than glucose. Regulation by CAP makes sense from the perspective of E. coli; E. coli always makes the enzymes to break down glucose, so if glucose is available the bacterium just eats the glucose. If glucose runs out, E. coli needs to find new food sources, so CAP turns on catabolic operons that produce enzymes for other food sources. That way, E. coli won’t run out of food. The details of how CAP responds to the presence of glucose are a bit complicated, but very similar to the workings of the lac repressor protein (see the preceding section “Feeling repressed”). Like the lac repressor, CAP is an allosteric protein with two important binding sites: A DNA-binding site that binds to a regulatory sequence of DNA called the CAP-binding site. The CAP-binding site is a sequence of DNA next to the promoters of catabolic operons. When CAP binds to the CAP-binding sites in the DNA, it enhances transcription of the adjacent operons. An allosteric site that binds to a signaling molecule named cyclic AMP (cAMP). When cAMP is bound to CAP, CAP is active. When cAMP isn’t bound to CAP, CAP is inactive. In other words, CAP needs cAMP in order to function. (Just like I need a cup of tea in the morning!) CAP and cAMP function as a team to monitor and respond to the presence of glucose. The amount of cAMP in the cell changes as the amount of glucose changes: When glucose levels are high, cAMP levels are low. When glucose levels are low, cAMP levels are high. You can think of cAMP like an alarm signal. When glucose runs out, more cAMP molecules run around the cell saying, “Oh no! We’re running out of food!” The cAMP molecules bind to CAP and activate it. Together, cAMP and CAP bind to the CAP binding site near the promoters of catabolic operons and turn them on, so E. coli makes enzymes to break down other food molecules besides glucose. The levels of cAMP change as glucose levels change because glucose acts as a regulator of the enzyme adenylate cyclase, which makes cAMP out of ATP. When glucose is available, it binds to an allosteric site on adenylate cyclase and inactivates the enzyme so that no cAMP is made. When glucose isn’t available, it can’t bind to adenylate cyclase. Adenylate cyclase is active and produces cAMP from ATP. To fully understand the regulation of the lac operon, you have to put the two regulatory systems together: negative control by the lac repressor combined with positive control by CAP. Remember that these two systems are independent of each other: Lactose is the environmental signal that interacts with the lac Glucose is the environmental signal that interacts with CAP. So, when you think about the regulation of the lac operon, consider these two systems separately. You can think of lactose as the on/off switch for the lac operon. When lactose is present, the operon is turned on. When lactose is absent, the operon is turned off. Glucose acts as volume control. When glucose is present, the volume of transcription on catabolic operons, including the lac operon, is very low. When glucose is absent, the volume of transcription of the lac operon gets cranked way up. The combined effects of these two systems determine the level of transcription of the lac operon: If glucose is present and lactose is absent, the volume is low, and the switch is off. No transcription of the lac operon occurs. If glucose and lactose are present, the volume is low, and the switch is on. Very low levels of transcription of the lac operon occur. If glucose is absent and lactose is present, the volume is high, and the switch is on. Very high levels of transcription of the lac operon occur. The hardest part of understanding gene regulation is getting the details straight on which molecules bind where and understanding their effects. The best strategy I’ve found for learning these details is to practice drawing the regulation of the lac operon in different conditions (different sugars available). In other words, practice re-creating the figure for yourself on a blank piece of paper. Draw the lac operon and then say to yourself, “If lactose is present, what is the effect?” Draw all the regulatory molecules onto the lac operon, describing what is happening out loud. Repeat your drawings for all the conditions shown. The combination of drawing, seeing, and hearing will help reinforce the information. Practice until you can re-create the figure with ease, narrating as you go.

Article / Updated 04-10-2020

Metabolism is a vast interlocking web of chemical reactions. If you put your finger on one of the dots (in the following figure) that represents a particular chemical, you can trace a path from that dot, along lines, to other dots, and so on. The path your finger travels represents a subset of the many chemical reactions that are occurring in the cell. A single path like the one you traced is called a metabolic pathway. Metabolic pathways have several key characteristics: Metabolic changes are broken down into small steps, each of which is a single chemical reaction. Several reactions in a series make up a metabolic pathway. Enzymes are very important to a functioning metabolism. They speed up chemical reactions by lowering the energy of activation so that metabolism occurs quickly enough to support life. Electrons are transferred from one molecule to another during many metabolic reactions. Molecules that lose electrons are oxidized; those that gain them are reduced. Electron carriers, such as nicotinamide adenine dinucleotide (NADH), shuttle electrons between reactions. Energy is transferred during metabolic reactions. The energy carrier ATP transfers energy to or from reactions. Taking baby steps during chemical reactions In cells, chemical reactions usually happen in many small steps rather than one quick change. By doing many small reactions, cells control the energy changes and prevent cellular damage. For example, a cell that needs to make molecule F out of molecule A might do so in five small steps: A→ B→ C→ D→ E→ F A represents the starting molecule, or substrate. F represents the ending molecule, or product. B, C, D, and E all represent molecules that were made during the conversion of A to F; they’re called intermediates. Every arrow represents one step, or reaction, as a chemical change occurred. Metabolic pathways connect with each other forming a complex interlocking web. The connections and complexities in metabolism occur when: The product of one pathway is the substrate of another. A pathway may have one or more branches as intermediates connect with other pathways. Some metabolic pathways are circular, re-creating the initial substrate during the pathway so that it can repeat, as shown. These types of pathways are called metabolic cycles. Helping hands from enzymes Life is very fast paced — too fast to just wait around for necessary chemical reactions to occur, even spontaneous reactions. Although spontaneous reactions are energetically favorable and can occur without energy input from the cell, there is no guarantee on exactly when they will occur. In order for a spontaneous reaction to happen, the reactants must find each other and then collide in just the right way and with enough kinetic energy to trigger the necessary changes for the reactants to convert into products. As the reactants interact, they form a temporary intermediate called the transition state intermediate. So, spontaneous reactions are just waiting to happen, but they need a little energy from the collision of the reactants to get to the transition state. The amount of energy necessary to trigger a reaction is called the energy of activation (Ea). Without help from enzymes, spontaneous reactions wouldn’t happen quickly enough to support life. For example, you probably know that if you eat sugar, your body will break it down in order to get some usable energy from the sugar. The breakdown of sugar is a spontaneous, exergonic reaction that releases usable energy to cells. However, if you were to place a bowl of sugar on your kitchen table and stare at it, it’s highly unlikely that the sugar would begin to disappear before your very eyes. Outside of your cells, the sugar molecules don’t have enough kinetic energy to overcome the barrier (see the following figure). Cellular enzymes make a huge difference between the breakdown of sugar inside your cells and outside of your cells. Enzymes are important to cells because Enzymes lower the energy of activation for reactions, making it easier for collisions between reactants to provide enough activation energy (compare the Ea for the reaction in the figure with and without enzymes). Every reaction that occurs in cells is catalyzed by an enzyme. Because enzymes are very specific and can bind to only a certain substrate, each reaction requires a unique enzyme. For example, look at this simple metabolic pathway in which molecule A is converted to molecule F by five reactions: A→ B→ C→ D→ E→ F Each reaction in this pathway would be catalyzed by a different enzyme, requiring a total of five enzymes to complete the pathway. If you refer to Figure 10-1 and look at all the reactions drawn on the metabolic map, you can get an idea of the hundreds of enzymes that may be needed at any one time in a cell. Enzymes lower the activation energy of reactions, making it easier for reactants to have productive collisions. Productive collisions are those that have enough energy to overcome the energy of activation. In order for productive collisions to occur: The particular reactants for a reaction must collide with each other. The reactants must be oriented toward each other in the right way so that the correct chemical groups come into contact. The reactants must have enough kinetic energy to overcome the energy of activation. Enzymes do several things to make it more likely that a collision will be productive: Enzymes bind reactants (substrates) in their active sites, bringing the necessary reactants for a reaction together in the proper orientation for the reaction to occur. The functional groups on the amino acids that make up the enzyme interact with the reactants, altering chemical bonds so that the changes necessary to reach the transition state are more likely to happen. The combined effects of these interactions between enzymes and reactants (substrates) result in the lowering of the activation energy for the reaction. Thus, it’s more likely that the kinetic energy of the reactants will be enough to cause the reaction to occur. Giving and taking electrons in redox reactions During metabolic reactions, electrons are often transferred from one molecule to another. Molecules change when they give or take electrons (as shown): When a molecule gives up an electron, it’s oxidized. When a molecule accepts an electron, it’s reduced. A good example of oxidation and reduction is the reaction between sodium (Na) and chlorine (Cl-). When sodium and chlorine come into contact with each other, chlorine steals an electron from sodium. Sodium is oxidized and becomes the sodium ion (Na+). Chlorine is reduced and becomes the chloride ion (Cl). Because oxidation and reduction reactions occur together — one molecule is oxidized, and one is reduced — these reactions are called redox reactions. It seems backwards to think that when a molecule gains an electron, it’s reduced. Reduced means less, right, so how can gaining an electron make you reduced? The reason for this contradiction is because elements are compared to their most oxidized state. So, if you think of most oxidized as the max, then every electron a molecule accepts moves it away from the max, or reduces it. Too confusing? Then just remember this friendly little sentence, “LEO the lion goes GER.” This stands for Loss of Electrons is Oxidation (LEO); Gain of Electrons is Reduction (GER). This shortcut never fails. Shuttling electrons with electron carriers Sometimes electrons are moved directly from one molecule to another during metabolism. Frequently, however, cells use an intermediate molecule, called an electron carrier. Electron carriers act like electron shuttle busses, accepting electrons from one reaction and then transferring those electrons to another reaction. During metabolism, these electrons are often moved as part of hydrogen atoms (H) that are stripped from one molecule and then given to another. Electron carriers cycle between two forms, an oxidized form and a reduced form, as they shuttle electrons (or hydrogen atoms) around the cell. The oxidized form of a carrier accepts electrons from reactions. When it accepts electrons, it becomes reduced. The reduced form of a carrier donates electrons to reactions. When it donates electrons, it becomes oxidize Nicotinamide adenine dinucleotide (NAD+/NADH), shown in the following figure, is a good example of an electron carrier. It’s made of two nucleotides hooked together. The nitrogenous base of the upper nucleotide is the part of the molecule that accepts and donates electrons. As NAD+/NADH shuttles electrons, it alternates between two forms: When the carrier is in its oxidized form, the nitrogenous ring carries a positive charge. This form of the carrier is NAD+. The carrier is reduced when it accepts one electron, which neutralizes the charge, plus one entire hydrogen atom. The reduced form of the carrier is NADH + H+. Whenever NAD+ accepts electrons, it’s converted to NADH + H+. The +H+ seems like a little brother always following the NADH around. During metabolism, electrons are often stripped off molecules as part of hydrogen atoms. Each hydrogen atom consists of one proton and one electron. When two hydrogen atoms are removed from a molecule during redox reactions, NAD+ can carry one electron, plus one whole hydrogen atom, in its nitrogenous ring. However, it can’t accept one proton. This proton is released into the cell, which is shown by writing +H+, which represents a proton, after the NADH. You can easily remember which form of an electron carrier is the oxidized form and which one is the reduced just by looking at its name. When electron carriers are reduced, they’re carrying their electron passengers in the form of hydrogen atoms. They show that they are carrying passengers by putting the letter H for hydrogen in their name, as in NADH. The oxidized form of the electron carrier doesn’t have the H, as in NAD+, which reveals that it’s not carrying any passengers. Getting what you need at the cellular level Metabolism is all about getting what you need to stay alive. You know what you need on the big scale — good old food, clothing, and shelter. But on the small scale, on the cellular level, what you need to keep your cells functioning comes down to a different three things: Building blocks for growth and repair. Your cells need a constant supply of materials to obtain the building blocks for the molecules that make up the cell. Food molecules are broken down by catabolism, and their building blocks are rearranged to form the molecules of the cell by anabolism. Energy for cellular work. Your cells need a constant supply of energy to allow cellular work, such as building molecules, moving things, and organizing cellular components. Food molecules are broken down by catabolism, allowing the transfer of energy from food to the cell. Reducing power. Your cells need a constant supply of electrons during anabolism in order to build the molecules that make up the cell. During catabolic reactions, electrons from food are transferred to electron carriers. These electron carriers then provide the needed electrons during anabolism.