Biochemistry Notes - Lecture 1
Biochemistry Notes - Lecture 1 Bch4053
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This 5 page Class Notes was uploaded by Hannah Hartman on Tuesday September 6, 2016. The Class Notes belongs to Bch4053 at Florida State University taught by Dr. Hong Li in Fall 2016. Since its upload, it has received 51 views. For similar materials see General Biochemistry I in Biochemistry at Florida State University.
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lunes, 29 de agosto de 2016 11:41 AM Lecture 1: an Introduction to Biochemistry August 29, 2016 Why do we study biochemistry? • Biochemistry principles guide biological processes in all organisms including the humans. • We can use biochemistry to study a variety of human pathogens in other organisms, such as the prion disease (proteinaceous pathogen) ○ This pathogen is also seen in sheep and involves a similar protein • Biochemistry is used to study and treat cancer- How do anticancer drugs work? ○ Examples of anticancer drugs: § Alklating agens § Topisomerase inhibitors § Antimitotic agents § RNA/DNA antimetabolites Cells are the Smallest Units of Life • Cellsare the smallest units of life. • A cell is capable of growth, replicating, energy transforming and metabolizing. • All living cells fall into two distinct classifications: ○ Prokaryotic: single celled; lack nuclei - includes Archaea [which has some eukaryotic characteristics] ○ Eukaryotic:multicellular; contains organelles (e.g. mitochondria) § Various types of cells (specialization) • Cells share a common biochemistry: ○ Genes that code for enzymes for essential biological processes are conserved between some bacteria and humans! ○ Living organisms are highly organized and consist bfi omolecular hierarchy § Atoms - molecules - larger molecular assemblies Cell Structures - Differences between prokaryotes and eukaryotes • Both have biological membranes that are extremely important. Both have DNA (genetic material) • Prokaryotes: no subcellular organization • Eukaryotes: subcellular organization such as organelles Atoms - molecules - larger molecular assemblies § Cell Structures - Differences between prokaryotes and eukaryotes • Both have biological membranes that are extremely important. Both have DNA (genetic material) • Prokaryotes: no subcellular organization • Eukaryotes: subcellular organization such as organelles Chemistry of biomolecules: • Biomolecules, or macromolecules, are composed of carbon. Carbon outer shell electrons have three possible hybridization states which allow them to form three kinds of covalent bonds with other atoms: ○ Sp3 - single bonds ○ Sp2 - forms double bonds ○ Sp - triple bonds ○ Various hybridizations change the properties of the molecules. • Limited sets of possible combinations of C, H, O, P, S and N atoms are found in biomolecules. • Biomolecule precursors are water(HO), carbon dioxide (CO ), and inorganic + - 2 2 nitrogen compounds (NH ,4NO , 3 )2 ○ The nitrogen is produced predominantly from bacteria and plants. ○ Precursor molecules are built into slightly bigger molecules called metabolites. • Biomolecules are constructed from several simple molecules according to a hierarchy of structure complexity • Precursors are converted to metabolites which mediate cellular energy transformation and biosynthesis of various sets of building blocks (amino acids, sugars, nucleotides, fatty acids and glycerol) • Macromolecules serve functional purposes: ○ Macromolecule building bocks - macromoles § Amino acids -proteins § Nucleotides - nucleic acids (DNA/RNA) § Fatty acids - lipid molecules End of August 29, 2016 lecture August 31, 2016 Bonding and chemistry of biomolecules (slide 7) • Hydrogen bonds will be extremely important in biochemistry! Lone pairs can form these hydrogen bonds. These bonds define thespecificityof the molecule. Biomolecule Directionalit- all large molecules are made with directionality. • Peptides - peptides construct proteins Bonding and chemistry of biomolecules (slide 7) • Hydrogen bonds will be extremely important in biochemistry! Lone pairs can form these hydrogen bonds. These bonds define thespecificityof the molecule. Biomolecule Directionalit- all large molecules are made with directionality. • Peptides - peptides construct proteins ○ Proteins are important for taking the building blocks and building the macromolecule ○ Proteins are important enzymes in biological processes such as the genesis of ATP and the contraction of muscle. • Carbohydrates ○ This is our major source of energy and ATP for the body. ○ Carbohydrates can be used in post-translational modification (glycoprotein) and the identification of viruses and bacteria. • Nucleic acids ○ Goes from the 5' to the 3'direction (this is how the nucleotide is read) ○ Human DNA has 3 billion such nucleotides, with a matching pair! ○ RNA will have a hydrogen group at the 3', where a DNA will have an OH at the 3' Features of macromolecules: • Macromolecules are synthesized from building blocks and have a sense of directionality (important for three dimensional architecture); • Macromolecules are informational (important for replication). • Biomolecules have characteristic three-dimensional architecture - structural functional relationship is extremely important! • Weak forcesinclude hydrogen bonding, van der Waals forces, ionic interactions and hydrophobic interactions (noncovalent interactions). These forces maintain biological structure and determine biomolecular interactions. ○ Van der Waals interaction - ANY pair of atoms will feel this interaction ○ Hydrophobic interaction- interactions that arise from molecules trying to "avoid" water interaction § These molecules do not interact with water. § These are nonpolar interactions, along with these molecules being in water. ○ Why are these called weak forces? Covalent bonds are much stronger than noncovalent bonds (which biomolecular interactions are) § We are talking of interactionsbtweenmolecules, or folding of molecule itself. • Weak forcesalso mediate biomolecule recognition; • Structural complementarity (similar to in that in lock -and-key or pieces of a puzzle) determines biomolecule interaction. Water as a solvent • Think about all of our molecules existing in water. • Water is capable of forming hydrogen bonds (partial overlapping of electrons) • Structural complementarity (similar to in that in lock -and-key or pieces of a puzzle) determines biomolecule interaction. Water as a solvent • Think about all of our molecules existing in water. • Water is capable of forming hydrogen bonds (partial overlapping of electrons) • Calathrate • It is capable of dissolving ions. This is due to the slight negative and positive charge of water (polarization) • Water is amphipathic = nonpolar + polar Properties of Water: • Chemical formula: H O2 • Its shape (or structure) determines its function. Water is good solvent for ionic substances (salt), nonionic but polar (sugar, alcohols, amines, aldehydes and ketones); ○ Water is extremely good at shielding the electrostatic interactions. • Dielectric Constant DT :he ability of water to surround ions in dipole interactions in order to diminish their electrostatic attractions is a measure of its dielectric constant, D. The larger D is, the smaller the Columbic force between the negative and positive ions is: F = e1e2/Dr^2 ○ The further they are the weaker it is, the closer they are the stronger it is. ○ This is the measure of how effectively the water will shield the electrostatic attractions ○ This depends on the property of our solvent. Pure water is 80. • H-bonds: H-bonds occur between polar groups. The oxygen in water is a good H-bond acceptor and hydrogens are good H -bond donors. Thus water can form H-bonds with many polar groups (I.,e, C=O, N3 , OH); ○ This ordering process costs energy • Hydrophobic interaction:s When non-polar molecules are dissolved in water, water molecules reorganize to form a cage -like structure (clathrate) that surrounds each solute molecule. This process is accompanied by significant ordering of the solvent or negative entropy. Under these conditions, non -polar molecule experience a net attraction for one another that is called hydrophobic interaction. In another word, two nonpolar molecules have a tendency to stay close together in water. Objectives of Lecture 1: • Textbook Chapter 1 • Concepts: ○ Definition of a cell. Review the processes supported by biological molecules ○ ○ Know the names of atoms that make up biological molecules ○ Describe structural features of the prokaryotic and the eukaryotic cells; ○ Can state general features of macromolecules ○ Describe chemical features of water as solvent. ○ Definition of a cell. ○ Review the processes supported by biological molecules ○ Know the names of atoms that make up biological molecules ○ Describe structural features of the prokaryotic and the eukaryotic cells; ○ Can state general features of macromolecules ○ Describe chemical features of water as solvent. ○ Know these terms: Dielectric constant, H -bond, Clathrate, Amphipathic. ○ Can illustrate schematically how water dissolve ions • Home work and practice questions: ○ Chap. 1: 1, 2 (2 and 3 eds.)