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RNA structure, Transcription, Central Dogma
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SB2. Obtain, evaluate, and communicate information to analyze how genetic information is expressed in cells. a. Construct an explanation of how the structures of DNA and RNA lead to the expression of information within the cell via the processes of replication, transcription, and translation. Learning Targets _______Identify the structural components of DNA and RNA Success Criteria _______Can accurately identify the key structural components of DNA (deoxyribose sugar, phosphate group, nitrogenous bases: adenine, thymine, cytosine, guanine). _______Can identify the key structural components of RNA (ribose sugar, phosphate group, nitrogenous bases: adenine, uracil, cytosine, guanine). _______Can describe the differences in the sugar backbone of DNA and RNA (deoxyribose vs. ribose). _______Can identify the double-stranded structure of DNA and the single-stranded structure of RNA. _______Identify the parts of protein synthesis and the location of each process Success Criteria _______Can identify and describe the two main processes of protein synthesis: transcription and translation. _______Can correctly explain that transcription occurs in the nucleus where DNA is transcribed into mRNA. _______Can explain that translation occurs in the cytoplasm at ribosomes where mRNA is translated into amino acid sequences to form proteins. _______Compare and Contrast DNA to RNA Success Criteria _______Can clearly identify similarities between DNA and RNA, such as both being nucleic acids and containing nucleotide structures. _______Can explain differences in DNA and RNA, including sugar types (deoxyribose vs. ribose), strand number (double-stranded DNA vs. single-stranded RNA), and nitrogenous base usage (thymine in DNA vs. uracil in RNA). _______Can describe the function of DNA as genetic storage and the function of RNA in protein synthesis (mRNA, tRNA, rRNA). _______Analyze the reasoning for enzymes usage in both DNA replication and protein synthesis. Success Criteria _______Can identify key enzymes involved in DNA replication (e.g., helicase, DNA polymerase, ligase) and explain their functions (e.g., helicase-unwinding DNA, DNA polymerase-synthesizing new DNA strands, ligase-sealing nicks in the DNA backbone). _______Can identify enzymes involved in protein synthesis (e.g., RNA polymerase) and explain their role in transcribing DNA into mRNA. _______Can analyze why enzymes are essential for speeding up chemical reactionsâŚ(ensuring accuracy, and catalyzing steps in replication and protein synthesis) _______Can provide specific examples of how enzyme malfunction can impact genetic replication or protein synthesis. _______Perform the steps of DNA replication and protein synthesis in order to demonstrate their understanding of how the structure of DNA supports the genetic expression in successive generations. Success Criteria _______Can demonstrate a step-by-step understanding of DNA replication, including unwinding, complementary base pairing, and proofreading. _______Can demonstrate the steps of transcription (formation of mRNA from DNA) and translation (conversion of mRNA into a polypeptide). _______Can show how DNA's structure (double helix, base pairing) ensures accurate replication for passing genetic information to offspring. _______Can illustrate how changes in DNA sequence can lead to changes in protein structure and function, thus affecting traits in successive generations.DNA and RNA StructureDNA and RNA structure and rolesPCR, DNA sequencing, DNA paternity testing, Structure of RNAMost of the functions of a eukaryotic cell are controlled by the nucleus, shown in Figure 4-12. The nucleus is filled with a jellylike liquid called the nucleoplasm, which holds the contents of the nucleus and is similar in function to a cellâs cytoplasm. The nucleus houses and protects the cellâs genetic information. The hereditary information that contains the instructions for the structure and function of the organism is coded in the organismâs DNA, which is contained in the nucleus. When a cell is not dividing, the DNA is in the form of a threadlike material called chromatin. When a cell is about to divide, the chromatin condenses to form chromosomes. Chromosomes are structures in the nucleus made of DNA and protein. The nucleus is the site where DNA is transcribed into ribonucleic acid (RNA). RNA moves through nuclear pores to the cytoplasm, where, depending on the type of RNA, it carries out its function. Nuclear Envelope The nucleus is surrounded by a double membrane called the nuclear envelope. The nuclear envelope is made up of two phos- pholipid bilayers. Covering the surface of the nuclear envelope are tiny, protein-lined holes, which are called nuclear pores. The nuclear pores provide passageways for RNA and other materials to enter and leave the nucleus. Nucleolus Most nuclei contain at least one denser area, called the nucleolus (noo-KLEE-uh-luhs). The nucleolus (plural, nucleoli) is the site where DNA is concentrated when it is in the process of making ribosomal RNA. Ribosomes (RIE-buh-SOHMZ) are organelles made of protein and RNA that direct protein synthesis in the cytoplasm. The nucleus of a cell is surrounded by a double membrane called the nuclear envelope. The nucleus stores the cellâs DNA. FIGURE 4-12 Nuclear envelope Nucleolus Nuclear pores DNA (chromatin) Copyright Š by Holt, Rinehart and Winston. All rights reserved. 80 CHAPTER 4 MITOCHONDRIA Mitochondria (MIET-oh-KAHN-dree-uh) (singular, mitochondrion) are tiny organelles that transfer energy from organic molecules to adenosine triphosphate (ATP). ATP ultimately powers most of the cellâs chemical reactions. Highly active cells, such as muscle cells, can have hundreds of mitochondria. Cells that are not very active, such as fat-storage cells, have few mitochondria. Like a nucleus, a mitochondrion has an inner and an outer phos- pholipid membrane, as shown in Figure 4-13. The outer membrane separates the mitochondrion from the cytosol. The inner membrane has many folds, called cristae (KRIS-tee). Cristae contain proteins that carry out energy-harvesting chemical reactions. Mitochondrial DNA Mitochondria have their own DNA and can reproduce only by the division of preexisting mitochondria. Scientists think that mito- chondria originated from prokaryotic cells that were incorporated into ancient eukaryotic cells. This symbiotic relationship provided the prokaryotic invaders with a protected place to live and pro- vided the eukaryotic cell with an increased supply of ATP. RIBOSOMES Ribosomes are small, roughly spherical organelles that are respon- sible for building protein. Ribosomes do not have a membrane. They are made of protein and RNA molecules. Ribosome assembly begins in the nucleolus and is completed in the cytoplasm. One large and one small subunit come together to make a functioning ribosome, shown in Figure 4-14. Some ribosomes are free within the cytosol. Others are attached to the rough endoplasmic reticulum.Understanding the differences between bacteria and viruses is important because they affect our health differently. In this study guide, we'll explore the key distinctions between these two microorganisms. Section 1: Bacteria What are Bacteria? Bacteria are tiny, single-celled living organisms. They are found everywhere, including in soil, water, and inside our bodies. Shape and Structure: Bacteria have different shapes like rods, spheres, and spirals. They have a cell wall that surrounds their cell membrane. Reproduction: Bacteria reproduce by dividing in half, a process called binary fission. This allows them to multiply quickly. Living or Nonliving: Bacteria are considered living because they can grow, reproduce, and respond to their environment. Section 2: Viruses What are Viruses? Viruses are smaller than bacteria and are not considered living organisms. They are made up of genetic material (either DNA or RNA) surrounded by a protein coat. Shape and Structure: Viruses come in various shapes but are much simpler than bacteria. They lack the cell structures found in bacteria. Reproduction: Viruses cannot reproduce on their own. They need a host cell (like a human cell) to replicate and make more viruses. Living or Nonliving: Viruses are considered nonliving because they cannot perform life processes without a host cell. Section 3: Differences Now, let's compare bacteria and viruses: Size: Bacteria are larger than viruses. Living or Nonliving: Bacteria are living organisms. Viruses are non-living entities. Reproduction: Bacteria reproduce on their own through binary fission. Viruses need a host cell to replicate. Structure: Bacteria have complex structures with cell walls. Viruses are simpler, consisting of genetic material and a protein coat. Treatment: Bacterial infections are treated with antibiotics. Viral infections are typically managed with antiviral medications (if available) or through the body's immune response. Section 4: Examples Examples of bacteria-related and virus-related illnesses: Bacterial Infections: Strep throat, Urinary tract infections (UTIs), Tuberculosis Viral Infections: Influenza (Flu), Common cold, HIV/AIDS Conclusion: Understanding the differences between bacteria and viruses can help us stay healthy and make informed decisions about treatment. Remember that while bacteria can be both helpful and harmful, viruses rely on our cells to replicate and cause infections.What is a Plant Cell? Plant cells are eukaryotic cells that vary in several fundamental factors from other eukaryotic organisms. Both plant and animal cells contain a nucleus along with similar organelles. One of the distinctive aspects of a plant cell is the presence of a cell wall outside the cell membrane. Plant Cell Structure Just like different organs within the body, plant cell structure includes various components known as cell organelles that perform different functions to sustain itself. These organelles include: Cell Wall It is a rigid layer which is composed of polysaccharides cellulose, pectin and hemicellulose. It is located outside the cell membrane. It also comprises glycoproteins and polymers such as lignin, cutin, or suberin. The primary function of the cell wall is to protect and provide structural support to the cell. The plant cell wall is also involved in protecting the cell against mechanical stress and providing form and structure to the cell. It also filters the molecules passing in and out of it. The formation of the cell wall is guided by microtubules. It consists of three layers, namely, primary, secondary and the middle lamella. The primary cell wall is formed by cellulose laid down by enzymes. Cell membrane It is the semi-permeable membrane that is present within the cell wall. It is composed of a thin layer of protein and fat. The cell membrane plays an important role in regulating the entry and exit of specific substances within the cell. For instance, cell membrane keeps toxins from entering inside, while nutrients and essential minerals are transported across. Nucleus The nucleus is a membrane-bound structure that is present only in eukaryotic cells. The vital function of a nucleus is to store DNA or hereditary information required for cell division, metabolism and growth. 1. Nucleolus: It manufactures cellsâ protein-producing structures and ribosomes. 2. Nucleopore: Nuclear membrane is perforated with holes called nucleopore that allow proteins and nucleic acids to pass through. Plastids They are membrane-bound organelles that have their own DNA. They are necessary to store starch and to carry out the process of photosynthesis. It is also used in the synthesis of many molecules, which form the building blocks of the cell. Some of the vital types of plastids and their functions are stated below: Leucoplasts They are found in the non-photosynthetic tissue of plants. They are used for the storage of protein, lipid and starch. Chromoplasts They are heterogeneous, colored plastid which is responsible for pigment synthesis and for storage in photosynthetic eukaryotic organisms. Chromoplasts have red-, orange- and yellow-colored pigments which provide color to all ripe fruits and flowers. Central Vacuole It occupies around 30% of the cellâs volume in a mature plant cell. Tonoplast is a membrane that surrounds the central vacuole. The vital function of the central vacuole apart from storage is to sustain turgor pressure against the cell wall. The central vacuole consists of cell sap. It is a mixture of salts, enzymes and other substances. Golgi Apparatus They are found in all eukaryotic cells, which are involved in distributing synthesized macromolecules to various parts of the cell. Ribosomes They are the smallest membrane-bound organelles which comprise RNA and protein. They are the sites for protein synthesis, hence, also referred to as the protein factories of the cell. Mitochondria They are the double-membraned organelles found in the cytoplasm of all eukaryotic cells. They provide energy by breaking down carbohydrate and sugar molecules, hence they are also referred to as the âPowerhouse of the cell.â Lysosome Lysosomes are called suicidal bags as they hold digestive enzymes in an enclosed membrane. They perform the function of cellular waste disposal by digesting worn-out organelles, food particles and foreign bodies in the cell. In plants, the role of lysosomes is undertaken by the vacuoles. Chloroplasts It is an elongated organelle enclosed by phospholipid membrane. The chloroplast is shaped like a disc and the stroma is the fluid within the chloroplast that comprises a circular DNA. Each chloroplast contains a green colored pigment called chlorophyll required for the process of photosynthesis. The chlorophyll absorbs light energy from the sun and uses it to transform carbon dioxide and water into glucose. Structure of Chloroplast Chloroplasts are found in all higher plants. It is oval or biconvex, found within the mesophyll of the plant cell. The size of the chloroplast usually varies between 4-6 Âľm in diameter and 1-3 Âľm in thickness. They are double-membrane organelle with the presence of outer, inner and intermembrane space. There are two distinct regions present inside a chloroplast known as the grana and stroma. ⢠Grana are made up of stacks of disc-shaped structures known as thylakoids or lamellae. The granum of the chloroplast consists of chlorophyll pigments and are the functional units of chloroplasts. ⢠Stroma is the homogenous matrix which contains grana and is similar to the cytoplasm in cells in which all the organelles are embedded. Stroma also contains various enzymes, DNA, ribosomes, and other substances. Stroma lamellae function by connecting the stacks of thylakoid sacs or grana. The chloroplast structure consists of the following parts: Membrane Envelope It comprises inner and outer lipid bilayer membranes. The inner membrane separates the stroma from the intermembrane space. Intermembrane Space The space between inner and outer membranes. Thylakoid System (Lamellae) The system is suspended in the stroma. It is a collection of membranous sacs called thylakoids or lamellae. The green colored pigments called chlorophyll are found in the thylakoid membranes. It is the sight for the process of light-dependent reactions of the photosynthesis process. The thylakoids are arranged in stacks known as grana and each granum contains around 10-20 thylakoids. Stroma It is a colorless, alkaline, aqueous, protein-rich fluid present within the inner membrane of the chloroplast present surrounding the grana. Grana Stack of lamellae in plastids is known as grana. These are the sites of conversion of light energy into chemical energy. Chlorophyll It is a green photosynthetic pigment that helps in the process of photosynthesis. Functions of Chloroplast Following are the important chloroplast functions: ⢠The most important function of the chloroplast is to synthesize food by the process of photosynthesis. ⢠Absorbs light energy and converts it into chemical energy. ⢠Chloroplast has a structure called chlorophyll which functions by trapping the solar energy and is used for the synthesis of food in all green plants. ⢠Produces NADPH and molecular oxygen (O 2 ) by photolysis of water. ⢠Produces ATP â Adenosine triphosphate by the process of photosynthesis. ⢠The carbon dioxide (CO2) obtained from the air is used to generate carbon and sugar during the Calvin Cycle or dark reaction of photosynthesis. Mitochondria âMitochondria are membrane-bound organelles present in the cytoplasm of all eukaryotic cells, that produce adenosine triphosphate (ATP), the main energy molecule used by the cell.â What are Mitochondria? Popularly known as the âPowerhouse of the cell,â mitochondria (singular: mitochondrion) are a double membrane-bound organelle found in most eukaryotic organisms. They are found inside the cytoplasm and essentially function as the cellâs âdigestive system.â They play a major role in breaking down nutrients and generating energy-rich molecules for the cell. Many of the biochemical reactions involved in cellular respiration take place within the mitochondria. The term âmitochondrionâ is derived from the Greek words âmitosâ and âchondrionâ which means âthreadâ and âgranules-likeâ, respectively. It was first described by a German pathologist named Richard Altmann in the year 1890. Structure of Mitochondria ⢠The mitochondrion is a double-membraned, rod-shaped structure found in both plant and animal cell. ⢠Its size ranges from 0.5 to 1.0 micrometers in diameter. ⢠The structure comprises an outer membrane, an inner membrane, and a gel-like material called the matrix. ⢠The outer membrane and the inner membrane are made of proteins and phospholipid layers separated by the intermembrane space. ⢠The outer membrane covers the surface of the mitochondrion and has a large number of special proteins known as porins. Cristae The inner membrane of mitochondria is rather complex in structure. It has many folds that form a layered structure called cristae, and this helps in increasing the surface area inside the organelle. The cristae and the proteins of the inner membrane aid in the production of ATP molecules. The inner mitochondrial membrane is strictly permeable only to oxygen and ATP molecules. A number of chemical reactions take place within the inner membrane of mitochondria. Mitochondrial Matrix The mitochondrial matrix is a viscous fluid that contains a mixture of enzymes and proteins. It also comprises ribosomes, inorganic ions, mitochondrial DNA, nucleotide cofactors, and organic molecules. The enzymes present in the matrix play an important role in the synthesis of ATP molecules. Functions of Mitochondria The most important function of mitochondria is to produce energy through the process of oxidative phosphorylation. It is also involved in the following process: 1. Regulates the metabolic activity of the cell 2. Promotes the growth of new cells and cell multiplication 3. Helps in detoxifying ammonia in the liver cells 4. Plays an important role in apoptosis or programmed cell death 5. Responsible for building certain parts of the blood and various hormones like testosterone and estrogen 6. Helps in maintaining an adequate concentration of calcium ions within the compartments of the cell 7. It is also involved in various cellular activities like cellular differentiation, cell signaling, cell senescence, controlling the cell cycle and in cell growth. Disorders Associated with Mitochondria Any irregularity in the way mitochondria function can directly affect human health, but often, it is difficult to identify because symptoms differ from person to person. Disorders of the mitochondria can be quite severe; in some cases, they can even cause an organ to fail.CARBOHYDRATES Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen in a ratio of about one carbon atom to two hydrogen atoms to one oxygen atom. The number of carbon atoms in a carbohydrate varies. Some carbohydrates serve as a source of energy. Other carbohydrates are used as structural materials. Carbohydrates can exist as monosaccharides, disaccharides, or polysaccharides. Monosaccharides A monomer of a carbohydrate is called a monosaccharide (MAHN-oh-SAK-uh-RIED). A monosaccharideâor simple sugarâ contains carbon, hydrogen, and oxygen in a ratio of 1:2:1. The gen- eral formula for a monosaccharide is written as (CH2O)n, where n is any whole number from 3 to 8. For example, a six-carbon mono- saccharide, (CH2O)6, would have the formula C6H12O6. The most common monosaccharides are glucose, fructose, and galactose, as shown in Figure 3-6. Glucose is a main source of energy for cells. Fructose is found in fruits and is the sweetest of the monosaccharides. Galactose is found in milk. Notice in Figure 3-6 that glucose, fructose, and galactose have the same molecular formula, C6H12O6, but differing structures. The different structures determine the slightly different properties of the three compounds. Compounds like these sugars, with a single chemical formula but different structural forms, are called isomers (IE-soh-muhrz). SECTION 2 OBJECTIVES â Distinguish between monosaccharides, disaccharides, and polysaccharides. â Explain the relationship between amino acids and protein structure. â Describe the induced fit model of enzyme action. â Compare the structure and function of each of the different types of lipids. â Compare the nucleic acids DNA and RNA. VOCABULARY carbohydrate monosaccharide disaccharide polysaccharide protein amino acid peptide bond polypeptide enzyme substrate active site lipid fatty acid phospholipid wax steroid nucleic acid deoxyribonucleic acid (DNA) ribonucleic acid (RNA) nucleotide C HO H C H OH C OH H C CH2OH H C H OH O Glucose C OH C O H OH C OH H CH2OH C H CH2OH Fructose C H HO C OH H C OH H C CH2OH H C H OH O Galactose Glucose, fructose, and galactose have the same chemical formula, but their structural differences result in different properties among the three compounds. FIGURE 3-6 Copyright Š by Holt, Rinehart and Winston. All rights reserved. 56 CHAPTER 3 Disaccharides and Polysaccharides In living things, two monosaccharides can combine in a condensa- tion reaction to form a double sugar, or disaccharide (die-SAK-e-RIED). For example in Figure 3-4, the monosaccharides fructose and glu- cose can combine to form the disaccharide sucrose. A polysaccharide is a complex molecule composed of three or more monosaccharides. Animals store glucose in the form of the polysaccharide glycogen. Glycogen consists of hundreds of glucose molecules strung together in a highly branched chain. Much of the glucose that comes from food is ultimately stored in your liver and muscles as glycogen and is ready to be used for quick energy. Plants store glucose molecules in the form of the polysaccha- ride starch. Starch molecules have two basic formsâhighly branched chains that are similar to glycogen and long, coiled, unbranched chains. Plants also make a large polysaccharide called cellulose. Cellulose, which gives strength and rigidity to plant cells, makes up about 50 percent of wood. In a single cellu- lose molecule, thousands of glucose monomers are linked in long, straight chains. These chains tend to form hydrogen bonds with each other. The resulting structure is strong and can be broken down by hydrolysis only under certain conditions. PROTEINS Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen. Like most of the other biological macromolecules, proteins are formed from the linkage of monomers called amino acids. Hair and horns, as shown in Figure 3-7a, are made mostly of proteins, as are skin, muscles and many biological catalysts (enzymes). Amino Acids There are 20 different amino acids, and all share a basic structure. As Figure 3-7b shows, each amino acid contains a central carbon atom covalently bonded to four other atoms or functional groups. A single hydrogen atom, highlighted in blue in the illustration, bonds at one site. A carboxyl group, âCOOH, highlighted in green, bonds at a second site. An amino group, âNH2, highlighted in yel- low, bonds at a third site. A side chain called the R group, high- lighted in red, bonds at the fourth site. The main difference among the different amino acids is in their R groups. The R group can be complex or it can be simple, such as the CH3 group shown in the amino acid alanine in Figure 3-7b. The differences among the amino acid R groups gives different proteins very different shapes. The different shapes allow pro- teins to carry out many different activities in living things. Amino acids are commonly shown in a simplified way such as balls, as shown in Figure 3-7c. (a) Many structures, such as hair and horns are made of proteins. (b) Proteins are made up of amino acids. Amino acids differ only in the type of R group (shown in red) they carry. Polar R groups can dissolve in water, but nonpolar R groups cannot. (c) Amino acids have complex structures, so, in this and other textbooks, they are often simplified into balls. FIGURE 3-7 (b) Alanine (an amino acid) (c) Simplified version of amino acid CH3 H N OH C C H O H (a) Copyright Š by Holt, Rinehart and Winston. All rights reserved. BIOCHEMISTRY 57 H H N C C OH H O H CH3 H2O Glycine Alanine H N OH C C H O H H H N C C H O H CH3 N OH C C H O H (a) (b) (a) The peptide bond (shaded blue) that binds amino acids together to form a polypeptide results from a condensation reaction that produces water. (b) Poly- peptides are commonly shown as a string of balls in this textbook and elsewhere. Each ball represents an amino acid. FIGURE 3-8 Substrate Products Enzyme 1 2 3 In the induced fit model of enzyme action, the enzyme can attach only to a substrate (reactant) with a specific shape. The enzyme then changes and reduces the activation energy of the reaction so reactants can become products. The enzyme is unchanged and is available to be used again. 3 2 1 FIGURE 3-9 Dipeptides and Polypeptides Figure 3-8a shows how two amino acids bond to form a dipeptide (die-PEP-TIED). In this condensation reaction, the two amino acids form a covalent bond, called a peptide bond (shaded in blue in Figure 3-8a) and release a water molecule. Amino acids often form very long chains called polypeptides (PAHL-i-PEP-TIEDZ). Proteins are composed of one or more polypep- tides. Some proteins are very large molecules, containing hun- dreds of amino acids. Often, these long proteins are bent and folded upon themselves as a result of interactionsâsuch as hydrogen bondingâbetween individual amino acids. Protein shape can also be influenced by conditions such as temperature and the type of solvent in which a protein is dissolved. For exam- ple, cooking an egg changes the shape of proteins in the egg white. The firm, opaque result is very different from the initial clear, runny material. Enzymes EnzymesâRNA or protein molecules that act as biological catalystsâare essential for the functioning of any cell. Many enzymes are proteins. Figure 3-9 shows an induced fit model of enzyme action. Enzyme reactions depend on a physical fit between the enzyme molecule and its specific substrate, the reactant being catalyzed. Notice that the enzyme has folds, or an active site, with a shape that allows the substrate to fit into the active site. An enzyme acts only on a specific substrate because only that substrate fits into its active site. The linkage of the enzyme and substrate causes a slight change in the enzymeâs shape. The change in the enzymeâs shape weakens some chemical bonds in the substrate, which is one way that enzymes reduce activation energy, the energy needed to start the reaction. After the reaction, the enzyme releases the products. Like any catalyst, the enzyme itself is unchanged, so it can be used many times. An enzyme may not work if its environment is changed. For example, change in temperature or pH can cause a change in the shape of the enzyme or the substrate. If such a change happens, the reaction that the enzyme would have catalyzed cannot occur.