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Biochemistry BBMB 301 Week 1 Notes

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by: Emily

Biochemistry BBMB 301 Week 1 Notes BBMB 301

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About this Document

This includes notes for lectures 1, 2, and 3.
Survey of Biochemistry
Robert Thornburg
Class Notes
biochemistry, BBMB




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This 6 page Class Notes was uploaded by Emily on Thursday February 4, 2016. The Class Notes belongs to BBMB 301 at Iowa State University taught by Robert Thornburg in Spring 2016. Since its upload, it has received 47 views. For similar materials see Survey of Biochemistry in General Science at Iowa State University.

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Date Created: 02/04/16
Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 1 - CHAPTER 1 – THE UNITY OF LIFE By: Emily Settle  Characteristics of Life Systems o Self-sustaining o Controlled catalysis o Molecules organized in separable physical units – CELLS o Informational molecules o Adaptation of the system o Capture energy from environment  Core essential biochemical processes is shared by all organisms – present in a common ancestor.  Systems adapt until they become distinct. o Species – distinct chemical systems  Similar characteristics reveal relationships.  Bacterial systems o Outer physical boundary only, no internal boundary. o Information processing specific to groups.  Eukaryotic systems o Internal boundaries physically separate, sub-cellular subgroups of molecules. o Information processing specific to groups.  Archael systems o Physical organization like bacteria. o Information processing like eukaryotes.  Organic chemistry – C, H, O, N and also S and P o Sp3 and sp2 bonding of C  Water o Aqueous and non-aqueous environments in cells  Name functional groups given a structure – alcohol, amine, ketone, aldehyde, carboxylic acid, phosphoric acid, sulfhydryl, ester, amide, phosphoester, phosphodiester.  Classes of biomolecules – proteins, carbohydrates, lipids, nucleic acids, (vitamins).  Proteins o Monomers – amino acids  Sp3 carbon with 4 functional groups – amino, carboxylic acid, proton, R group. o Monomers linked into polymer by amide groups o Polymer is a polypeptide – fold into complex 3D structures.  Carbohydrates o Monomers – monosaccharides (simple sugars) o Linked by glycoside bonds to form polysaccharides  Nucleic Acids o Monomers – nucleotides o Monosaccharide, heterocylic aromatic ring, phosphate groups o Linked into polymers by phosphodiester groups o Two polymers associate form into double helix (DNA)  Lipids – NOT a true polymer o Monomers – fatty acids  Alkane or alkene + carboxylic acid o Small carbohydrate backbone – glycerol, ester group linkages.  Information flows through the Central Dogma o DNA  RNA  Protein  DNA  DNA – DNA Replication  DNA  RNA – Transcription  RNA  Protein – Translation o DNA is inherited o RNA info is transitory – used by an individual organism.  Exception – some viruses o Proteins are the functional entities… activities of proteins determine the activities of cells.  Groups of biomolecules are separated into compartments – compartmentalization o Lipids form boundaries, protein imbedder in or attached to lipids. o Membrane interior is hydrophobic – impermeable to water. o Prokaryotes – outer boundary – single compartment (bacteria and archaea) o Eukaryotes – outer and internal boundaries – multiple compartments.  Compartments are specialized (different functions)  Two subdivisions – plants and animals  Endomembrane system – transport of molecules between compartments.  Mitochondria (animal cells) and chloroplasts (plant cells) - energy conversion compartments  Membrane bound organelles with outer boundary  Internal membranes – multiple compartments within the organelle  Mitochondria – produce ATP  Chloroplasts – light energy  chemical energy  Cytoskeleton – macromolecular assemblies o Structural filaments made of proteins o Physical connections between organelles  Structure and function of main organelles o Nucleus – information center of cell, genomic information is expressed here. o Mitochondria – found in animal cells, produces ATP, two membranes. o Chloroplast – found in plant cells, converts light energy into chemical energy. o Endoplasmic reticulum – smooth or rough, processes drugs (includes alcohol) o Golgi complex – processing of proteins, sorts, mailroom. o Ribosomes – synthesize proteins. o Plasma membrane – separates the inside of the cell from the outside, selective permeability, holds cell together. Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 2 - CHAPTER 2 – WATER AND WEAK BONDS By: Emily Settle  Functions of water: o Solvent – dissolves polymers, building block molecules, small organic molecules (metabolites) o Compartmentalization – alkane/alkenes for membrane barriers that separate compartments o Proton concentration and temperature resistant to change  stabilize temperature and pH. o Water resists temperature change o Liquid in the temperatures that occur on earth o Solid is less dense than liquid – critical for life because ice floats o Participates in chemical reactions such as in a hydrolysis reaction or in photosynthesis. o Structure – sp3 bonding of oxygen, tetrahedral.  Paired electrons in two of the orbitals  Electron shared with H nucleus in the other two sp3 orbitals  Asymmetric charge distribution  Polar molecule  Partial positive on H  Partial negative on O  Partial charges on H and O can interact with ions. o Partial charges allow hydrogen bonds  Electrostatic interactions between δ+ and δ-  Strongest – three atoms in straight line  Hydrogen bonds between water molecules form network o Weak proton donor (acid) o Dissociation frequency determined by nuclear properties (equilibrium constant)  Hydrogen bonds occur with other polar functional groups o Ex  Adenine – Thymine Guanine – Cytosine (double stranded DNA)  Hydrogen bonds can exchange  Weak chemical interactions o Covalent bonds – strength, link monomers into stable polymers. o Weak interactions are formed and broken quickly with little energy input allowing conformational changes. o Weak interactions can mediate specificity of interaction.  Four types of weak chemical interactions o Ionic bonds – fully charged groups (ions), attractive or repulsive force, ions occur on amino, carboxyl, other functional groups. o Hydrogen bonds – described above. o Van der Waals bond – transient asymmetric charge distribution, short distances, individually weak needs a large surface area, close fit required with a narrow distance range. o Hydrophobic interaction – non-polar groups separate from polar molecules  Driven by entropic effect – less interaction between polar and non-polar groups  max entropy (second law of thermodynamics)  Main determinant of protein and DNA structure.  Amphipathic molecules – polar and non-polar functional on same molecule (compartmentalization)  Interaction of polar water molecule with non-polar compound restricts the freedom of water.  Cage of water surrounds non-polar molecules.  Ex  water and oil don’t mix.  pH scale: pH = -log[H+] o pH of water = 7  neutral solution o Acidic solutions – pH less than 7 (concentration of H greater than that of water) o Basic solutions – pH greater than 7 ([H+] less than water)  Conjugate acid – conjugate base  Acid donates protons, base accepts protons.  pKa = -logKa lower pKa  stronger acid  Charge between acid and conjugate base differs by 1.  Polyprotic acids have multiple ionizable groups  Weak acid ex  acetic acid, citric acid, lactic acid, etc. o All groups are carboxylic acids except the amino in glutamic acid. Biochemistry 301 – Survey of Biochemistry Professor Robert Thornburg LECTURE 3 - CHAPTER 3 – AMINO ACIDS By: Emily Settle  Proteins: o Not all proteins are expressed in all cells o Approx. 5,000 in eukaryotic cells o Expression of a gene results in the presence of a polypeptide. o Functions:  Structural proteins – cell architecture, aids physical movement of cell  Transporters and carriers of small molecules across membranes.  Enzymes – reaction catalysts  Protection – antibodies, toxins, detoxification  Signal detection and transmission o Composition:  One or more polypeptide chains – polymers of amino acids linked by peptide bonds.  Peptides – polypeptides with fewer than 50 amino acids  Prosthetic groups – non-amino acid parts that are covalently or non-covalently bound to polypeptide  Amino acids: o Twenty different amino acids in proteins o Structure:  central α carbon (usually chiral)  amino group – neutral pH (7)  carboxylic acid group – neutral pH (7)  hydrogen atom  one of twenty different R groups – chemical properties vary  Types of R groups:  non-polar/hydrophobic – greasy o Hydrophobic effect – non-polar functional groups tend to separate from water. Neutral R group  Aliphatic – glycine, alanine, valine, etc.  Aromatic – phenylalanine, tryptophan  polar, uncharged, hydrophilic – alcohols/sulfhydryls o neutral at pH = 7  Aliphatic – threonine, serine, glutamine, etc.  Aromatic - tyrosine  charged, hydrophilic – acidic, basic o negative at pH = 7 (acidic)  aspartate, glutamate o positive at pH = 7 (basic)  lysine, arginine, histidine (hist. can be positive or negative) o Chirality:  Four different constituents on α carbon  Enantiomers – D and L (mostly L)  Exception – glycine because R group is a second H o Ionization:  Zwitter – German for hybrid  Zwitterion – molecule contains two charged groups pH = 7  All amino acids have at least two ionizable groups, some have three (amino and carboxyl groups)  Both an acid and a base o Acid: α carboxyl group pKa = about 2 o Base: α amino group pKa = about 9.5  Some R groups can accept or donate H+  Acids: Asp, Glu  Bases: Lys, Arg, His  Titration of Amino Acids – two or three inflection points o Isoelectric point (pl) – pH at which the net charge is 0  Ionization of Histidine – pKa of the imidazole nitrogen is near pH = 7 o Either in protonated or dissociated form - can convert back and forth  Important at a proton acceptor/donor in many catalytic mechanisms  Essential Amino Acids: nine amino acids that our bodies can’t make – required in the diet. o Histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.  Non-protein functions of amino acids: o Metabolic intermediates used to produce:  Neurotransmitters: GABA, serotonin  Synthesis of nucleic acid bases, heme, chlorophyll  Nitrogen excretion cycle – citrulline, ornithine  Hormones – indole acetic acid


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