DNA Structure

A cell’s complete complement of DNA is called its genome. In plants and animals the DNA is found in an organelle called the nucleus.  
In plants and animals, the complete genetic code for the organism is made of several double-stranded, DNA molecules. The DNA is coiled and condensed into chromosomes. Each species has a specific number of chromosomes in its cells. Human body cells have 46 chromosomes. Human body cells contain two matched sets of chromosomes, a configuration known as diploid. Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm, or haploid.
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The matched pairs of chromosomes in a diploid organism are called homologous chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments, called genes, in exactly the same location on the chromosome. Genes determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic. For example, the shape of earlobes is a characteristic with traits of free or attached.
Each copy of the homologous pair of chromosomes comes from a different parent; therefore, the copies of each of the genes themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two different sequences, such as AB.
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Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes; other than a small amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.
​The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base and sugar phosphate backbone. The nucleotide is named depending on the nitrogenous base. There are only four nitrogenous bases,  adenine (A), guanine (G), cytosine (C), and thymine (T). The fact that all life on Earth uses these same four bases in their DNA is evidence for evolution. 
Base pairs are formed with the nitrogenous base from one strand of DNA forms a weak hydrogen bond with a nitrogenous base from the other strand of DNA. Nitrogenous bases always pair up the same way. An adenine can only bond with a thymine and a guanine only forms bonds with a cytosine. These bonded nitrogenous bases are called base pairs. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. A and T form 2 hydrogens bonds between them while G and C form 3 hydrogen bonds between them. 
Section Summary:
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The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. The two strands that make up the double helix are complementary. The sugar phosphate backbone wraps around the nitrogenous bases, which are stacked inside.  Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other into the double helix shape. 

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DNA Replication

When a cell divides, it is important that each daughter cell receives an identical copy of the DNA. This is accomplished by the process of DNA replication. The replication of DNA occurs during interphase, before the cell enters mitosis or meiosis.

Because DNA strands are complementary, having one strand means that it is possible to recreate the other strand. During replication, the two strands of the double helix separate  and each strand serves as a template from which the new complementary strand is copied.
 The new strand will be complementary to the parental or “old” strand. Each new double strand consists of one parental strand and one new daughter strand. This is known as semiconservative replication. When two DNA copies are formed, they have an identical sequence of nucleotide bases and are divided equally into two daughter cells.
DNA Replication in Plants and Animals
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Because plants and animal genomes are very complex, DNA replication is a very complicated process that involves several enzymes and other proteins. First, the DNA must be opened so that other enzymes can build the complementary strands. The enzyme helicase unwinds and opens up the DNA helix. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication, and these get extended in both directions as replication proceeds. 
Next, an enzyme called DNA polymerase adds DNA nucleotides to the 3' end of the template. Because DNA polymerase can only add new nucleotides at the end of a backbone, a primer sequence, which provides this starting point, is added with complementary RNA nucleotides. This primer tells the DNA polymerase where to start building the new DNA strand. One strand, which is complementary to the parental DNA strand, is made continuously toward the replication fork as the DNA polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand.

​Because DNA polymerase can only synthesize DNA in a 5' to 3' direction, the other new strand is put together in short pieces called Okazaki fragments. The Okazaki fragments each require a primer made of RNA to start the synthesis. The strand with the Okazaki fragments is known as the lagging strand. As synthesis continues, an enzyme removes the RNA primer, which is then replaced with DNA nucleotides, and the gaps between fragments are sealed by an enzyme called DNA ligase.
The process of DNA replication can be summarized as follows:
  1. DNA unwinds at the origin of replication.
  2. New bases are added to the new strands, complementary to the original strands. One new strand is made continuously, while the other strand is made in pieces.
  3. Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase.
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Protein Synthesis

​DNA provides a “blueprint” for the cell structure. DNA contains the information necessary for the cell to build one very important type of molecule: the protein. Most structural components of the cell are made up, at least in part, by proteins and virtually all the functions that a cell carries out are completed with the help of proteins. One of the most important classes of proteins is enzymes. Some of these critical reactions include building larger molecules from smaller components (such as occurs during DNA replication) and breaking down larger molecules into smaller components (such as during cellular respiration). Whatever the cellular process may be, it is almost sure to involve proteins. 

Protein synthesis begins with genes. A gene is a segment of DNA that provides the genetic information necessary to build a protein. Each particular gene provides the code necessary to construct a particular protein. 
​Proteins are polymers, or chains, of many amino acid building blocks. The sequence of bases in a gene (that is, its sequence of A, T, C, G nucleotides) translates to an amino acid sequence. A triplet is a section of three DNA bases in a row that codes for a specific amino acid. Similar to the way in which the three-letter code d-o-g signals the image of a dog, the three-letter DNA base code signals the use of a particular amino acid. For example, the DNA triplet CAC (cytosine, adenine, and cytosine) specifies the amino acid valine. 
From DNA to RNA: Transcription
DNA is kept within the nucleus, and protein synthesis takes place in the cytoplasm, thus there must be some sort of messenger that leaves the nucleus and manages protein synthesis. This intermediate messenger is messenger RNA (mRNA), a single-stranded nucleic acid that carries a copy of the genetic code for a single gene out of the nucleus and into the cytoplasm where it is used to produce proteins.
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There are several different types of RNA, each having different functions in the cell. The structure of RNA is similar to DNA with a few small exceptions. For one thing, unlike DNA, most types of RNA, including mRNA, are single-stranded and contain no complementary strand. Second, instead of the base thymine, RNA contains the base uracil. This means that adenine will always pair up with uracil during the protein synthesis process.

Protein synthesis begins with the process called transcription, in which  strand of mRNA that is complementary to the gene of interest is made. This process is called transcription because the mRNA is like a transcript, or copy, of the gene’s DNA code. Transcription begins somewhat like DNA replication, in that a region of DNA unwinds and the two strands separate, however, only that small portion of the DNA will be split apart. 
Stage 1: Initiation. A region at the beginning of the gene called a promoter—a particular sequence of nucleotides—triggers the start of transcription.Stage 2: Elongation. Transcription starts when RNA polymerase unwinds the DNA segment. One strand, referred to as the coding strand, becomes the template with the genes to be coded. The polymerase then aligns the correct nucleic acid (A, C, G, or U) with its complementary base on the coding strand of DNA. RNA polymerase is an enzyme that adds new nucleotides to a growing strand of RNA. This process builds a strand of mRNA.Stage 3: Termination. When the polymerase has reached the end of the gene, one of three specific triplets (UAA, UAG, or UGA) codes a “stop” signal, which triggers the enzymes to terminate transcription and release the mRNA transcript.
During transcription, an RNA polymerase enzyme binds to the DNA and opens the DNA to form a little bubble. The RNA polymerase then reads the DNA and built a complementary strand the RNA. Like with DNA, the RNA is built by adding to the 3' end. Once the RNA polymerase reaches a terminator the mRNA is 
From RNA to Protein: Translation

Like translating a book from one language into another, the codons on a strand of mRNA must be translated into the amino acid alphabet of proteins. Translation is the process of synthesizing a chain of amino acids called a polypeptide. When an mRNA molecule is ready to be translated, the ribosomes attach to the mRNA. The ribosome brings together and aligning the mRNA molecule with the molecular “translators” that must decipher its code.
The other major requirement for protein synthesis is the translator molecules that physically “read” the mRNA codons. Transfer RNA (tRNA) is a type of RNA that ferries the appropriate corresponding amino acids to the ribosome, and attaches each new amino acid to the last, building the polypeptide chain one-by-one. Thus tRNA transfers specific amino acids from the cytoplasm to a growing polypeptide. The tRNA molecules must be able to recognize the codons on mRNA and match them with the correct amino acid. On one end of the tRNA is a binding site for a specific amino acid. On the other end is a base sequence that matches the codon specifying its particular amino acid. This sequence of three bases on the tRNA molecule is called an anticodon. For example, a tRNA responsible for shuttling the amino acid glycine contains a binding site for glycine on one end. On the other end it contains an anticodon that complements the glycine codon (GGA is a codon for glycine, and so the tRNAs anticodon would read CCU). Equipped with its particular cargo and matching anticodon, a tRNA molecule can read its recognized mRNA codon and bring the corresponding amino acid to the growing chain .
Much like the processes of DNA replication and transcription, translation consists of three main stages: initiation, elongation, and termination. 
  • Initiation takes place with the binding of a ribosome to an mRNA transcript. 
  • The elongation stage involves the recognition of a tRNA anticodon with the next mRNA codon in the sequence. Once the anticodon and codon sequences are bound (remember, they are complementary base pairs), the tRNA presents its amino acid cargo and the growing polypeptide strand is attached to this next amino acid. This attachment takes place with the assistance of various enzymes and requires energy. The tRNA molecule then releases the mRNA strand, the mRNA strand shifts one codon over in the ribosome, and the next appropriate tRNA arrives with its matching anticodon. 
  • This process continues until the final codon on the mRNA is reached which provides a “stop” message that signals termination of translation and triggers the release of the complete, newly synthesized protein. Thus, a gene within the DNA molecule is transcribed into mRNA, which is then translated into a protein product.
​CHAPTER REVIEW:
DNA stores the information necessary for instructing the cell to perform all of its functions. Cells use the genetic code stored within DNA to build proteins, which ultimately determine the structure and function of the cell. This genetic code lies in the particular sequence of nucleotides that make up each gene along the DNA molecule. To “read” this code, the cell must perform two sequential steps. In the first step, transcription, the DNA code is converted into a RNA code. A molecule of messenger RNA that is complementary to a specific gene is synthesized in a process similar to DNA replication. The molecule of mRNA provides the code to synthesize a protein. In the process of translation, the mRNA attaches to a ribosome. Next, tRNA molecules shuttle the appropriate amino acids to the ribosome, one-by-one, coded by sequential triplet codons on the mRNA, until the protein is fully synthesized. When completed, the mRNA detaches from the ribosome, and the protein is released. 
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MUTATIONS:
A mutation is a change in the nucleotide sequence of an organisms DNA. A common example would be binding a cytosine in place of a thymine. These mistakes can be made during DNA replication, transcription, or translation. Mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body.
​Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations. These silent mutations have no affect on the resulting protein. The most common silent mutations are point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. 
If the mutation results the code for a different amino acid then the resulting protein will be changed. This change could be beneficial or detrimental, or it could result in no change in the function of the protein. The mutation that causes sickle cell anemia is caused by one amino acid being exchanged for another. The result of this amino acid switch is a change the in the shape of the red blood cell that contains the haemoglobin protein. The resulting red blood cells are sickle shaped. This thin and pointy shape makes them prone to getting stuck in blood vessels, causing clots. These sickle shaped red blood cells are not able to carry as much oxygen as their normal counterparts. However, the gene for sickle cell anemia is not all bad, people with the gene are protected from malaria.
​Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia. 
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Enzymes

A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up of chains of amino acids, and they perform the critical task of lowering the amount of energy needed for the chemical reaction to take place inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily.
The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme’s active site. The active site is where the “action” happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acids in the enzyme's active site. The unique combination of amino acid, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates, enzymes are known for their specificity. The “best fit” results from the shape and the attraction to the substrate of the amino acids in the active site . There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction. Each enzyme will work with only one type of substrate. This is called the "lock and key" hypothesis.
​The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment. This means that changing the local pH or temperature can change the nature of the active site, changing how it is attracted to the substrate. Increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the natural properties of a substance. Likewise, the pH of the local environment can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature. 
Section Summary
Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acids. This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with lock and key fit, which means that enzyme's active site matches with a specific substrate. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.

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Environmental factors influence enzyme activity

The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment. The environmental conditions can include temperature, pH, salinity and presence of heavy metals. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the natural properties of a substance. Likewise, the pH of the local environment can also affect enzyme function. Active site amino acids have their own acidic or basic properties that are optimal for catalysis. These amino acids are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature an the rates of the reaction decrease.
The temperatures and pHs that are most effective will change with each enzyme. Enzymes in the human body are most affective at a temperature of 37 degrees celsius as this is the normal body temperature. If you have a fever your body temperature increases making enzymes less effective. This is your body's natural defense to invaders. The idea is that the invaders will die as their enzymes will no longer work. However, if your fever increases too much your enzymes will also be affected and you may also die. 

The enzymes in your body are also most functional at specific pH levels. In the stomach there is a high acidity due to the hydrochloric acid used to break down food and kill bacteria. As a result, only protease (the enzymes that break down proteins) are functional in the stomach as they have an optimum pH of about 2. Amylase, which is functional in the mouth and small intestine works at a much higher pH, one much closer to 6. 

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