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Section 2 Biochemical Building Blocks. Chapter 5 Amino Acids, Peptides, & Proteins.

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Presentation on theme: "Section 2 Biochemical Building Blocks. Chapter 5 Amino Acids, Peptides, & Proteins."— Presentation transcript:

1 Section 2 Biochemical Building Blocks

2 Chapter 5 Amino Acids, Peptides, & Proteins

3 Section 5.1: Amino Acids  Proteins are molecular tools  They are a diverse and complex group of macromolecules Figure 5.1 Protein Diversity

4 Section 5.1: Amino Acids  Proteins can be distinguished by the number, composition, and sequence of amino acid residues  Amino acid polymers of 50 or less are peptides; polymers greater than 50 are proteins or polypeptides  There are 20 standard amino acids

5 Section 5.1: Amino Acids  19 have the same general structure: central (  ) carbon, an amino group, carboxylate group, hydrogen atom, and an R group (proline is the exception)  At pH 7, the carboxyl group is in its conjugate base form (-COO - ) while the amino group is its conjugate acid form (- NH 3 + ); therefore, it is amphoteric  Molecules that have both positive and negative charges on different atoms are zwitterions and have no net charge at pH 7  The R group is what gives the amino acid its unique properties Figure 5.3 General Structure of the  - Amino Acids

6 Section 5.1: Amino Acids  Amino Acid Classes  Classified by their ability to interact with water  Nonpolar amino acids contain hydrocarbon groups with no charge Figure 5.2 The Standard Amino Acids

7 Section 5.1: Amino Acids  Amino Acid Classes Continued  Polar amino acids have functional groups that can easily interact with water through hydrogen bonding  Contain a hydroxyl group (serine, threonine, and tyrosine) or amide group (asparagine) Figure 5.2 The Standard Amino Acids

8 Section 5.1: Amino Acids  Amino Acid Classes Continued  Acidic amino acids have side chains with a carboxylate group that ionizes at physiological pH  Basic amino acids bear a positive charge at physiological pH  At physiological pH, lysine is its conjugate acid (-NH 3 + ), arginine is permanently protonated, and histidine is a weak base, because it is only partly ionized Figure 5.2 The Standard Amino Acids

9 Section 5.1: Amino Acids

10  Biologically Active Amino Acids  Amino acids can have other biological roles 1. Some amino acids or derivatives can act as chemical messengers  Neurotransmitters (tryptophan- derivative serotonin) and hormones (tyrosine-derivative thyroxine) Figure 5.5 Some Derivatives of Amino Acids

11 Section 5.1: Amino Acids 2. Act as precursors for other molecules (nucleotides and heme) 3. Metabolic intermediates (arginine, ornithine, and citrulline in the urea cycle) Figure 5.6 Citruline and Ornithine

12 Section 5.1: Amino Acids  Modified Amino Acids in Proteins  Some proteins have amino acids that are modified after synthesis  Serine, threonine, and tyrosine can be phosphorylated   -Carboxyglutamate (prothtrombin), 4-hydroxyproline (collagen), and 5-hydroxylysine (collagen) Figure 5.7 Modified Amino Acid Residues Found in Polypeptides

13 Section 5.1: Amino Acids  Amino Acid Stereoisomers  Because the  -carbon (chiral carbon) is attached to four different groups, they can exist as stereoisomers  Except glycine, which is the only nonchiral standard amino acid  The molecules are mirror images of one another, or enantiomers  They cannot be superimposed over one another and rotate plane, polarized light in opposite directions (optical isomers) Figure 5.8 Two Enantiomers

14 Section 5.1: Amino Acids  Molecules are designated as D or L (glyceraldehyde is the reference compound for optical isomers)  D or L is used to indicate the similarity of the arrangement of atoms around the molecule’s asymmetric carbon to the asymmetric carbon of the glyceraldehyde isomers  Chirality has a profound effect on the structure and function of proteins Figure 5.9 D- and L-Glyceraldehyde

15 Section 5.1: Amino Acids  Titration of Amino Acids  Free amino acids contain ionizable groups  The ionic form depends on the pH  When amino acids have no net charge due to ionization of both groups, this is known as the isoelectric point (pI) and can be calculated using: pK 1 + pK 2 pI = 2 This formula only works if there is no pK R. If there is a pK R, then you will need to determine which pK values are on either side of zero net charge!

16 Section 5.1: Amino Acids

17  Alanine is a simple amino acid with two ionizable groups  Alanine loses two protons in a stepwise fashion upon titration with NaOH  Isoelectric point is reached with deprotonation of the carboxyl group Figure 5.10 Titration of Two Amino Acids: Alanine

18 Section 5.1: Amino Acids  Amino acids with ionizable side chains have more complex titration curves  Glutamic acid is a good example, because it has a carboxyl side chain group  Glutamic acid has a +1 charge at low pH  Glutamic acid’s isoelectric point as base is added and the  - carboxyl group loses a proton  As more base is added, it loses protons to a final net charge of -2 Figure 5.10 Titration of Two Amino Acids: Glutamic Acid pK 1 +pK R = pK I 2

19 Section 5.1: Amino Acids  Amino Acid Reactions  Amino acids, with their carboxyl, amino, and various R groups, can undergo many chemical reactions  Peptide bond and disulfide bridge are of special interest because of the effect they have on structure Figure 5.11 Formation of a Dipeptide

20 Section 5.1: Amino Acids  Peptide Bond Formation: polypeptides are linear polymers of amino acids linked by peptide bonds  Peptide bonds are amide linkages formed by nucleophilic acyl substitution  Dehydration reaction  Linkage of two amino acids is a dipeptide Figure 5.11 Formation of a Dipeptide

21 Section 5.1: Amino Acids  Linus Pauling was the first to characterize the peptide bond as rigid and flat  Found that C-N bonds between two amino acids are shorter than other C-N bonds  Gives them partial double- bond characteristics (they are resonance hybrids)  Because of the rigidity, one-third of the bonds in a polypeptide backbone cannot rotate freely  Limits the number of conformational possibilities Figure 5.12 The Peptide Bond

22 Section 5.1: Amino Acids  Cysteine oxidation leads to a reversible disulfide bond  A disulfide bridge forms when two cysteine residues form this bond  Helps stabilize polypeptides and proteins Figure 5.13 Oxidation of Two Cysteine Molecules to Form Cystine

23 Section 5.2: Peptides  Less structurally complex than larger proteins, peptides still have biologically important functions  Glutathione is a tripeptide found in most all organisms and is involved in protein and DNA synthesis, toxic substance metabolism, and amino acid transport  Vasopressin is an antidiuretic hormone that regulates water balance, appetite, and body temperature  Oxytocin is a peptide that aids in uterine contraction and lactation From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press

24 Section 5.3: Proteins  Of all the molecules in a living organism, proteins have the most diverse set of functions:  Catalysis (enzymes)  Structure (cell and organismal)  Movement (amoeboid movement)  Defense (antibodies)  Regulation (insulin is a peptide hormone)  Transport (membrane transporters)  Storage (ovalbumin in bird eggs)  Stress Response (heat shock proteins)

25 Section 5.3: Proteins  Due to recent research, numerous multifunction proteins have been identified  Proteins are categorized into families based on sequence and three-dimensional shape  Superfamilies are more distantly related proteins (e.g., hemoglobin and myoglobin to neuroglobin)  Proteins are also classified by shape: globular and fibrous  Proteins can be classified by composition: simple (contain only amino acids) or conjugated  Conjugated proteins have a protein and nonprotein component (i.e., lipoprotein or glycoprotein)

26 Section 5.3: Proteins  Protein Structure  Proteins are extraordinarily complex; therefore, simpler images highlighting specific features are useful  Space-filling and ribbon models  Levels of protein structure are primary, secondary, tertiary, and quaternary Figure 5.15 The Enzyme Adenylate Kinase

27 Section 5.3: Proteins  Primary Structure is the specific amino acid sequence of a protein  Homologous proteins share a similar sequence and arose from the same ancestor gene  When comparing amino acid sequences of a protein between species, those that are identical are invariant and presumed to be essential for function Figure 5.16 Segments of  -chain in HbA and HbS

28 Section 5.3: Proteins Figure 5.18 The  -Helix  Secondary Structure: Polypeptide secondary structure has a variety of repeating structures  Most common include the  -helix and  - pleated sheet  Both structures are stabilized by hydrogen bonding between the carbonyl and the N-H groups of the polypeptide’s backbone  The  -helix is a rigid, rod-like structure formed by a right-handed helical turn   -Helix is stabilized by N-H hydrogen bonding with a carbonyl four amino acids away  Glycine and proline do not foster  -helical formation

29 Section 5.3: Proteins Figure 5.19  -Pleated Sheet  The  -pleated sheets form when two or more polypeptide chain segments line up, side by side

30 Section 5.3: Proteins  Each  strand is fully extended and stabilized by hydrogen bonding between N-H and carbonyl groups of adjacent strands  Parallel sheets are much less stable than antiparallel sheets Figure 5.19  -Pleated Sheet

31 Section 5.3: Proteins  Many proteins form supersecondary structures (motifs) with patterns of  -helix and  -sheet structures (a)  unit (b)  -meander (c)  unit (d)  -barrel (e) Greek key Figure 5.20 Selected Supersecondary Structures

32 Section 5.3: Proteins  Tertiary Structure refers to unique three- dimensional structures formed by globular proteins  Also prosthetic groups  Protein folding is the process by which a nascent molecule acquires a highly organized structure  Information for folding is contained within the amino acid sequence  Interactions of the side chains are stabilized by electrostatic forces  Tertiary structure has several important features 1. Many polypeptides fold in a way to bring distant amino acids into close proximity 2. Globular proteins are compact because of efficient packing

33 Section 5.3: Proteins  Tertiary structure has several important features 1. Many polypeptides fold in a way to bring distant amino acids into close proximity 2. Globular proteins are compact because of efficient packing 3. Large globular proteins (200+ amino acids) often contain several domains  Domains are structurally independent segments that have specific functions  Core structural element of a domain is called a fold 4. A number of proteins called mosaic or modular proteins consist of repeated domains  Fibronectin has three repeated domains (F1, F2, and F3)  Domain modules are coded for by genetic sequences created by gene duplications

34 Section 5.3: Proteins Figure 5.21 Selected Domains Found in Large Numbers of Proteins

35 Section 5.3: Proteins  Interactions that stabilize tertiary structure are hydrophobic interactions, electrostatic interactions (salt bridges), hydrogen bonds, covalent bonds, and hydration Figure 5.23 Interactions That Maintain Tertiary Structure

36 Section 5.3: Proteins  Quaternary structure: a protein that is composed of several polypeptide chains (subunits)  Multisubunit proteins may be composed, at least in part, of identical subunits and are referred to as oligomers (composed of protomers) Figure 5.25 Structure of Immunoglobulin G

37 Section 5.3: Proteins  Reasons for common occurrence of multisubunit proteins: 1. Synthesis of subunits may be more efficient 2. In supramolecular complexes replacement of worn-out components can be handled more effectively 3. Biological function may be regulated by complex interactions of multiple subunits Figure 5.25 Structure of Immunoglobulin G

38 Section 5.3: Proteins  Polypeptide subunits held together with noncovalent interactions  Covalent interactions like disulfide bridges (immunoglobulins) are less common  Other covalent interactions include desmosine and lysinonorleucine linkages Figure 5.26 Desmosine and Lysinonorleucine linkages

39 Section 5.3: Proteins  Interactions between subunits are often affected by ligand binding  An example of this is allostery, which controls protein function by ligand binding  Can change protein conformation and function (allosteric transition)  Ligands triggering these transitions are effectors and modulators

40 Section 5.3: Proteins  Unstructured proteins: Some proteins are partially or completely unstructured  Unstructured proteins referred to as intrinsically unstructured proteins (IUPs) or natively unfolded proteins  Often these proteins are involved in searching out binding partners (i.e., KID domain of CREB) Figure 5.27 Disordered Protein Binding

41  Loss of Protein Structure: Because of small differences between the free energy of folded and unfolded proteins, they are susceptible to changes in environmental factors  Disruption of protein structure is denaturation (reverse is renaturation)  Denaturation does not disrupt primary protein structure Figure 5.28 The Anfinsen Experiment Section 5.3: Proteins

42  The Folding Problem  The direct relationship between a protein’s primary sequence and its final three-dimensional conformation is among the most important assumptions in biochemistry  Painstaking work has been done to be able to predict structure by understanding the physical and chemical properties of amino acids  X-ray crystallography, NMR spectroscopy, and site- directed mutagenesis Section 5.3: Proteins

43  Important advances have been made by biochemists in protein-folding research  This research led to the understanding that it is not a single pathway  A funnel shape best describes how an unfolded protein negotiates its way to a low-energy, folded state  Numerous routes and intermediates Figure 5.29 The Energy Landscape for Protein Folding Section 5.3: Proteins

44  Small polypeptides (<100 amino acids) often form with no intermediates  Larger polypeptides often require several intermediates (molten globules)  Many proteins use molecular chaperones to help with folding and targeting Figure 5.30 Protein Folding Section 5.3: Proteins

45  Molecular chaperones assist protein folding in two ways:  Preventing inappropriate protein-protein interactions  Helping folding occur rapidly and precisely  Two major classes: Hsp70s and Hsp60s (chaperonins) Figure 5.31 Space-Filling Model of the E. Coli Chaperonin, called the GroES-GroEL Complex Section 5.3: Proteins

46  Hsp70s are a family of chaperones that bind and stabilize proteins during the early stages of folding  Hsp60s (chaperonins) mediate protein folding after the protein is released by Hsp70  Increases speed and efficiency of the folding process  Both use ATP hydrolysis  Both are also involved in refolding proteins  If refolding is not possible, molecular chaperones promote protein degradation Figure 5.32 The Molecular Chaperones Section 5.3: Proteins

47  Fibrous Proteins  Typically contain high proportions of  -helices and  -pleated sheets  Often have structural rather than dynamic roles and are water insoluble  Keratin (  -helices) and silk fibroin (  -sheets) Figure 5.33  -Keratin Section 5.3: Proteins

48  Globular Proteins  Biological functions often include precise binding of ligands  Myoglobin and hemoglobin  Both have a specialized heme prosthetic group used for reversible oxygen binding Figure 5.36 Heme Section 5.3: Proteins

49  Myoglobin: found in high concentrations in cardiac and skeletal muscle  The protein component of myoglobin, globin, is a single protein with eight  -helices  Encloses a heme [Fe 2+ ] that has a high affinity for O 2 Figure 5.37 Myoglobin Section 5.3: Proteins

50  Hemoglobin is a roughly spherical protein found in red blood cells  Primary function is to transport oxygen from the lungs to tissues  HbA molecule is composed of 2  -chains and 2  -chains (  2  2 )  2% of hemoglobin contains  - chains instead of  -chains (HbA 2 )  Embryonic and fetal hemoglobin have  - and  -chains that have a higher affinity for O 2 Figure 5.38 The Oxygen- Binding Site of Heme Created by a Folded Globin Chain Section 5.3: Proteins

51  Comparison of myoglobin and hemoglobin identified several invariant residues, most having to do with oxygen binding  Four chains of hemoglobin arranged as two identical  dimers Figure 5.39 Hemoglobin Section 5.3: Proteins

52  Hemoglobin shows a sigmoidal oxygen dissociation curve due to cooperative binding  Binding of first O 2 changes hemoglobin’s conformation making binding of additional O 2 easier  Myoglobin dissociation curve is a hyperbolic simpler binding pattern Figure 5.41 Equilibrium Curves Measure the Affinity of Hemoglobin and Myoglobin for Oxygen Section 5.3: Proteins

53  Binding of ligands other than oxygen affects hemoglobin’s oxygen-binding properties  pH decrease enhances oxygen release from hemoglobin (Bohr effect)  The waste product CO 2 also enhances oxygen release by increasing H + concentration  Binding of H + to several ionizable groups on hemoglobin shifts it to its T state Section 5.3: Proteins

54  2,3-Bisphosphoglycerate (BPG) is also an important regulator of hemoglobin function  Red blood cells have a high concentration of BPG, which lowers hemoglobin’s affinity for O 2  In the lungs, these processes reverse Figure 5.42 The Effect of 2,3- Bisphosphoglycerate (BPG) on the Affinity Between Oxygen and Hemoglobin Section 5.3: Proteins

55  Molecular Machines  Purposeful movement is a hallmark of living things  This behavior takes a myriad of forms  Biological machines are responsible for these behaviors  Usually ATP or GTP driven  Motor proteins fall into the following categories: 1.Classical motors (myosins, dyneins, and kinesin) 2.Timing devices (EF-Tu in translation) 3.Microprocessing switching devices (G proteins) 4.Assembly and disassembly factors (cytoskeleton assembly and disassembly) Section 5.4: Molecular Machines

56 Chapter 7 Carbohydrates

57  Carbohydrates are the most abundant biomolecule in nature  Have a wide variety of cellular functions: energy, structure, communication, and precursors for other biomolecules  They are a direct link between solar energy and chemical bond energy Chapter 7: Overview

58 Section 7.1: Monosaccharides  Monosaccharides, or simple sugars, are polyhydroxy aldehydes or ketones  Sugars with an aldehyde functional group are aldoses  Sugars with an ketone functional group are ketoses Figure 7.1 General Formulas for the Aldose and Ketose Forms of Monosaccharides

59 Section 7.1: Monosaccharides  Monosaccharide Stereoisomers  An increase in the number of chiral carbons increases the number of possible optical isomers  2 n where n is the number of chiral carbons  Almost all naturally occurring monosaccharides are the D form  All can be considered to be derived from D -glyceraldehyde or nonchiral dihydroxyacetone Figure 7.3 The D Family of Aldoses

60 Section 7.1: Monosaccharides  Cyclic Structure of Monosaccharides  Sugars with four or more carbons exist primarily in cyclic forms  Ring formation occurs because aldehyde and ketone groups react reversibly with hydroxyl groups in an aqueous solution to form hemiacetals and hemiketals Figure 7.5 Formation of Hemiacetals and Hemiketals

61 Section 7.1: Monosaccharides  The two possible diastereomers that form because of cyclization are called anomers  Hydroxyl group on hemiacetal occurs on carbon 1 and can be in the up position (above ring) or down position (below ring)  In the D -sugar form, because the anomeric carbon is chiral, two stereoisomers of the aldose can form the  - anomer or  -anomer Figure 7.6 Monosaccharide Structure

62 Section 7.1: Monosaccharides  Haworth Structures — these structures more accurately depict bond angle and length in ring structures than the original Fischer structures  In the D-sugar form, when the anomer hydroxyl is up it gives a  -anomeric form (left in Fischer projection) while down gives the  -anomeric form (right) Figure 7.7 Haworth Structures of the Anomers of D -Glucose

63 Section 7.1: Monosaccharides  Five-membered rings are called furanoses and six- membered rings are pyranoses  Cyclic form of fructose is fructofuranose, while glucose in the pyranose form is glucopyranose Figure 7.8 Furan and Pyran Figure 7.9 Fischer and Haworth Representations of D -Fructose

64 Section 7.1: Monosaccharides  Reaction of Monosaccharides  The carbonyl and hydroxyl groups can undergo several chemical reactions  Most important include oxidation, reduction, isomerization, esterification, glycoside formation, and glycosylation reactions

65 Section 7.1: Monosaccharides  Glycoside Formation — hemiacetals and hemiketals react with alcohols to form the corresponding acetal and ketal  When the cyclic hemiacetal or hemiketal form of the monosaccharide reacts with an alcohol, the new linkage is a glycosidic linkage and the compound a glycoside Figure 7.17 Formation of Acetals and Ketals

66 Section 7.1: Monosaccharides  Naming of glycosides specifies the sugar component  Acetals of glucose and fructose are glucoside and fructoside Figure 7.18 Methyl Glucoside Formation

67 Section 7.1: Monosaccharides  If an acetal linkage is formed between the hemiacetal hydroxyl of one monosaccharide and the hydroxyl of another, this forms a disaccharide  In polysaccharides, large numbers of monosaccharides are linked together through acetal linkages

68 Section 7.1: Monosaccharides  Glycosylation Reactions attach sugars or glycans (sugar polymers) to proteins or lipids  Catalyzed by glycosyl transferases, glycosidic bonds are formed between anomeric carbons in certain glycans and oxygen or nitrogen of other types of molecules, resulting in N- or O-glycosidic bonds

69 Section 7.1: Monosaccharides  Glycation is the reaction of reducing sugars with nucleophilic nitrogen atoms in a nonenzymatic reaction  Most researched example of the glycation reaction is the nonenzymatic glycation of protein (Maillard reaction)  The Schiff base that forms rearranges to a stable ketoamine, called the Amadori product  Can further react to form advanced glycation end products (AGEs)  Promote inflammatory processes and involved in age-related diseases

70 Section 7.1: Monosaccharides Figure 7.20 The Maillard Reaction

71 Section 7.1: Monosaccharides  Important Monosaccharides  Glucose ( D -Glucose) — originally called dextrose, it is found in large quantities throughout the natural world  The primary fuel for living cells  Preferred energy source for brain cells and cells without mitochondria (erythrocytes) Figure 7.21  - D -glucopyranose

72 Section 7.1: Monosaccharides  Fructose ( D -Fructose) is often referred to as fruit sugar, because of its high content in fruit  On a per - gram basis, it is twice as sweet as sucrose; therefore, it is often used as a sweetening agent in processed food Figure 7.22  -D-fructofuranose

73 Section 7.1: Monosaccharides  Galactose is necessary to synthesize a variety of important biomolecules  Important biomolecules include lactose, glycolipids, phospholipids, proetoglycan, and glycoproteins  Galactosemia is a genetic disorder resulting from a missing enzyme in galactose metabolism Figure 7.23  -D-galactopyranose

74 Section 7.2: Disaccharides  Disaccharides  Two monosaccharides linked by a glycosidic bond  Linkages are named by  - or  -conformation and by which carbons are connected (e.g.,  (1,4) or  (1,4)) Figure 7.27 Glycosidic Bonds

75 Section 7.2: Disaccharides  Disaccharides Continued  Lactose (milk sugar) is the disaccharide found in milk  One molecule of galactose linked to one molecule of glucose (  (1,4) linkage)  It is common to have a deficiency in the enzyme that breaks down lactose (lactase)  Lactose is a reducing sugar Figure 7.28  - and  -lactose

76 Section 7.2: Disaccharides  Disaccharides Continued  Sucrose is common table sugar (cane or beet sugar) produced in the leaves and stems of plants  One molecule of glucose linked to one molecule of fructose, linked by an ,  (1,2) glycosidic bond  Glycosidic bond occurs between both anomeric carbons  Sucrose is a nonreducing sugar Figure 7.31 Sucrose

77 Section 7.3: Polysaccharides  Polysaccharides (glycans) are composed of large numbers of monosaccharides connected by glycosidic linkages  Smaller glycans made of 10 to 15 monomers called oligosaccharides, most often attached to polypeptides as glycoproteins  Two broad classes : N- and O-linked oligosaccharides

78 Section 7.3: Polysaccharides  O-Glycosidic linkages attach glycans to the side chain hydroxyl of serine or threonine residues or the hydroxyl oxygens of membrane lipids Figure 7.32 Oligosaccharides Linked to Polypeptides  N-linked oligosaccharides are attached to polypeptides by an N-glycosidic bond with the side chain amide nitrogen from the amino acid asparagine  Three major types of asparagine-linked oligosaccharides: high mannose, hybrid, and complex

79 Section 7.3: Polysaccharides  Homoglycans  Have one type of monosaccharide and are found in starch, glycogen, cellulose, and chitin (glucose monomer)  Starch and glycogen are energy storage molecules while chitin and cellulose are structural  Chitin is part of the cell wall of fungi and arthropod exoskeleton  Cellulose is the primary component of plant cell walls  No fixed molecular weight, because the size is a reflection of the metabolic state of the cell producing them

80 Section 7.3: Polysaccharides  Starch — the energy reservoir of plant cells and a significant source of carbohydrate in the human diet  Two polysaccharides occur together in starch: amylose and amylopectin  Amylose is composed of long, unbranched chains of D - glucose with  (1,4) linkages between them Figure 7.33 Amylose

81 Section 7.3: Polysaccharides  Amylose typically contains thousands of glucose monomers and a molecular weight from 150,000 to 600,000 Da  The other form is amylopectin, which is a branched polymer containing both  (1,6) and  (1,4) linkages  Branch points occur every 20 to 25 residues Figure 7.33 Amylose

82 Section 7.3: Polysaccharides  Glycogen is the carbohydrate storage molecule in vertebrates found in greatest abundance in the liver and muscle cells  Up to 8–10% of the wet weight of liver cells and 2–3% in muscle cells  Similar in structure to amylopectin, with more branch points  More compact and easily mobilized than other polysaccharides

83 Section 7.3: Polysaccharides Figure 7.34 (a) Amylopectin and (b) Glycogen

84 Section 7.3: Polysaccharides  Cellulose is a polymer of D -glucopyranosides linked by  (1,4) glycosidic bonds  It is the most important structural polysaccharide of plants (most abundant organic substance on earth) Figure 7.35 The Disaccharide Repeating Unit of Cellulose

85 Section 7.3: Polysaccharides  Pairs of unbranched cellulose molecules (12,000 glucose units each) are held together by hydrogen bonding to form sheetlike strips, or microfibrils  Each microfibril bundle is tough and inflexible with a tensile strength comparable to that of steel wire  Important for dietary fiber, wood, paper, and textiles Figure 7.36 Cellulose Microfibrils

86 Section 7.3: Polysaccharides  Heteroglycans  High-molecular-weight carbohydrate polymers that contain more than one type of monosaccharide  Major types: N- and O-linked glycosaminoglycans (glycans), glycosaminoglycans, glycan components of glycolipids, and GPI (glycosylphosphatidylinositol) anchors  GPI anchors and glycolipids will be discussed in Chapter 11

87 Section 7.3: Polysaccharides  Heteroglycans Continued  N- and O-Glycans — many proteins have N- and O- linked oligosacchaarides  N-linked (N-glycans) are linked via a  -glycosidic bond  O-linked (O-glycans) have a disaccharide core of galactosyl-  -(1,3)-N-acetylgalactosamine linked via an  -glycosidic bond to the hydroxyl of serine or threonine residues  Glycosaminoglycans (GAGs) are linear polymers with disaccharide repeating units  Five classes: hyaluronic acid, chondroitin sulfate, dermatan sulfate, heparin and heparin sulfate, and keratin sulfate  Varying uses based on repeating unit

88 Section 7.4: Glycoconjugates  Glycoconjugates result from carbohydrates being linked to proteins and lipids  Proteoglycans  Distinguished from other glycoproteins by their high carbohydrate content (about 95%)  Occur on cell surfaces or are secreted to the extracellular matrix Figure 7.38 Proteoglycan Aggregate From McKee and McKee, Biochemistry, 5th Edition, © 2011 Oxford University Press

89 Section 7.4: Glycoconjugates  Glycoproteins  Commonly defined as proteins that are covalently linked to carbohydrates through N- and O-linkages  Several addition reactions in the lumen of the endoplasmic reticulum and Golgi complex are responsible for final N-linked oligosaccharide structure  O-glycan synthesis occurs later, probably initiating in the Golgi complex  Carbohydrate could be 1%–85% of total weight  Glycoprotein Functions occur in cells as soluble and membrane-bound forms and are nearly ubiquitous in living organisms  Vertebrate animals are particularly rich in glycoproteins

90 Section 7.4: Glycoconjugates Figure 7.39 The Glycocalyx

91 Section 7.5: The Sugar Code  Living organisms require large coding capacities for information transfer  Profound complexity of functioning systems  To succeed as a coding mechanism, a class of molecules must have a large capacity for variation  Glycosylation is the most important posttranslational modification in terms of coding capacity  More possibilities with hexasaccharides than hexapeptides

92 Section 7.5: The Sugar Code  In addition to their immense combinatorial possibilities they are also relatively inflexible, which makes them perfect for precise ligand binding  Lectins  Lectins, or carbohydrate-binding proteins, are involved in translating the sugar code  Bind specifically to carbohydrates via hydrogen bonding, van der Waals forces, and hydrophobic interactions

93 Section 7.5: The Sugar Code Figure 7.40 Role of Oligosaccharides in Biological Recognition  Lectins Continued  Biological processes include binding to microorganisms, binding to toxins, and involved in leukocyte rolling

94 Section 7.5: The Sugar Code  The Glycome  Total set of sugars and glycans in a cell or organism is the glycome  Constantly in flux depending on the cell’s response to environment  There is no template for glycan biosynthesis; it is done in a stepwise process  Glycoforms can result based upon slight variations in glycan composition of each glycoprotein

95 Chapter 11 Lipids and Membranes

96  Fatty Acids  Monocarboxylic acids that typically contain hydrocarbon chains of variable lengths (12 to 20 or more carbons)  Numbered from the carboxylate end, and the  - carbon is adjacent to the carboxylate group  Terminal methyl carbon is denoted the omega (  ) carbon  Important in triacylglycerols and phospholipids Figure 11.1 Fatty Acid Structure Section 11.1: Lipid Classes


98  Most naturally occurring fatty acids have an even number of carbons in an unbranched chain  Fatty acids that contain only single carbon-carbon bonds are saturated  Fatty acids that contain one or more double bonds are unsaturated  Can occur in two isomeric forms: cis (like groups on the same side) and trans (like groups are on opposite sides) Figure 11.2 Isomeric Forms of Unsaturated Molecules Section 11.1: Lipid Classes

99  The double bonds in most naturally occurring fatty acids are cis and cause a kink in the fatty acid chain  Unsaturated fatty acids are liquid at room temperature; saturated fatty acids are usually solid  Monounsaturated fatty acids have one double bond while polyunsaturated fats have two or more Figure 11.3 Space-Filling and Conformational Models Section 11.1: Lipid Classes

100  Plants and bacteria can synthesize all fatty acids they require from acetyl-CoA  Animals acquire most of theirs from dietary sources  Nonessential fatty acids can be synthesized while essential fatty acids must be acquired from the diet  Omega-3 fatty acids (i.e.,  -linolenic acid and its derivatives) may promote cardiovascular health  Certain fatty acids attach to proteins called acylated proteins; the groups (acyl groups) help facilitate interactions with the environment  Myristoylation and palmitoylation Section 11.1: Lipid Classes

101  Eicosanoids  A diverse group of powerful, hormone-like (generally autocrine) molecules produced in most mammalian tissues  Include prostaglandins, thromboxanes, and leukotrienes  Mediate a wide variety of physiological processes: smooth muscle contraction, inflammation, pain perception, and blood flow regulation Figure 11.4a Eicosanoids Section 11.1: Lipid Classes

102  Eicosonoids are often derived from arachidonic acid or eicosapentaenoic acid (EPA)  Prostaglandins contain a cyclopentane ring and hydroxyl groups at C-11 and C-15  Prostaglandins are involved in inflammation, digestion, and reproduction Figure 11.4a Eicosanoids Section 11.1: Lipid Classes

103 Figure 11.4b Eicosanoids Section 11.1: Lipid Classes  Thromboxanes differ structurally from other eicosanoids in that they have a cyclic ether  Synthesized by polymorphonuclear lymphocytes  Involved in platelet aggregation and vasoconstriction following tissue injury

104  Leukotrienes were named from their discovery in white blood cells and triene group in their structure  LTC 4, LTD 4, and LTE 4 have been identified as components of slow-reacting substance of anaphylaxis  Other effects of leukotrienes: blood vessel fluid leakage, white blood cell chemoattractant, vasoconstriction, edema, and bronchoconstriction Figure 11.4c Eicosanoids Section 11.1: Lipid Classes

105  Triacylglycerols  Triacylglycerols are esters of glycerol with three fatty acids  Neutral fats because they have no charge  Contain fatty acids of varying lengths and can be a mixture of saturated and unsaturated Figure 11.5 Triacylglycerol Section 11.1: Lipid Classes

106  Depending on fatty acid composition, can be termed fats or oils  Fats are solid at room temperature and have a high saturated fatty acid composition  Oils are liquid at room temperature and have a high unsaturated fatty acid composition Figure 11.6 Space-Filling and Conformational Models of a Triacylglycerol Section 11.1: Lipid Classes

107  Roles in animals: energy storage (also in plants), insulation at low temperatures, and water repellent for some animals’ feathers and fur  Better storage form of energy for two reasons: 1. Hydrophobic and coalesce into droplets; store an equivalent amount of energy in about one-eighth the space 2. More reduced and thus can release more electrons per molecule when oxidized Figure 11.5 Triacylglycerol Section 11.1: Lipid Classes

108  Wax Esters  Waxes are complex mixtures of nonpolar lipids  Protective coatings on the leaves, stems, and fruits of plants and on the skin and fur of animals  Wax esters composed of long-chain fatty acids and long-chain alcohols are prominent constituents of most waxes  Examples include carnuba (melissyl cerotate) and beeswax Figure 11.8 The Wax Ester Melissyl Cerotate Section 11.1: Lipid Classes

109  Phospholipids  Amphipathic with a polar head group (phosphate and other polar or charged groups) and hydrophobic fatty acids  Act in membrane formation, emulsification, and as a surfactant  Spontaneously rearrange into ordered structures when suspended in water Figure 11.9 Phospholipid Molecules in Aqueous Solution Section 11.1: Lipid Classes

110  Two types of phospholipids: phosphoglycerides and sphingomyelins  Sphingomyelins contain sphingosine instead of glycerol (also classified as sphingolipids)  Phosphoglycerides contain a glycerol, fatty acids, phosphate, and an alcohol  Simplest phosphoglyceride is phosphatidic acid composed of glycerol-3-phosphate and two fatty acids  Phosphatidylcholine (lecithin) is an example of alcohol esterified to the phosphate group as choline Section 11.1: Lipid Classes


112  Another phosphoglyceride, phosphatidylinositol, is an important structural component of glycosyl phosphatidylinositol (GPI) anchors  GPI anchors attach certain proteins to the membrane surface  Proteins are attached via an amide linkage Figure GPI Anchor Section 11.1: Lipid Classes

113  Phospholipases  Hydrolyze ester bonds in glycerophospholipid molecules  Three major functions: membrane remodeling, signal transduction, and digestion  Membrane remodeling—removal of fatty acids to adjust the ratio of saturated to unsaturated or repair a damaged fatty acid Figure Phospholipases Section 11.1: Lipid Classes

114  Phospholipases Continued  Signal Transduction—phospholipid hydrolysis initiates the signal transduction by numerous hormones  Digestion—pancreatic phospholipases degrade dietary phospholipids in the small intestine  Toxic Phospholipases—various organisms use membrane-degrading phospholipases as a means of inflicting damage  Bacterial  -toxin and necrosis from snake venom (PLA 2 ) Section 11.1: Lipid Classes

115  Sphingolipids  Important components of animal and plant membranes  Sphingosine (long-chain amino alcohol) and ceramide in animal cells Figure Sphingolipid Components Section 11.1: Lipid Classes

116  Sphingomyelin is found in most cell membranes, but is most abundant in the myelin sheath of nerve cells Figure Space-Filling and Conformational Models of Sphingolmyelin Section 11.1: Lipid Classes

117  The ceramides are also precursors of glycolipids  A monosaccharide, disacchaaride, or oligosaccharide attached to a ceramide through an O-glycosidic bond  Most important classes are cerebrosides, sulfatides, and gangliosides (may bind bacteria and their toxins) Figure 11.14a Selected Glycolipids Section 11.1: Lipid Classes

118  Cerebrosides have a monosaccharide for their head group  Galactocerebroside is found in brain cell membranes  Sulfatides are negatively charged at physiological pH  Gangliosides possess oligosaccharide groups; occur in most animal tissues and G M2 is involved in Tay-Sachs disease Figure 11.14b Selected Glycolipids Section 11.1: Lipid Classes

119  Isoprenoids  Vast array of biomolecules containing repeating five- carbon structural units, or isoprene units  Isoprenoids consist of terpenes and steroids  Terpenes are classified by the number of isoprene units they have  Monoterpenes (used in perfumes), sesquiterpines (e.g., citronella), tetraterpenes (e.g., carotenoids) Figure Isoprene Section 11.1: Lipid Classes

120  Carotenoids are the orange pigments found in plants  Mixed terpenoids consist of a nonterpene group attached to the isoprenoid group (prenyl groups)  Include vitamin K and vitamin E Figure Vitamin K, a Mixed Terpenoid Section 11.1: Lipid Classes

121  A variety of proteins are covalently attached to prenyl groups (prenylation): farnesyl and geranylgeranyl groups  Unknown function, but may be involved in cell growth Figure Prenylated Proteins Section 11.1: Lipid Classes

122  Steroids are derivatives of triterpenes with four fused rings (e.g., cholesterol)  Found in all eukaryotes and some bacteria  Differentiated by double-bond placement and various substituents Figure Structure of Cholesterol Section 11.1: Lipid Classes

123  Cholesterol is an important molecule in animal cells that is classified as a sterol, because C-3 is oxidized to a hydroxyl group  Essential in animal membranes; a precursor of all steroid hormones, vitamin D, and bile salts  Usually stored in cells as a fatty acid ester  The term steroid is commonly used to describe all derivatives of the steroid ring structure Section 11.1: Lipid Classes

124 Figure Animal Steroids Section 11.1: Lipid Classes

125  Lipoproteins  Term most often applied to a group of molecular complexes found in the blood plasma of mammals  Transport lipid molecules through the bloodstream from organ to organ  Protein components (apolipoproteins) for lipoproteins are synthesized in the liver or intestine Figure Plasma Lipoproteins Section 11.1: Lipid Classes

126  Lipoproteins are classified according to their density:  Chylomicrons are large lipoproteins of extremely low density that transport triacylglycerol and cholesteryl esters (synthesized in the intestines)  Very low density lipoproteins (VLDL) are synthesized in the liver and transport lipids to the tissues  Low density lipoproteins (LDL) are principle transporters of cholesterol and cholesteryl esters to tissues  High density lipoprotein (HDL) is a protein-rich particle produced in the liver and intestine that seems to be a scavenger of excess cholesterol from membranes Section 11.1: Lipid Classes

127  A membrane is a noncovalent heteropolymer of lipid bilayer and associated proteins (fluid mosaic model)  Membrane Structure  Proportions of lipid, protein, and carbohydrate vary considerably among cell types and organelles Section 11.2: Membranes

128  Membrane lipids: phospholipids form bimolecular layers at relatively low concentrations; this is the basis of membrane structure  Membrane lipids are largely responsible for many membrane properties  Membrane fluidity refers to the viscosity of the lipid bilayer  Rapid lateral movement is apparently responsible for normal membrane function Figure Lateral Diffusion in Biological Membranes Section 11.2: Membranes

129  The movement of molecules from one side of a membrane to the other requires a flipase  Membrane fluidity largely depends on the percentage of unsaturated fatty acids and cholesterol  Cholesterol contributes to stability with its rigid ring system and fluidity with its flexible hydrocarbon tail Figure Diagrammatic View of a Lipid Bilayer Section 11.2: Membranes

130  Selective permeability is provided by the hydrophobic chains of the lipid bilayer, which is impermeable to most all molecules (except small nonpolar molecules)  Membrane proteins help regulate the movement of ionic and polar substances  Small nonpolar substances may diffuse down their concentration gradient  Self-sealing is a result of the lateral flow of lipid molecules after a small disruption  Asymmetry of biological membranes is necessary for their function  The lipid composition on each side of the membrane is different Section 11.2: Membranes

131  Membrane Proteins—most functions associated with the membrane require membrane proteins  Classified by their relationship with the membrane: peripheral or integral Figure Integral and Peripheral Membrane Proteins Section 11.2: Membranes

132  Integral proteins embed in or pass through the membrane  Red blood cell anion exchanger  Peripheral proteins are bound to the membrane primarily through noncovalent interactions  Can be linked covalently through myristic, palmitic, or prenyl groups  GPI anchors link a wide variety of proteins to the membrane Figure Red Blood Cell Integral Membrane Proteins Section 11.2: Membranes

133  Membrane Microdomains—lipids and proteins in membranes are not uniformly distributed  Specialized microdomains like “lipid rafts” can be found in the external leaflet of the plasma membrane Figure Lipid Rafts Section 11.2: Membranes

134  Lipid rafts often include cholesterol, sphingolipids, and certain proteins  Lipid molecules are more ordered (less fluid) than non- raft regions  Lipid rafts have been implicated in a number of processes: exocytosis, endocytosis, and signal transduction Figure The Lipid Raft Environment Section 11.2: Membranes

135  Membrane Function  There are a vast array of membrane functions, including transport of polar and charged substances and the relay of signals Figure Transport across Membranes Section 11.2: Membranes

136  Membrane Transport—the mechanisms are vital to living organisms  Ions and molecules constantly move across the plasma membrane and membranes of organelles  Important for nutrient intake, waste excretion, and the regulation of ion concentration  Biological transport mechanisms are classified according to whether they require energy Section 11.2: Membranes

137  In passive transport, there is no energy input, while in active transport, energy is required  Passive is exemplified by simple diffusion and facilitated diffusion (with the concentration gradient)  Active transport uses energy to transport molecules against a concentration gradient Figure Transport across Membranes Section 11.2: Membranes

138  Simple diffusion involves the propulsion of each solute by random molecular motion from an area of high concentration to an area of low concentration  Diffusion of gases O 2 and CO 2 across membranes is proportional to their concentration gradients  Does not require a protein channel  Facilitated diffusion uses channel proteins to move large or charged molecules down their concentration gradient  Examples include chemically gated Na + channel and voltage-gated K + channel Section 11.2: Membranes

139  Active transport has two forms: primary and secondary  In primary active transport, transmembrane ATP- hydrolyzing enzymes provide the energy to drive the transport of ions or molecules  Na + -K + ATPase Figure The Na + -K + ATPase and Glucose Transport Section 11.2: Membranes

140  In secondary active transport, concentration gradients formed by primary active transport are used to move other substances across the membrane  Na + -K + ATPase pump in the kidney drives the movement of D -glucose against its concentration gradient Figure The Na + -K + ATPase and Glucose Transport Section 11.2: Membranes

141  Membrane Receptors provide mechanisms by which cells monitor and respond to changes in their environment  Chemical signals bind to membrane receptors in multicellular organisms for intracellular communication  Other receptors are involved in cell-cell recognition  Binding of ligand to membrane receptor causes a conformational change and programmed response Section 11.2: Membranes

142 Chapter 17 Nucleic Acids

143  Scientists have studied how organisms organize and process genetic information, revealing the following principles: 1. DNA directs the function of living cells and is transmitted to offspring  DNA is composed of two polydeoxynucleotide strands forming a double helix Figure 17.2 Two Models of DNA Structure Section 17.1: DNA

144  A gene is a DNA sequence that contains the base sequence information to code for a gene product, protein, or RNA  The complete DNA base sequence of an organism is its genome  DNA synthesis, referred to as replication, involves complementary base pairing between the parental and newly synthesized strand Figure 17.2 Two Models of DNA Structure Section 17.1: DNA

145 2. The synthesis of RNA begins the process of decoding genetic information  RNA synthesis is called transcription and involves complementary base pairing of ribonucleotides to DNA bases  Each new RNA is a transcript  The total RNA transcripts for an organism comprise its transcriptome Figure 17.3a An Overview of Genetic Information Flow Section 17.1: DNA

146 3. Several RNA molecules participate directly in the synthesis of protein, or translation  Messenger RNA (mRNA) specifies the primary protein sequence  Transfer RNA (tRNA) delivers the specific amino acid  Ribosomal RNA (rRNA) molecules are components of ribosomes Figure 17.3b An Overview of Genetic Information Flow Section 17.1: DNA

147  The proteome is the entire set of proteins synthesized 4. Gene expression is the process by which cells control the timing of gene product synthesis in response to environmental or developmental cues  Metabolome refers to the sum total of low molecular weight metabolites produced by the cell Figure 17.3b An Overview of Genetic Information Flow Section 17.1: DNA

148  The Central dogma schematically summarizes the previous information  Includes replication, transcription, and translation  The central dogma is generally how the flow of information works in all organisms, except some viruses have RNA genomes and use reverse transcriptase to make DNA (e.g., HIV) Section 17.1: DNA DNARNAProtein

149  DNA consists of two polydeoxynucleotide strands that wind around each other to form a right-handed double helix  Each DNA nucleotide monomer is composed of a nitrogenous base, a deoxyribose sugar, and phosphate Figure 17.4 DNA Strand Structure Section 17.1: DNA

150  Nucleotides are linked by 3′,5′- phosphodiester bonds  These join the 3′-hydroxyl of one nucleotide to the 5′- phosphate of another Figure 17.4 DNA Strand Structure Section 17.1: DNA

151  The antiparallel nature of the two strands allows hydrogen bonds to form between the nitrogenous bases  Two types of base pair (bp) in DNA: (1) adenine (purine) pairs with thymine (pyrimidine) and (2) the purine guanine pairs with the pyrimidine cytosine Figure 17.5 DNA Structure Section 17.1: DNA

152  The dimensions of crystalline B -DNA have been precisely measured: 1. One turn of the double helix spans 3.32 nm and consists of 10.3 base pairs Figure 17.6 DNA Structure: GC Base Pair Dimensions Section 17.1: DNA

153 2. Diameter of the double helix is 2.37 nm, only suitable for base pairing a purine with a pyrimidine 3. The distance between adjacent base pairs is nm Figure 17.6 DNA Structure: AT Base Pair Dimensions Section 17.1: DNA

154  DNA is a relatively stable molecule with several noncovalent interactions adding to its stability 1. Hydrophobic interactions—internal base clustering 2. Hydrogen bonds—formation of preferred bonds: three between CG base pairs and two between AT base pairs 3. Base stacking—bases are nearly planar and stacked, allowing for weak van der Waals forces between the rings 4. Hydration—water interacts with the structure of DNA to stabilize structure 5. Electrostatic interactions—destabilization by negatively charged phosphates of sugar-phosphate backbone are minimized by the shielding effect of water on Mg 2+ Section 17.1: DNA

155  Mutation types — The most common are small single base changes, also called point mutations  This results in transition or transversion mutations  Transition mutations, caused by deamination, lead to purine for purine or pyrimidine for pyrimidine substitutions  Transversion mutations, caused by alkylating agents or ionizing radiation, occur when a purine is substituted for a pyrimidine or vice versa Section 17.1: DNA

156  Point mutations that occur in a population with any frequency are referred to as single nucleotide polymorphisms (SNPs)  Point mutations that occur within the coding portion of a gene can be classified according to their impact on structure and/or function:  Silent mutations have no discernable effect  Missense mutations have an observable effect  Nonsense mutations changes a codon for an amino acid to that of a premature stop codon Section 17.1: DNA

157  Insertions and deletions, or indels, occur from one to thousands of bases  Indels that occur within the coding region that are not divisible by three cause a frameshift mutation  Genome rearrangements can cause disruptions in gene structure or regulation.  Occur as a result of double strand breaks and can lead to inversions, translocations, or duplications Section 17.1: DNA

158  DNA Structure: The Genetic Material  In the early decades of the twentieth century, life scientists believed that of the two chromosome components (DNA and protein) that protein was most likely responsible for transmission of inherited traits  The work of several scientists would lead to another conclusion Section 17.1: DNA

159  DNA Structure: Variations on a Theme  Watson and Crick’s discovery is referred to as B-DNA (sodium salt)  Another form is the A-DNA, which forms when RNA/DNA duplexes form  Z-DNA (zigzag conformation) is left-handed DNA that can form as a result of torsion during transcription Figure A-DNA, B-DNA, and Z-DNA Section 17.1: DNA

160  DNA can form other structures, including cruciforms, which are cross-like structures, probably a result of palindromes (inverted repeats)  Packaging large DNA molecules to fit inside a cell or nucleus requires a process termed supercoiling Section 17.1: DNA

161  DNA Supercoiling  Facilitates several biological processes: packaging of DNA, replication, and transcription  Linear and circular DNA can be in a relaxed or supercoiled shape Figure Linear and Circular DNA and DNA Winding Section 17.1: DNA

162  Chromosomes and Chromatin  DNA is packaged into chromosomes  Prokaryotic and eukaryotic chromosomes differ significantly  Prokaryotes — the E. coli chromosome is a circular DNA molecule that is extensively looped and coiled  Supercoiled DNA complexed with a protein core Figure The E. coli Chromosome Removed from a Cell Section 17.1: DNA

163  Eukaryotes have extraordinarily large genomes when compared to prokaryotes  Chromosome number and length can vary by species  Each eukaryotic chromosome consists of a single, linear DNA molecule complexed with histone proteins to form nucleohistone  Chromatin is the term used to describe this complex Figure Electron Micrograph of Chromatin Section 17.1: DNA

164  Nucleosomes are formed by the binding of DNA and histone proteins  Nucleosomes have a beaded appearance when viewed by electron micrograph  Histone proteins have five major classes: H1, H2A, H2B, H3, and H4  A nucleosome is positively coiled DNA wrapped around a histone core (two copies each of H2A, H2B, H3, and H4) Figure Electron Micrograph of Chromatin Section 17.1: DNA

165  Prokaryotic Genomes — Investigation of E. coli has revealed the following prokaryotic features: 1. Genome size—usually considerably less DNA and fewer genes (E. coli 4.6 megabases) than eukaryotic genomes 2. Coding capacity—compact and continuous genes 3. Gene expression—genes organized into operons  Prokaryotes often contain plasmids, which are usually small and circular DNA with additional genes (e.g., antibiotic resistance) Section 17.1: DNA

166  Eukaryotic Genomes — Investigation has revealed the organization to be very complex  The following are unique eukaryotic genome features: 1. Genome size—eukaryotic genome size does not necessarily indicate complexity 2. Coding capacity—enormous protein coding capacity, but the majority of DNA sequences do not have coding functions 3. Coding continuity—genes are interrupted by noncoding introns, which can be removed by splicing from the primary RNA transcript Section 17.1: DNA

167  Existence of introns and exons allows eukaryotes to produce more than one polypeptide from each protein- coding gene  Alternative splicing allows for various combinations of exons to be joined to form different mRNAs  Intergenic sequences are those sequences that do not code for polypeptide primary sequence or RNAs Section 17.1: DNA

168  Of the 3,200 Mb of the human genome, only 38% comprise genes and related sequence  Only 4% codes for gene products  Humans have about 23,000 protein coding genesand several ncRNA genes Section 17.1: DNA

169  25% of known protein- coding genes are related to DNA synthesis and repair  21% signal transduction  17% general biochemical functions  38% other activities  Over 60% of the human genome is intergenic sequences Figure Human Protein-Coding Genes Section 17.1: DNA

170  Two classes: tandem repeats and interspersed genome- wide repeats  Tandem repeats (satellite DNA) are DNA sequences in which multiple copies are arranged next to each other  Certain tandem repeats play structural roles like centromeres and telomeres  Some are small, like microsatellites (1-4 bp) and minisatellites ( bp)  Used as markers in genetic disease, forensic investigations, and kinship Section 17.1: DNA

171  Interspersed genome-wide repeats are repetitive sequences scattered around the genome  Often involve mobile genetic elements that can duplicate and move around the genome  Transposons and retrotransposones  LINEs (long interspersed nuclear elements) and SINEs (short interspersed nuclear elements) are two types of transposons Section 17.1: DNA

172  RNA is a versatile molecule, not only involved in protein synthesis, but plays structural and enzymatic roles as well  Differences between DNA and RNA primary structure:  1. Ribose sugar instead of deoxyribose  2. Uracil nucleotide instead of thymine Figure Secondary Structure of RNA Section 17.2: RNA

173  3. RNA exists as a single strand that can form complex three- dimensional structures by base pairing with itself  4. Some RNA molecules have catalytic properties, or ribozymes (e.g., self-cleavages or cleave other RNA) Figure Secondary Structure of RNA Section 17.2: RNA

174  Transfer RNA  Transfer RNA (tRNA) molecules transport amino acids to ribosomes for assembly (15% of cellular RNA)  Average length: 75 bases  At least one tRNA for each amino acid  Structurally look like a warped cloverleaf due to extensive intrachain base pairing Figure 17.26a Transfer RNA Section 17.2: RNA

175  Amino acids are attached via specific aminoacyl-tRNA synthetases to the end opposite the three nucleotide anticodon  Anticodon allows the tRNA to recognize the correct mRNA codon and properly align its amino acid for protein synthesis  The tRNA loops help facilitate interactions with the correct aminoacyl-tRNA synthetases Section 17.2: RNA Figure 17.26b Transfer RNA

176  Ribosomal RNA  Ribosomal RNA (rRNA) is the most abundant RNA in living cells with a complex secondary structure  Components of ribosomes (eukaryotes and prokaryotes)  Similar in shape and function, both have a small and large subunit, but differ in size and chemical composition  Eukaryotic are larger (80S) with a 60S and 40S subunit, while prokaryotic are smaller (70S) with 50S and 30S subunits Section 17.2: RNA

177  rRNA plays a role in scaffolding as well as enzymatic functions  Ribosomes also have proteins that interact with rRNA for structure and function Section 17.2: RNA Figure rRNA Structure

178  Messenger RNA  Messenger RNA (mRNA) is the carrier of genetic information from DNA to protein synthesis (approximately 5% of total RNA)  mRNA varies considerably in size  Prokaryotic and eukaryotic mRNA differ in several respects  Prokaryotes are polycistronic while eukaryotes are usually monocistronic  mRNAs are processed differently; eukaryotic mRNA requires 5′ capping, 3′ tailing, and splicing Section 17.2: RNA

179  Noncoding RNA  RNAs that do not directly code for polypeptides are called noncoding RNAs (ncRNAs)  Micro RNAs and small interfering RNAs are among the shortest and involved in the RNA-induced silencing complex  Small Nucleolar RNAs (snoRNAs) facilitate chemical modifications to rRNA in the nucleolus Section 17.2: RNA

180  Noncoding RNA  Small interfering RNAs (siRNAs) are nt dsRNAs that play a crucial role in RNA interference (RNAi)  Small nuclear RNAs (snRNAs) combine with proteins to form small nuclear ribonucleoproteins (snRNPs) and are involved in splicing Section 17.2: RNA

181  Viruses lack the properties that distinguish life from nonlife (e.g., no metabolism)  Once a virus has infected a cell, its nucleic acid can hijack the host’s nucleic acid and protein- synthesizing machinery  The virus can then make copies of itself until it ruptures the host cell or integrates into the host cell’s chromosome Section 17.3: Viruses

182  A viral infection can provide biochemical insight, because it subverts the host cell’s function  Viruses can cause numerous different diseases, but have also been invaluable in the development of recombinant DNA technology  Human papillomavirus can cause cervical cancer Section 17.3: Viruses

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