Chapter4_berg_8e_mng Fall 2024_Part1 MNG.pdf

Chapter 4: Flow of genetic information (Part1) Structure of one chain of DNA Simple and elegant Double helix structure Other structures (Bacterial DNA,...

Chapter 4: Flow of genetic information (Part1) Structure of one chain of DNA Simple and elegant Double helix structure Other structures (Bacterial DNA, RNA) Family resemblance, very evident in this One such regulatory protein, a zinc-finger photograph of four sisters, results from having protein (zinc ion is blue, protein is red), is genes in common. Genes must be expressed to shown bound to a control region of DNA exert an effect, and proteins regulate such (black). expression.  Why do we need DNA? The flow of genetic information is from DNA to RNA to proteins, a scheme called the central dogma. DNA double helical structure discovered in 1953 Crick speaking at the 1963 Cold Crick’s first outline of the central dogma, from an Spring Harbor Symposium. unpublished note made in 1956. Crick FHC. Central dogma of molecular biology. Nature. 1970;227:561–563. Nucleic acids are long, linear polymers constructed from 4 types of monomers. Each monomer consists of a sugar, a phosphate and a base. The sequence of the bases is the information content of the nucleic acid. Nucleic acids are long, linear polymers constructed from 4 types of monomers. Each monomer consists of a sugar, a phosphate and a base. The sequence of the bases is the information content of the nucleic acid.  Reminder from the first lecture: Macromolecules in living cells Only six elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHNOPS) make up about 98% of the mass of all living organisms. The functions of macromolecules are directly related to their shapes and to the chemical properties of their monomers (same way that the arrangement of the letters in a word determine its sound and meaning.) http://www.contexo.info The sugar component of deoxyribonucleic acid (DNA) is deoxyribose, a ribose in which the 2-hydroxyl is replaced with a hydrogen. Ribonucleic acid (RNA) contains the sugar ribose. The backbones of DNA and RNA consist of sugars linked by phosphodiester bridges between the 3-hydroxyl of one sugar and the 5- hydroxyl of an adjacent sugar. Bases are attached to carbon atom 1 in the sugar. Two of the bases are purines (adenine and guanine) and two are pyrimidines (cytosine and thymine (DNA) or uracil (RNA)).  Backbones of DNA and RNA The backbones of DNA and RNA consist of sugars linked by phosphodiester bridges between the 3-hydroxyl of one sugar and the 5-hydroxyl of an adjacent sugar. A sugar unit is highlighted in red and a phosphate group in blue. Bases are attached to carbon atom 1 in the sugar. Negative charge in the backbone repels nucleophilic species such as hydroxide ion which can hydrolytically cleave the phosphodiester linkages.  The backbones of DNA and RNA consist of sugars linked by phosphodiester bridges https://chem.libretexts.org An ester is the compound obtained when the hydrogen atom in at least one hydroxy group in an oxoacid or a hydroxoacid is replaced by an alkyl group (alkyl ester) or an aryl group (aryl ester). Esters are a functional group that are commonly encountered in organic chemistry. In an ester molecule, the bond connecting the atom doubly bonded to oxygen and the oxygen atom bearing the alkyl or aryl group is called the ester bond or, in biochemistry, ester linkage. A form of dehydration synthesis  Ribose and deoxyribose. The sugar component of deoxyribonucleic acid (DNA) is deoxyribose, a ribose in which the 2-hydroxyl is replaced with a hydrogen Ribonucleic acid (RNA) contains the sugar ribose. Atoms in sugar units are numbered with primes to distinguish them from atoms in bases The absence of 2’-hydroxyl group in DNA further increases resistance to nucleophilic species and hydrolysis.  The absence of 2’-hydroxyl group in DNA further increases resistance to nucleophilic species and hydrolysis. Free hydroxide ions in solution can easily deprotonate the 2’ OH of the ribose, enabling the deprotonated 2′ hydroxyl's nucleophilic attack on the adjacent phosphorus. Phosphodiester bond is broken, cleaving the RNA https://bio.libretexts.org/ backbone. Reminder: Stability of DNA A digital recreation of a Homo antecessor fossil found in Spain. Livescience.com  Bases: Purines and pyrimidines. Two of the bases are purines (adenine and guanine) and two are pyrimidines (cytosine and thymine (DNA) or uracil (RNA)); double ring structure vs single ring. Atoms within bases are numbered without primes. A base bound to a sugar is called a nucleoside. The nucleosides of DNA are deoxyadenosine, deoxyguanosine, deoxycytidine and deoxythymidine. By convention, deoxythymidine, which rarely occurs in RNA, is simply called thymidine. The nucleosides of RNA are adenosine, guanosine, cytidine and uridine. In all cases, the C-1 of the sugar is attached to the N-9 of the purine or the N-1 of the pyrimidine by a β-glycosidic bond. A nucleotide is a nucleoside with one or more phosphoryl groups attached. Nucleotide triphosphates are the building blocks of DNA and RNA.  β-Glycosidic linkage in a nucleoside (deoxyadenosine). A base bound to a sugar is called a nucleoside. The nucleosides of DNA are deoxyadenosine, deoxyguanosine, deoxycytidine and deoxythymidine. By convention, deoxythymidine, which rarely occurs in RNA, is simply called thymidine. The nucleosides of RNA are adenosine, guanosine, cytidine and uridine. In all cases, the C-1 of the sugar is attached to the N-9 of the purine or the N-1 of the pyrimidine by a β-glycosidic bond.  β-Glycosidic linkage in a nucleoside A glycosidic bond or glycosidic linkage is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate Ribose deoxyadenosine linear form cyclic form Carbon # 1 is now called the anomeric carbon; the carbon that was the carbonyl carbon in acyclic form. The Beta position is defined as the -OH being on the same side of the ring. In the ring structure this results in a upward projection. The Alpha position is defined as the -OH being on the opposite side of the ring. In the ring structure this results in a downward projection. https://chem.libretexts.org/ Phosphoester and glycosidic bonds (Dehydration synthesis reactions) https://upendrats.blogspot.com/2017/11/  e e e https://www.differencebetween.com Nucleotides adenosine 5-triphosphate (5-ATP) and deoxyguanosine 3-monophosphate (3-dGMP). A nucleotide is a nucleoside with one or more phosphoryl groups attached. Nucleotide triphosphates are the building blocks of DNA and RNA. Nucleic acid chains are represented by abbreviations such as pApGpCpT, pAGCT or more simply AGCT. Nucleic acid chains have directionality in that the two ends are different. One end has a phosphoryl group attached to the 5 carbon atom of the sugar and one end has a free hydroxyl attached to the 3 carbon of the sugar. Nucleic acid sequences are written in the 5 to 3 direction.  Structure of a DNA chain. (Has directionality) Glycosidic linkage The chain has a 5 end, which is usually attached to a phosphoryl group, and a 3 end, which is usually a free hydroxyl group. Nucleic acid chains are represented by abbreviations such as pApGpCpT, pAGCT or more simply AGCT. Nucleic acid sequences are written in the 5 to 3 direction. DNA molecules can be extremely long, some consisting of more than 1 billion nucleotides. Electron micrograph of part of the E. coli genome  The Indian muntjac (an Asiatic deer) and its chromosomes Cells from a female Indian muntjac contain three pairs of very large chromosomes (stained orange). The cell shown is a hybrid containing a pair of human chromosomes (stained green) for comparison. Human genome comprises approx. 3 billion nucleotides per DNA strand divided among 23 pairs of chromosomes. Indian muntjac as large but only has 3 chromosomes. Largest has 1 billion nucleotides- more than a foot in length. Human cells- 6 billion base pairs of information Would be 3.6m in length if all of the molecules were laid end to end 10 trillion cells DNA if strung end to end would reach the Sun and back about 65 times Adenine always forms hydrogen bonds with thymine while guanine forms hydrogen bonds with cytosine. The helix is stabilized by hydrogen bonds between base pairs as well as by hydrophobic interactions, called stacking forces, between adjacent bases. Because of the base pairing rules, the sequence of one strand determines the sequence of the partner strand. The two strands can be separated and complementary sequences synthesized to generate two identical daughter strands. Because the two daughter helices have one parent strand and one newly synthesized strand, the replication process is called semiconservative replication.  X-ray diffraction photograph of a hydrated DNA fiber - Critical evidence in identifying the structure of DNA Photo 51, the diffraction pattern from DNA in its so-called B configuration (51st photograph) Rosalind Franklin and Raymond Gosling  X-ray diffraction photograph of a hydrated DNA fiber - Critical evidence in identifying the structure of DNA https://ib.bioninja.com.au Photo 51 and the structure of DNA (year 1952). The photo revealed that B-form DNA was a double helix with 10 nucleotide base pairs within a complete turn of the helix. The “X” indicates a helix. The dark patches indicate the bases. https://www.biointeractive.org/sites/ default/files/media/file/2020- 03/DoubleHelix-Educator-film.pdf (good read) Watson and Crick’s model of double helical DNA published in 1953 Watson–Crick model of double-helical DNA Putting the Evidence Together Adjacent bases are separated by 3.4 Å. The structure repeats along the helical axis (vertical) at intervals of 34 Å, which corresponds to approximately 10 nucleotides on each chain. Axial view, looking down the helix axis, reveals a rotation of 36° per base and shows that the bases are stacked on top of one another 900-word paper, published in Nature, concluded, famously, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Published in Nature, April 25, 1953 titled “ Molecular structure of nucleic acids: Structure for deoxyribose nucleic acid” pg 737-738 Structures of the base pairs proposed by Watson and Crick 900-word paper, published in Nature, concluded, famously, "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." Published in Nature, April 25, 1953 titled “ Molecular structure of nucleic acids: Structure for deoxyribose nucleic acid” pg 737-738 Adenine always forms hydrogen bonds with thymine while guanine forms hydrogen bonds with cytosine. The helix is stabilized by hydrogen bonds between base pairs as well Because of the base pairing rules, the sequence of one strand determines the sequence of the partner strand. The two strands can be separated, and complementary sequences synthesized to generate two identical daughter strands. Because the two daughter helices have one parent strand and one newly synthesized strand, the replication process is called semiconservative replication. Adenine always forms hydrogen bonds with thymine while guanine forms hydrogen bonds with cytosine. These base-pairing rules account for the observation, originally made by Erwin Chargaff in 1950, that the ratios of adenine to thymine and of guanine to cytosine are nearly the same in all species studied, whereas the adenine-to-guanine ratio varies considerably. Chargaff (professor of biochemistry at Columbia University medical school) met Francis Crick and James D. Watson at Cambridge in 1952, and, despite not getting along with them personally, he explained his findings to them. Chargaff's research would later help the Watson and Crick laboratory team to deduce the double helical structure of DNA. (Wikipedia) Van der Waals interactions between stacked bases, called stacking forces, help to stabilize the double helix.  A side view of DNA Van der Waals interactions between stacked bases, called stacking forces, help to stabilize the double helix.  Different ways of depicting molecular structures Lewis structures Skeletal formula of isobutanol, (CH3)2CHCH2OH Condensed formula CH3CH2OH (ethanol) Stereochemistry (3D arrangement) in skeletal formula (of strychnine) https://en.wikipedia.org Fischer Projection https://www.slideshare.net/  Different ways of depicting molecular structures Molecular Representations. Comparison of (A) space-filling, (B) ball-and- stick, and (C) skeletal models of ATP. Space-Filling Models. Structural formulas and space-filling representations of selected molecules are shown. Alternative Representations of Protein Structure. (A) A ribbon diagram (B) and a surface representation of a key protein from the immune system emphasize different aspects of structure. https://www.ncbi.nlm.nih.gov/books/NBK22407/ In the cell, the most commonly seen form of DNA double helix is called the B form or the Watson-Crick helix. The double helix can also exist in an A form, which is shorter and wider than the B form with the bases at an angle rather than perpendicular to the helix axis. In the A forms, the sugar is in the C-3-endo conformation, while the sugar is in C-2-endo configuration in the B form. The A form is seen in RNA double helices and in RNA-DNA hybrid helices, structures observed in transcription and RNA processing. In the cell, the most commonly seen form of DNA double helix is called the B form or the Watson-Crick helix. The double helix can also exist in an A form, which is shorter and wider than the B form with the bases at an angle rather than perpendicular to the helix axis. When DNA is less hydrated A-DNA The A form is seen in RNA double helices and in RNA-DNA hybrid helices, structures observed in transcription and RNA processing. FIGURE 4.15 Sugar pucker (Dictionary meaning of pucker a tightly gathered wrinkle or small fold) In A-form DNA, the C-3 carbon atom lies above the approximate plane defined by the four other sugar nonhydrogen atoms (called C-3-endo). In B-form DNA, each deoxyribose is in a C-2- endo conformation, in which C-2 lies out of the plane.  Sugar pucker B vs A DNA https://x3dna.org C-3’-endo puckering in A-DNA leads to an 11-degree tilting of the base pairs away from perpendicular to the helix. RNA helices are further induced to take the A-DNA form because of steric hindrance from the 2’- hydroxyl group: the 2’ -oxygen atom would be too close to three atoms of the adjoining phosphoryl group and to one atom in the next base. In an A-form helix, in contrast, the 2’-oxygen atom projects outward, away from other atoms. The phosphoryl and other groups in the A-form helix bind fewer H 2 O molecules than do those in B-DNA. Hence, dehydration favors the A form. The double helix can also form Z-DNA. Z-DNA is left-handed and the backbone is zigzagged, accounting for the name “Z-DNA”. The double helix can also form Z-DNA. Z-DNA is left-handed and the backbone is zigzagged, accounting for the name “Z-DNA”. DNA is a flexible, dynamic molecule whose parameters are not as fixed as depictions suggest The biological role of Z-DNA is still under investigation  Structure of one chain of DNA Simple and elegant Double helix structure Other structures (Bacterial DNA, RNA) Human cells- 6 billion base pairs of information Would be 3.6m in length if all of the molecules were laid end to end 10 trillion cells DNA if strung end to end would reach the Sun and back about 65 times How does a bacteria compact its DNA? E. coli (bacteria) chromosome, fully extended, would be about 1000 times as long as the greatest diameter of the bacterium. (Reminder: No nucleus) DNA molecules can be extremely long, some consisting of more than 1 billion nucleotides. Electron micrograph of part of the E. coli genome  In order to fit inside a cell, the DNA molecule must be compacted. In E. coli, the DNA double helix is a circular molecule that is twisted into a superhelix by the process of supercoiling. The relaxed circular DNA and the superhelix form are topological isomers of each other. Shutterstock.com The term circular refers to the continuity of the DNA strands, not to their geometric form  Electron micrographs of circular DNA from mitochondria. (A) Relaxed form. (B) Supercoiled form. E. coli chromosome, fully extended, would be about 1000 times as long as the greatest diameter of the bacterium. (Reminder: No nucleus) In order to fit inside a cell, the DNA molecule must be compacted. In E. coli, the DNA double helix is a circular molecule that is twisted into a superhelix by the process of supercoiling. The relaxed circular DNA and the superhelix form are topological isomers of each other.  Structure of one chain of DNA Simple and elegant Double helix structure Other structures (Bacterial DNA, RNA) A common structural motif seen in nucleic acids, most notably RNA, is the stem-loop, which occurs when complementary sequences in the same strand form a double helix. Non-Watson-Crick base pairs occur frequently in RNA. More elaborate structures may form, often stabilized by Mg2+ ions. Stem-loop structures. Stem-loop structures can be formed from single-stranded DNA and RNA molecules. The simplest and most-common structural motif formed is a stem-loop, created when two complementary sequences within a single strand come together to form double-helical structures. In many cases, these double helices are made up entirely of Watson–Crick base pairs. In other cases, however, the structures include mismatched base pairs or unmatched bases that bulge out from the helix. Such mismatches destabilize the local structure but introduce deviations from the standard double helical structure that can be important for higher-order folding and for function  Complex structure of an RNA molecule A single-stranded RNA molecule can fold back on itself to form a complex structure. Often, three or more bases interact to stabilize these structures. In such cases, hydrogen-bond donors and acceptors that do not participate in Watson–Crick base pairs participate in hydrogen bonds to form nonstandard pairings. Metal ions such as magnesium ion (Mg2+ )often assist in the stabilization of these more elaborate structures.  Complex structure of an RNA molecule These complex structures allow RNA to perform a host of functions that the double- stranded DNA molecule cannot. Indeed, the complexity of some RNA molecules rivals that of proteins, and these RNA molecules perform a number of functions that had formerly been thought the exclusive domain of proteins. Has other functions too The relative sizes of a globular protein and the mRNA that codes for it Has other functions too http://book.bionumbers.org