Chapter 3 AP Bio Review

Lipids properties and functions

Most lipids (which include fats, waxes, phospholipids, and steroids) are nonpolar in nature due to most of the lipids' hydrocarbons mostly nonpolar carbon-carbon or carbon-hydrogen bonds. Cells store energy in the form of fats for long-term use. Lipids are act as natural insulation for plants and animals Lipids make up important hormones and important feature of the cell membrane wall.

Dehydration Synthesis

Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is known as dehydration synthesis, which means "to put together while losing water." In a dehydration synthesis reaction, the hydrogen of one monomer combines with the hydroxyl group (-OH) of another monomer, releasing a molecule of water. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer.

Quaternary Structure

Some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between subunits help to stabilize the structure. A protein consisting of more than one amino acid chain

Protein Structure

The shape of a protein is critical to its function. The four levels of protein structure: primary, secondary, tertiary, and quaternary.

The Four Categories of Macromolecules

Carbohydrates, lipids, proteins, and nucleic acids.

6 Main Elements of Biological Macromolecules

elements—sulfur, phosphorus, oxygen, nitrogen, carbon, and hydrogen (SPONCH)

Monosaccharides

) po)Monosaccharides (mono- = "one"; sacchar- = "sweet") are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R'), it is known as a ketose. Sugars may be known as trioses (3 carbons), pentoses (5 carbons), and hexoses (6 carbons), depending on the # of carbs in the sugar. Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in ring forms. In a ring shape, in this case for glucose, if the hydroxyl group is below carbon number 1 (anomeric carbon), it is in the alpha (α) position, and if it is above, it is in the beta (β) position.

Fats and Oils

A fat molecule (aka triacylglycerols or triglycerides, depending on their chemical structure) consists of mainly glycerol and fatty acids. Glycerol is an organic compound (alcohol) with 3 carbons, 5 hydrogens, and 3 hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached, hence the name "fatty acid." In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through an oxygen atom Ester bond: the bond between an alcohol group (-OH) and a carboxylic acid group (-COOH), formed by the elimination of a molecule of water (H2O). Mammals store fats in specialized cells called adipocytes. Plants store fat or oil in many seeds and is used as a source of energy during seedling development.

Polysaccharides

A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = "many"). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more depending on the number of monomers joined.

Polysaccharides: Chitin

A nitrogen-containing polysaccharide. It is made of repeating units of N-acetyl-β-d-glucosamine, a modified sugar. Chitin is also a major part of fungal cell walls, as well as makes up the exoskeleton of arthropods.

Difference between Polypeptides and Proteins

A polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications.

Hydrolysis

A reaction in which a water molecule is used during the breakdown of another compound. During these reactions, the polymer is broken into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH-) from a split water molecule.

Amino Acids

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom/group of atoms bonded to the central atom known as the R group. Each R group is different for each amino acid. 9 of the 20 amino acids in proteins are essential in humans because the human body can't produce them, so they are obtained from the diet. Essential amino acids refer to those necessary for the construction of proteins in the body, although not produced by the body; which amino acids are essential varies from organism to organism (isoleucine, leucine, and cysteine).

3.2 Carbohydrates Summary

Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that are formed as a result of dehydration reactions, forming disaccharides and polysaccharides with the elimination of a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides, whereas common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide, whereas amylopectin, a constituent of starch, is a highly branched molecule. Storage of glucose, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause excessive water uptake by the cell.

Carbohydrate ratio

Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. stoichiometric formula: relating to or denoting quantities of reactants in simple integral ratios, as prescribed by an equation or formula.

Benefits of Carbohydrates

Carbohydrates should be supplemented with proteins, vitamins, and fats to be parts of a well-balanced diet. Carbohydrates contain soluble and insoluble elements; the insoluble part is known as fiber, which is mostly cellulose. Fiber has many uses; it promotes regular bowel movement by adding bulk, and it regulates the rate of consumption of blood glucose. Fiber also helps to remove excess cholesterol from the body: fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream, and then cholesterol exits the body via the feces. Without the consumption of carbohydrates, the availability of "instant energy" that is the result of glucose being broken down and producing ATP during cellular repiration, would be reduced.

Cis and Trans Fats

Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same side, it is referred to as a cis fat. If hydrogen atoms are on different sides it is referred to as a trans fat. The cis double bond causes a bend or a "kink" that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. In the food industry, oils are artificially hydrogenated to make them semi-solid and of a consistency desirable for many processed food products. During hydrogenation process, double bonds of the cis- conformation in the hydrocarbon chain may be converted to double bonds in the trans- conformation. Studies have shown that the increase in consuming fatty acids may lead to increase in lipoproteins(LDL) aka bad cholesterol. This has the potential to plaque deposition in the arteries, leading to heart issues.

The Central Dogma of Life,

DNA dictates the structure of mRNA in a process known as transcription, and RNA dictates the structure of protein in a process known as translation DNA -> RNA -> Protein This is true for all organisms (besides some exceptions connected with viral infections)

DNA

DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. The entire genetic content of a cell is known as its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. DNA controls all of the cellular activities by turning the genes "on" or "off."

Features of DNA and RNA Summarized

DNA: Function: Carries genetic information Location: Remains in the nucleus Structure: Double Helix Sugar: Deoxyribose Pyrimidines: Cytosine, thymine Purines: Adenine, guanine RNA: Function: Involved in protein synthesis Location: Leaves the nucleus Structure: Usually single-stranded Sugar: Ribose Pyrimidines: Cytosine, uracil Purines: Adenine, guanine

Dehydration Synthesis, Hydrolysis and Enzymes

Dehydration and hydrolysis reactions are catalyzed, or "sped up," by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. Each macromolecule is broken down by a specific enzyme. For instance, carbohydrates are broken down by amylase, sucrase, lactase, or maltase. Proteins are broken down by the enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken down by lipases. Breakdown of these macromolecules provides energy for cellular activities.

Denaturation and Protein Folding

Denaturation is when, due to changes in temperature, changes in pH, or exposure to chemicals, the protein structure may change, losing its shape, but does not lose its primary sequence. Although usually reversible, irreversible denaturation can lead to loss of function (Ex. when an egg is fried). Protein folding is critical to its function. Protein helpers (chaperones) help their target protein during the folding process by preventing the aggregation of polypeptides that make up the complete protein structure. Chaperones disassociate from the protein once the target protein is folded.

Protein Types and Functions Examples

Digestive Enzymes: Amylase, lipase, pepsin, trypsin Help in digestion of food by catabolizing nutrients into monomeric units Transport: Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural: Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones: Insulin, thyroxine Coordinate the activity of different body systems Defense: Immunoglobulins Protect the body from foreign pathogens Contractile: Actin, myosin Effect muscle contraction Storage: Legume storage proteins, egg white (albumin) Provide nourishment in early development of the embryo and the seedling

Dissacharides

Disaccharides (di- = "two") form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

Omega Fatty Acids

Essential fatty acids are fatty acids required but not synthesized by the human body and therefore have to be supplemented via the diet. Omega-3 (as well as omega-6) are the only known essential fatty acids. These are polyunsaturated fatty acids and are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. The farthest carbon away from the carboxyl group is numbered as the omega (ω) carbon, and if the double bond is between the third and fourth carbon from that end, it is known as an omega-3 fatty acid. omega-3 fatty acids include polyunsaturated fatty acids alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). These are nutritionally important since the body does not make them. Omega-3 fatty acids reduce the risk of sudden death from heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. Many vitamins are fat soluble, and fats serve as a long-term storage form of fatty acids: a source of energy. They also provide insulation for the body. Therefore, "healthy" fats in moderate amounts should be consumed on a regular basis.

3.3 Lipids Summary

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are made up of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are known as saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids make up the matrix of membranes. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the fluid nature of the membrane. It is also the precursor of steroid hormones such as testosterone.

Phospholipids

Major constituents of the plasma membrane, the outermost layer of all living cells. They are composed of fatty acid chains attached to a glycerol or sphingosine backbone. Phospholipids contain 2 fatty acids attached, forming a diacylglycerol, and the 3rd fatty acid is occupied by a modified phosphate group. A phosphate group alone attached to a diacylglycerol does not qualify as a phospholipid. It is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. The phosphate group is modified by an alcohol. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are found in plasma membranes. A phospholipid is an amphipathic molecule, meaning it has a hydrophobic (tails) and a hydrophilic part (heads). The fatty acid chains are hydrophobic and cannot interact with water, whereas the phosphate-containing group is hydrophilic and interacts with water. Phospholipids form a bilayer, with the fatty acid tails facing inside away from water, the the phosphate group heads face outwards towards the water.

3.5 Nucleic Acids Summary

Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. MicroRNA regulates the use of mRNA for protein synthesis.

Nucleic Acids: DNA and RNA

Nucleic acids are the most important macromolecules for the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of a nitrogenous base, a pentose (5-carbon) sugar, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

Polysaccharides: Starch

Plants are able to synthesize glucose, and the excess glucose, beyond the plant's immediate energy needs, is stored as starch in different plant parts, including roots and seeds. Starch in seeds provides food for plant seeds, as well as humans and animals. After the starch is consumed by a human, enzymes (like salivary amylases) break it down into smaller molecules (like maltose and glucose). The cells then absorb glucose. Starch is made up of glucose monomers that are joined by α 1-4 or α 1-6 glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond.

3.4 Proteins Summary

Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers, or hormones. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that is linked to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide. Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the unique sequence of amino acids. The local folding of the polypeptide to form structures such as the α helix and β-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is known as the quaternary structure of a protein. Protein shape and function are intricately linked; any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.

Types and Functions of Proteins

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. They may be structural, regulatory, contractile, or protective and may serve in transport, storage, or membranes, as well as be toxins or enzymes. All proteins are polymers of amino acids arranged in a linear sequence. Enzymes are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on. Enzymes that break down their substrates are called catabolic enzymes, enzymes that build more complex molecules from their substrates are called anabolic enzymes, and enzymes that affect the rate of reaction are called catalytic enzymes. All enzymes increase the rate of reaction and, therefore, are considered to be organic catalysts. Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. Protein shape is critical to its function, and this shape is maintained by many different types of chemical bonds. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to loss of function, known as denaturation. All proteins are made up of the 20 most common types of amino acids.

3.1 Synthesis of Biological Macromolecules Summary

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. Macromolecules are made up of single units known as monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients; this is an important advantage in the maintenance of cellular osmotic conditions. A monomer joins with another monomer with the release of a water molecule, leading to the formation of a covalent bond. These types of reactions are known as dehydration or condensation reactions. When polymers are broken down into smaller units (monomers), a molecule of water is used for each bond broken by these reactions; such reactions are known as hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.

RNA

RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester bonds, as well as mostly involved in protein synthesis. Even though the RNA is single-stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function. 4 major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. mRNA is synthesized in the nucleus and is complementary to the DNA sequence it was copied from (besides replacing T with U). In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery. The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the ribosomes. The rRNA of the ribosome also has an enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70-90 nucleotides long. It carries the correct amino acid to the site of protein synthesis (base pairing between tRNA and mRNA that allows for correct amino acid order in the polypeptide chain). microRNAs are the smallest RNA molecules and their role involves the regulation of gene expression by interfering with the expression of certain mRNA messages.

Steroids

Steroids have a fused ring structure and they are hydrophobic and insoluble in water. Steroids have four linked carbon rings and several of them, like cholesterol, have a short tail. Many steroids also have the -OH functional group, which puts them in the alcohol classification (sterols). Cholesterol is the most common steroid. Cholesterol is mainly synthesized in the liver and is the precursor to many steroid hormones such as testosterone and estradiol, as well as a precursor to Vitamin D. It is a component of the plasma membrane of animal cells and is found within the phospholipid bilayer. The plasma membrane is responsible for the transport of materials and cellular recognition and it is involved in cell-to-cell communication.

Monosaccharides Glucose, Galactose and Fructose

The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of energy. Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers) because of the different arrangement of functional groups around the asymmetric carbon; all of these monosaccharides have more than one asymmetric carbon. Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have the same chemical formula but have slightly different structures. Glucose and galactose are aldoses, and fructose is a ketose.

R Groups of amino acids

The chemical nature of the side chain determines if an amino acid is acidic, basic, polar, or nonpolar. The amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic. Amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. Amino acids that are positively charged are known as basic amino acids (ex. lysine and arginine). Amino acids are represented by a single upper case letter or a three-letter abbreviation (ex. Valine = V or val). 1. nonpolar C-H bonds 2. polar uncharged bonds OH and SH bonds 3. polar charged acidic bonds COO- 4. polar charged basic bonds NH3+

Secondary Structure

The local folding of the polypeptide in some regions. The most common structures are the α-helix and β-pleated sheets. In the α-helix structure, the hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain. Every helical turn in an alpha helix has 3.6 amino acid residues. The R groups of the polypeptide protrude out from the α-helix chain. In the β-pleated sheet, the "pleats" are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons and extend above and below the folds of the pleat. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive hydrogen atom in the amino group and the partially negative oxygen atom in the carbonyl group of the peptide backbone.

Polysaccharides: Cellulose

The most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose; this provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds Cellulose has an important (especially to plant cells) rigidity and high tensile strength due to every other glucose monomer in cellulose being flipped over, packed tightly as extended long chains. While the β 1-4 linkage cannot be broken down by human digestive enzymes, herbivores such as cows, koalas, and buffalos are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria and protists reside in the digestive system of herbivores and secrete the enzyme cellulase.

DNA and RNA nucleotides

The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. DNA base pairs consist of adenine (A), guanine (G) cytosine (C), and thymine (T), with complementary pairing being A+T and C+G. RNA base pairs consist of adenine (A), guanine (G) cytosine (C), and uracil (U), with complementary pairing being A+U and C+G Adenine and guanine are classified as purines (two carbon-nitrogen rings structure). Cytosine, thymine, and uracil are classified as pyrimidines(single carbon-nitrogen ring structure). The pentose sugar in DNA is deoxyribose (hydrogen on the second carbon), and in RNA, the sugar is ribose (hydroxyl group on the second carbon). The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as "one prime"). The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′-3′ phosphodiester linkage. Phosphodiester linkage formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.

amino acids in protein synthesis

The sequence and the number of amino acids ultimately determine the protein's shape, size, and function. The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water(dehydration synthesis). The resulting bond is the peptide bond. Linked amino acids forms a peptide. As more amino acids join to this growing chain, the resulting chain is known as a polypeptide. Each polypeptide has a free amino group at one end. This end is called the N terminal (amino terminal), and the other end has a free carboxyl group (C or carboxyl terminal).

Polysaccharides: Glycogen

The storage form of glucose in humans and other vertebrates and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.

DNA Double-Helix Structure

The sugar and phosphate lie on the outside of the helix, forming the backbone of the DNA. The two strands of the helix run in opposite directions (antiparallel), meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. The base complementary rule: A+T, and G+C, aka DNA strands are complementary to each other. During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.

Primary Structure

The unique sequence of amino acids in a polypeptide chain is its primary structure. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Disulfide bonds can help connect chains together and helps to fold chains into the correct shapes. A change in the nucleotide sequence of the gene's coding region may lead to a different amino acid being added to the growing polypeptide chain, causing a change in protein structure and function. Point mutation: the mutation is caused by a single base change Types of point mutations: Silent mutation: a change in the sequence of bases in a DNA molecule, but do not result in a change in the amino acid sequence of a protein. Missense mutation: a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene Nonsense mutation: A nonsense mutation is also a change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.

Tertiary Structure

The unique three-dimensional structure of a polypeptide. The interactions among R groups create the complex three-dimensional tertiary structure of a protein. R groups with like charges repel each other, and R groups with different charges attract each other (ionic bonds). During protein folding, nonpolar hydrophobic amino acids turn inwards, while hydrophilic amino acids turn outwards. These are known as hydrophobic reactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond forming during protein folding. When a protein loses its three-dimensional shape, it may no longer be functional.

Waxes

Wax covers the feathers of some aquatic birds and the leaf surfaces of some plants. Because of the hydrophobic nature of waxes, they prevent water from sticking on the surface. Waxes are made up of long fatty acid chains esterified to long-chain alcohols.

saturated and unsaturated fatty acids

saturated fatty acids contain only single bonds between neighboring carbons in the hydrocarbon chain. The number of hydrogen atoms attached to the carbon skeleton is maximized. An unsaturated fatty acid is when the hydrocarbon chain contains a double bond. Most unsaturated fats are liquid at room temperature and are called oils. If a molecule contains one double bond, then it is a monosaturated fat (like olive oil). If there is more than one double bond, it is a polyunsaturated fat (like canola oil). Long straight fatty acids with single bonds (saturated) tend to get packed tightly and are solid at room temperature (ex. stearic acid which is found in meat). Unsaturated fats are usually from plants and cotnain cis unstaturated fatty acids. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries.