The backbone of the DNA ladder are

phosphate and deoxyribose sugar

DNA - RNA - Proteins (Part 1)

Basics of Molecular Biology, Introduction to DNA & RNA, Structural and Functional aspects of DNA, Structural and Functional aspects of RNA, Types and variants of RNAs (Coding & Noncoding), Central Dogma, Genes and Proteins, Prokaryotic & Eukaryotic CELL structures, Genome size - sequence complexity -Introns and Exons, Genome sequences and database subscriptions. Genome organization: Mitochondrial and Chloroplast genome.Genomic regulatory elements and their role: Promoters, Enhancers & CpG Islands; Genomic Repetitive Elements & their role: Long Repeats, Short Repeats, SSRs, Transposons / Transposable elements, Miniature Inverted Repeat TE, etc.; DNA Modifications: Variations and Base modifications, Polymorphisms: types of polymorphism Single Nucleotide Polymorphisms (SNPs), mutations, other genetic variations, Introduction to Structural Variation and implications on genomes.

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 reactions…(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.

Animal Cells Animal cells contain many organelles, which are subunits within the cell that perform specialized functions. The organelles may be membrane-bound (enclosed within a lipid bilayer) or non-membrane bound (free in the cytoplasm). Here is a list of animal cell components and organelles and their functions: • Cell Membrane: The cell membrane or plasma membrane is a selectively permeable lipid bilayer that encloses the contents of the cell and regulates the transport of materials into and out of it. • Cytoplasm: The cytoplasm is the jelly-like fluid that gives a cell is shape and contains the molecules the cell needs for its processes. • Cytoskeleton: The cytoskeleton is a network of protein fibers that provides structural support, maintains cell shape, and enables cell movement. It is composed of three main types of protein filaments: microfilaments, intermediate filaments, and microtubules. • Nucleus: The nucleus is the control center of the cell, containing DNA and regulating gene expression. It is surrounded by a double-layered nuclear envelope or nuclear membrane that has nuclear pores that allow the exchange of materials between the nucleus and the cytoplasm. Nucleolus: Located within the nucleus, the nucleolus is the site of pre-ribosome production. • Mitochondria: Often referred to as the “powerhouse” of the cell, mitochondria are responsible for generating energy in the form of adenosine triphosphate (ATP) through cellular respiration. • Endoplasmic Reticulum (ER): The ER is a network of membrane-bound tubes and sacs involved in the synthesis, folding, and transport of proteins and lipids. There are two types of ER: the rough ER, which is studded with ribosomes and involved in protein synthesis, and the smooth ER, which is responsible for lipid synthesis and detoxification. • Ribosomes: These small structures, composed of RNA and proteins, are the sites of protein synthesis within the cell. They can be found either free-floating in the cytoplasm or attached to the rough ER. • Golgi Apparatus: The Golgi apparatus is responsible for modifying, sorting, and packaging proteins and lipids for transport to their final destinations within or outside the cell. • Lysosomes: Lysosomes are membrane-bound organelles containing enzymes that break down waste materials and cellular debris, playing a crucial role in the recycling of cellular components. • Peroxisomes: These small organelles contain enzymes that neutralize toxic substances and break down fatty acids, contributing to cellular detoxification and energy production. • Centrosome: The centrosome is an organelle found in animal cells but not plant cells. It is a small organelle near the nucleus with radiating tubules. The centrosome produces and organizes microtubules and regulates cell division so that the cell contents equally divide between daughter cells.

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 monosaccharide—or simple sugar— 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 ● Distinguish between monosaccharides, disaccharides, and polysaccharides. ● Explain the relationship between amino acids and protein structure. ● Describe the induced fit model of enzyme action. ● Compare the structure and function of each of the different types of lipids. ● 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 © 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 forms—highly 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, —COOH, highlighted in green, bonds at a second site. An amino group, —NH2, 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 © 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 interactions—such as hydrogen bonding—between 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 Enzymes—RNA or protein molecules that act as biological catalysts—are 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 enzyme’s shape. The change in the enzyme’s 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.

Lipids are large, nonpolar organic molecules. They do not dissolve in water. Lipids include triglycerides (trie-GLIS-uhr-IEDZ), phospho- lipids, steroids, waxes, and pigments. Lipid molecules have a higher ratio of carbon and hydrogen atoms to oxygen atoms than carbohydrates have. Because lipid molecules have larger numbers of carbon-hydrogen bonds per gram than other organic com- pounds do, they store more energy per gram. Fatty Acids Fatty acids are unbranched carbon chains that make up most lipids. Figure 3-10 shows that a fatty acid contains a long carbon chain (from 12 to 28 carbons) with a carboxyl group, —COOH, attached at one end. The two ends of the fatty-acid molecule have different properties. The carboxyl end is polar and is thus hydrophilic or attracted to water molecules. In contrast, the hydro- carbon end of the fatty-acid molecule is nonpolar. This end tends not to interact with water molecules and is said to be hydrophobic (HIE-droh-FOH-bik), or “water fearing.” In saturated fatty acids, such as palmitic acid, which is shown in Figure 3-10, each carbon atom is covalently bonded to four atoms. The carbon atoms are in effect full, or saturated. In contrast, linoleic acid, also shown in Figure 3-10, has carbon atoms that are not bonded to the maximum number of atoms to which they can bond. Instead, they have formed double bonds within the carbon chain. This type of fatty acid is said to be unsaturated. Triglycerides Three classes of lipids important to living things contain fatty acids: triglycerides (fats), phospholipids, and waxes. A triglyceride is composed of three molecules of fatty acid joined to one molecule of the alcohol glycerol. Saturated triglycerides are composed of saturated fatty acids. They typically have high melting points and tend to be hard at room temperature. Common dietary saturated triglycerides include butter and fats in red meat. In contrast, unsaturated triglycerides are composed of unsaturated fatty acids and are usually soft or liquid at room temperature. Unsaturated triglycerides are found primarily in plant seeds where they serve as an energy and carbon source for germinating plants. Phospholipids Phospholipids have two, rather than three, fatty acids attached to a molecule of glycerol. They have a phosphate group attached to the third carbon of the glycerol. As shown in Figure 3-11, the cell membrane is made of two layers of phospholipids, called the lipid bilayer. The inability of lipids to dissolve in water allows the mem- brane to form a barrier between the inside and outside of the cell. Hydrophilic “head” Phospholipids Hydrophobic “tail” Phospholipids Water Water The lipid bilayer of a cell membrane is a double row of phospholipids.The “tails” face each other.The “head” of a phospholipid, which contains a phosphate group, is polar and hydrophilic.The two tails are two fatty acids and are nonpolar and hydrophobic. FIGURE 3-11 H C H C O OH H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H H C H C H H H H C H H C H H C H H C H H C H C O OH H C H H C H H C H C H C H C H H C H H C H C H H C H H C H C H H H H C H Fatty acids have a polar carboxyl head, highlighted in purple, and a nonpolar hydrocarbon tail, highlighted in green. FIGURE 3-10 Palmitic acid Linoleic acid mb06se_bchs02.qxd 5/18/07 10:49 AM Page 59 60 CHAPTER 3 1. Compare the structure of monosaccharides, dis- accharides, and polysaccharides. 2. How are proteins constructed from amino acids? 3. How do amino acids differ from one another? 4. Describe a model of enzyme action. 5. Why do phospholipids orient in a bilayer when in a watery environment, such as a cell? 6. Describe how the three major types of lipids differ in structure from one another. 7. What are the functions of the two types of nucleic acids? CRITICAL THINKING 8. Applying Information Before a long race, run- ners often “carbo load.” This means that they eat substantial quantities of carbohydrates. How might this help their performance? 9. Recognizing Relationships High temperatures can weaken bonds within a protein molecule. How might this explain the effects of using a hot curling iron or rollers in one’s hair? 10. Applying Information You want to eat more unsaturated than saturated fats. Name examples of foods you would eat more of and less of. SECTION 2 REVIEW Waxes A wax is a type of structural lipid consisting of a long fatty-acid chain joined to a long alcohol chain. Waxes are waterproof, and in plants, form a protective coating on the outer surfaces. Waxes also form protective layers in animals. For example, earwax helps pre- vent microorganisms from entering the ear canal. Steroids Unlike most other lipids, which are composed of fatty acids, steroid molecules are composed of four fused carbon rings with various functional groups attached to them. Many animal hor- mones, such as the male hormone testosterone, are steroid com- pounds. One of the most familiar steroids in humans is cholesterol. Cholesterol is needed by the body for nerve and other cells to func- tion normally. It is also a component of the cell membrane. NUCLEIC ACIDS Nucleic acids are very large and complex organic molecules that store and transfer important information in the cell. There are two major types of nucleic acids: deoxyribonucleic acid and ribonucleic acid. Deoxyribonucleic acid, or DNA, contains information that deter- mines the characteristics of an organism and directs its cell activi- ties. Ribonucleic (RIE-boh-noo-KLEE-ik) acid, or RNA, stores and transfers information from DNA that is essential for the manufactur- ing of proteins. Some RNA molecules can also act as enzymes. Both DNA and RNA are polymers, composed of thousands of linked monomers called nucleotides (NOO-klee-uh-TIEDS). As shown in Figure 3- 12, each nucleotide is made of three main components: a phosphate group, a five-carbon sugar, and a ring-shaped nitrogenous base.

RNA translation. The genetic information in DNA is used to synthesize proteins through the processes of RNA Transcription and RNA Translation. The sequence of three-letter code words in the gene determines the sequence of amino acids in a polypeptide chain. RNA Transcription DNA serves as a template for the synthesis of RNA. There are 3 major types of RNA that participate in the process of proteins synthesis. 1.5% of the genome encodes for proteins via mRNA, but an unknown % of the genome codes for noncoding RNA (ncRNA)

Origin recognition ORC,MCM proteins helicase activity, ssDNA RPA, Primer synthesis polymers alpha/primase,Sliding clamp PCNA, primer removal RNase H, FEN1.Pol α/Primase synthesizes an RNA chain of 10 nucleotides followed by another 20 nucleotides of initiator DNA (iDNA). Because Pol α/Primase has no proofreading ability, this whole section of RNA/iDNA is removed. The exonucleases RNase H removes the RNA and Fen1 removed the iDNA. The gap is filled in by Pol δ and DNA ligase joins the 2 ends.Eukaryotic DNA Replication All have 5’ to 3’ Polymerase activity.

Most 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 cell’s cytoplasm. The nucleus houses and protects the cell’s genetic information. The hereditary information that contains the instructions for the structure and function of the organism is coded in the organism’s 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 cell’s DNA. FIGURE 4-12 Nuclear envelope Nucleolus Nuclear pores DNA (chromatin) Copyright © 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 cell’s 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.

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