Ch01_Biochemical Principles_berg_8e_mng Fall 2024.pdf

The biological world is magnificently diverse However, great unity of all living things at the biochemical level. Nobel Prize winners Peter Agre, M.D., and Carol Greider, P...

The biological world is magnificently diverse However, great unity of all living things at the biochemical level. Nobel Prize winners Peter Agre, M.D., and Carol Greider, Ph.D., -used biochemical techniques to study the structure and function of proteins. Large biochemical machines comprise many thousands of atoms Yet, the functions of these elaborate assemblies depend on simple chemical processes such as the protonation and deprotonation of the carboxylic acid groups  DNA vs RNA? Deoxyribose Nucleic Acid vs Ribose Nucleic Acid Difference in the 2’ C of the sugar moiety: presence or absence of Oxygen Structure at the biochemical level and function of macromolecules are interlinked. ie., Form and Function are interliked A digital recreation of a Homo antecessor fossil found in Spain. Livescience.com Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)  The biological world is magnificently diverse However, great unity of all living things at the biochemical level. Biochemistry is the study of the chemistry of life processes. Biological diversity yet unity at the biochemical level eg., built up of cells, DNA is the hereditary material At the biochemical level there are many common features; cells with common functions Central Dogma of Biology Biochemistry is the study of the chemistry of life processes. Two classes of biochemically important molecules are macromolecules and small molecules called metabolites, such as glucose and glycerol. Macromolecules, such as proteins, that play similar roles in different organisms have Macromolecules are polymers similar structures. assembled by chemical linkage of monomers  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  Biological diversity and similarity in Macromolecules The shape of a key molecule in gene regulation (the TATA-box-binding protein) is similar in three very different organisms that are separated from one another by billions of years of evolution.  Biological diversity and similarity in Macromolecules While there are similarities, different organisms have specific needs, depending on the particular biological niche. Challenges are addressed by the adaptation of existing macromolecules to new roles rather than by the evolution of entirely new ones. Quora.com Hemoglobin is found in red blood cells or erythrocytes (red blood cells), myoglobin is found muscle cells. To perform its job, myoglobin (Mb) must effectively bind with any oxygen released from hemoglobin (Hb). Myoglobin therefore needs to have a higher oxygen affinity than hemoglobin. Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)  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 DNA is a linear polymer composed of monomers consisting of deoxyribose sugar, a phosphate and one of four bases. The linked sugar and phosphate compose the backbone of the DNA. The two strands of a DNA double helix are formed by hydrogen bonds between specific base pairs in the different strands: A binds to T G binds to C FIGURE 1.5 The double helix. The double-helical structure of DNA proposed by Watson and Crick. The sugar–phosphate backbones of the two chains are shown in red and blue, and the bases are shown in green, purple, orange, and yellow. The two strands are antiparallel, running in opposite directions with respect to the axis of the double helix, as indicated by the arrows.  Because of specific-base pairing, each strand can serve as a template for a new partner, allowing the generation of two identical daughter double helices from one parent strand. We will discuss this in the next chapter 900-word paper, published inNature, 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” pg737-738 Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)  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 Periodic table: Valence electrons shown by Lewis dot structures Only six elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHNOPS) make up about 98% of the mass of all living organisms. The ns2np2 valence electron configurations of group 14 (Carbon) https://manoa.hawaii.edu/  Valence electrons The ns2np2 valence electron configurations of group 14 (Carbon) p orbital can only hold 6. Non metals of interest have p in their highest energy shell. (N is the energy level, s is the orbital, number of electrons)  Atomic Orbitals (reminder) Chemlibretext.org The ns2np2 valence electron configurations of group 14 (Carbon)  1s2 2s2 2p2-4 3s2 3p3-4 The ns2np2 valence electron configurations of group 14 (Carbon) Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, and Sulfur (CHNO PS) ns2np2 to 4 CNO PS ns1 H  Octet rule The octet rule refers to the tendency of atoms to prefer to have eight electrons in the valence shell. When atoms have fewer than eight electrons, they tend to react and form more stable compounds. When discussing the octet rule, we do not consider d or f electrons. Only the s and p electrons are involved in the octet rule, making it useful for the main group elements (elements not in the transition metal or inner-transition metal blocks); an octet in these atoms corresponds to an electron configurations ending with ns2np6. Periodic table: Valence electrons shown by Lewis dot structures Only six elements carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHNOPS) make up about 98% of the mass of all living organisms. The ns2np2 valence electron configurations of group 14 (Carbon) https://manoa.hawaii.edu/  Slideplayer.org The ns2np2 valence electron configurations of group 14 (Carbon)  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 Electronegative elements like to gain electrons, Electropositive elements like to loose electrons. Basis for Electrostatic attraction= ionic/electrostatic bonds Electronegativity https://chem.libretexts.org The structure of the DNA double helix illustrates key chemical principles fundamental to living systems. Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place) Covalent bond  Covalent bond Covalent bonds, formed by electron sharing between two adjacent atoms, are the strongest bonds. A typical C-C covalent bond has a distance of 1.54 Å and a bond energy of 355 kJ mol-1 (85 kcal mol-1). Some molecules exhibit multiple covalent structures called resonance structures. Valence shell is complete https://www.khanacademy.org  Covalent bond (Octet rule) Methane CH4 The octet rule refers to the tendency of atoms to prefer to have eight electrons in the valence shell. When atoms have fewer than eight electrons, they tend to react and form more stable compounds. When discussing the octet rule, we do not consider d or f electrons. Only the s and p electrons are involved in the octet rule, making it useful for the main group elements (elements not in the transition metal or inner-transition metal blocks); an octet in these atoms corresponds to an electron configurations ending with ns2np6.  Polar and NonpolarCovalent bonds There are two basic types of covalent bonds: polar and nonpolar. In a polar covalent bond, the electrons are unequally shared by the atoms and spend more time close to one atom than the other. Because of the unequal distribution of electrons between the atoms of different elements, slightly positive (δ+) and slightly negative (δ–) charges develop in different parts of the molecule. https://www.khanacademy.org  Covalent bonds in DNA Covalent bonds Resonance structures of adenine For some molecules, more than one pattern of covalent bonding can be written. For example, adenine can be written in two nearly equivalent ways called resonance structures. A typical C-C covalent bond has a distance of 1.54 Å and a bond energy of 355 kJ mol-1 (85 kcal mol-1). Three of the bases in DNA include carbon– oxygen (C=O) double bonds. These bonds are even stronger than C-C single bonds, with energies near 730 kJ mol-1 (175 kcal mol-1 ) and are somewhat shorter.  Image by Bryon Inouye https://manoa.hawaii.edu/ Which illustration describes covalent bonds better?  Non-covalent bonds (ionic/electrostatic interaction)  Noncovalent bonds: 1) Ionic bond Noncovalent bonds Ionic interactions. Ionic interactions, also called electrostatic interactions, occur between oppositely charged molecules. Electrostatic interactions in water have a bond distance of ≈3 Å and a bond energy, given by Coulomb energy, of 5.86 kJ mol-1 (1.4 kcal mol-1)  Image by Bryon Inouye https://courses.lumenlearning.com  Noncovalent bonds: 1) Ionic bond https://courses.lumenlearning.com Formation of Sodium Flouride: The attraction of oppositely charged atoms and the transfer of electrons leads to the formation of an ionic compound. In this case, NaF. Noncovalent bonds: 1) Ionic bond  Image by Bryon Inouye https://manoa.hawaii.edu/  Noncovalent bonds: 2) Hydrogen bonds Hydrogen bonds occur between an electronegative atom and a hydrogen covalently bonded to another electronegative atom. Hydrogen bonds vary in bond distance from 1.5 Å to 2.6 Å with bond energies from 4-20 kJ mol-1 (1-5 kcal mol-1) Figure 1.9 Hydrogen bonds. Hydrogen bonds are depicted by dashed green lines. The positions of the partial charges (δ+ and δ-) are shown.  Noncovalent bonds: 3) van der Waals interactions Van der Waals interactions occur between two molecules sufficiently close (the van der Walls contact distance) such that transient electronic asymmetries in one molecule induce complementary interaction in the partner molecule. Van der Waals interactions have bond energies from 2-4 kJ mol-1 ( 0.5-1.0 kcal mol-1) Van der Waals forces include attractive forces arising from interactions between the partial electric charges and repulsive forces arising from the exclusion of electrons in overlapping orbitals. FIGURE 1.10 Energy of a van der Waals interaction as two atoms approach each other. The energy is most favorable at the van der Waals contact distance. Owing to electron– electron repulsion, the energy rises rapidly as the distance between the atoms becomes shorter than the contact distance.  Covalent bonds Electrostatic interaction Non-covalent bonds: (electrostatic interaction is the common feature) 1) Ionic bond Image by Bryon 2) Hydrogen bond Inouye 3) Van der Walls interaction  Covalent bonds Non-covalent bonds 1) 2) 3) van der Waal interactions https://courses.lumenlearning.com Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)  The structure of water (the solvent in which most biochemical processes take place) Properties of water. Water is a polar molecule. The charges on the molecule are not evenly distributed.  The structure of water (the solvent in which most biochemical processes take place) Properties of water. Water is highly cohesive. Water molecules interact with one another through hydrogen bonds.  The structure of water (the solvent in which most biochemical processes take place) The hydrophobic effect. Nonpolar molecules in water can be driven together by the hydrophobic effect which is powered by the increase in entropy of water. The associated interactions are called hydrophobic interaction. FIGURE 1.12 The hydrophobic effect. The aggregation of nonpolar groups in water leads to the release of water molecules, initially interacting with the nonpolar surface, into bulk water. The release of water molecules into solution makes the aggregation of nonpolar groups favorable.  The structure of water (the solvent in which most biochemical processes) The hydrophobic effect. Cell Membrane Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)  The structure of the DNA double helix illustrates key chemical principles fundamental to living systems. Hydrogen bond between bases Adenine base (Non-covalent bonds) (Covalent bonds) Hydrogen bonds form between bases, which are in the hydrophobic interior away from the disrupting effects of water. In the interior of the helix, bases are stacked and interact with one another through van der Waals interactions. Why?  The structure of water (the solvent in which most biochemical processes take place) The hydrophobic effect in DNA structure https://www.slideshare.net https://thatsinteresting.scienceblog.com The structure of the DNA double helix illustrates key chemical principles fundamental to living systems. Will study this in detail in the next chapter  DNA vs RNA? Deoxyribose Nucleic Acid vs Ribose Nucleic Acid Difference in the 2’ C of the sugar moiety: presence or absence of Oxygen How will this difference in 2’C can affect its stability in water Structure at the biochemical level and function of macromolecules are interlinked. ie., Form and Function are interlinked A digital recreation of a Homo antecessor fossil found in Spain. Livescience.com Types of chemical bonds The structure of water (the solvent in which most biochemical processes take place)