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Exam 1 Notes

by: tess2019

Exam 1 Notes 40763 - BMS 110 - B

GPA 4.0
Introduction to the Biomedical Sciences
Ivy J Fitzgerald

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Includes notes for Exam 1 for the following lectures: Atoms and Molecules Tonicity and Mixtures pH Scale Macromolecules Central Dogma
Introduction to the Biomedical Sciences
Ivy J Fitzgerald
Class Notes
atoms, Molecules, tonicity, Mixtures, pH, pH scale, Macromolecules, Fats, Lipids, Proteins, DNA, RNA, transcription, replication, translation, bms 110, missouri state, fizgerald, ivy fitzgerald
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This 21 page Class Notes was uploaded by tess2019 on Monday October 5, 2015. The Class Notes belongs to 40763 - BMS 110 - B at Missouri State University taught by Ivy J Fitzgerald in Fall 2015. Since its upload, it has received 39 views. For similar materials see Introduction to the Biomedical Sciences in Biomedical Sciences at Missouri State University.

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Date Created: 10/05/15
it Central Dogma Monday August 17 2015 1227 PM Overview Central Dogma quotDNA makes RNA makes Proteinquot DNAgt DNA Replication in nucleus DNA gt RNA Transcription in nucleus mRNAgt Protein Translation in cytosol Central Dogma of Molecular Biology The Central Dogma of biology says 0 Information is encoded and stored longterm in the DNA o DNA is stored in the nucleus 0 This info encodes how to make proteins 0 Info for makinga protein that is needed at a particular time is transcribed into mRNA 0 mRNA leaves the nucleus and goes to the cytosol where ribosomes are located Ribosomes are able to translate the information encoded in an mRNA into a protein which does thejob that the cell needs done How is DNA replicated Cell division requires duplication of DNA 1 Parental DNA strands separated by DNA helicase 2 DNA polymerase quotreadsquot parental template DNA and matches complementary base pairs to synthesize new DNA strands 3 Two identical strands of DNA are synthesized a Replication is semiconservative each new DNA duplex has one old strand and one new strand DNA is synthesized 539 gt 339 0 One strand is easy to synthesize A nlnnv Ir nnl Inlnrrpnrl n nnl IrIn n El 339 nlvrnInn 39 ULIICI DLICIIIU DYIILIICDILCU Ill DPUILDIII J 39D UIICLLIUII Transcription DNA encodes how to make proteins 0 Proteins are machines of cell 0 DNA sends info using mRNA 0 RNA polymerase makes a singlestranded mRNA copy ofa region of DNA 0 Unwinds DNA 0 Synthesizes new strand of RNAfrom DNA39s template strand 0 DNA coding strand strand that reads the same as the mRNA except for TU DNA template strand noncoding strand strand that is template for mRNA reverse complement of coding sequence mRNA The copied mRNA sequence isn39t ready to use immediately after transcription 0 The premRNA must be spliced 0 Cut out regions wo information 0 Paste together good parts 0 The premRNA must have 539 and 339 modifications added 0 mRNA modifications 0 lntronsnoncodingsequences o Exons coding sequence 0 Splicing cutting out introns and sticking together exons 0 539 cap protects 539 end funny backwards nucleotide o 339 polyadenylation polya protects 339 end 39 String of adenines AAAA Translation The mRNA is quotreadquot by the ribosome and translated from a nucleotide sequence to an amino acid sequence 0 In the cytosol the mRNA is translated into proteins by ribosomes o Ribosome is mostly made up of RNA and some proteins 0 Has 2 halves one larger than the other 39 Eukaryotes 40 amp 60 S subunits Make 80 S whole ribosome Ribosome reads mRNA 539 to 339 Ribosomes quot1 IIJ CJl39lll 1 I o 3 CIOCKIngSItes tortmwun ribosome 39 A site III tRNA starts here with 1 amino acid III Where the aminoacyltRNA enters ribosome AminoacyltRNAa tRNA quotchargedquot with an amino acid 39 P site III ribosome moves so tRNA is here holding all the amino acids III Where peptidyltRNA is located I E site III ribosome moves so that tRNA is in E site with no amino acids III Exit site 0 Start of translation is called initiation o The two halves ofthe ribosome come together with the mRNA and a methioninetRNA The extension ofthe polypeptide chain is called elongation o A new aminoacyltRNA enters the ribosome and binds in the A site 0 A new peptide bond forms bt the peptide chain in the P site and the amino acid in the A site The bond bt the peptide and the tRNA in the P site breaks 0 The ribosome shifts over 39 The peptide chain is now in the P site 39 The empty tRNA is now in the E site 0 The empty tRNA in the E site leaves the ribosome A new aminoacyl tRNA enters the ribosome at the A site 0 The end of translation is called termination 0 When the ribosome comes to a stop codon it stalls and then disassembles falls apart releasing the peptide the mRNA the tRNA and the two ribosome halves 0 tRNAs o AminoacyltRNA o PeptidlylRNA 0 Empty tRNA Genetic Code The quotgenetic codequot translates nucleotide bases to amino acids Polynucleotides are read 3 bases at a time codon 0 Each codon specifies an amino acid How does the ribosome know where to start 0 Readingframe the way a polynucleotide is divided into codons o Translationlnitiation 39 The start codon is AUG 39 The first amino acid ofan amino acid is always methionine 39 The ribosome scans forthe first AUG and assembles here 39 The start codon determines the reading frame How does the ribosome know where to stop 0 Three codons have no corresponding amino acids 0 When the ribosome runs into one ofthese it stops 0 This causes termination o The stop codon DOES NOT CODE FOR ANYAMINO ACIDS Genetic code is redundant 0 Multiple codons encode forthe same amino acids Genetic code is unambiguous 0 Each codon encodes foronly one amino acid 0 f give you a codon you can tell me with certainty what amino acid it encodes tRNA revisited 0 Each tRNA has an anticodon that base pairs to its codon in the mRNA 0 When an aminoacyltRNA39s anticodon matches the mRNAcodon in the Asite a peptide bond is formed bt the amino acid attached to the tRNA in the A site and the peptide in the Psite Atoms amp Molecules Tuesday August 4 2015 1006 PM Biological ions Magnesium Calcium Sodium Potassium Fluorine Chlorine Iodine Definitions Element a substance with a distinct atomic identity Atom the smallest unit displaying the characteristics of an element Nucleus core of an atom 0 Contains protons and neutrons all have a mass ofabout 1 amu Surrounded by an electron cloud Charges Atom uncharged Ion a charged state ofan atom contains a diff number of electrons than a neutral atom Cation positivelycharged ion Anion negativelycharged ion Electrolyte substance that ionizes when dissolved produces cations and anions Elemental Counting Atomic numbertells you of protons Atomic mass tells you of protons neutrons Protons are positive 1 Electrons are negative 1 A neutral atom must have an equal numberof protons and electrons of neutrons atomic mass atomic number For atoms atomic numberalso equals of electrons in a NEUTRALatom Electron Shells Electron shells describe the electron densityaround the nucleus The first she holds 2 electrons 2nd she holds up to 8 electrons 3rd she holds up to 18 electrons Elements with more electrons will have more shes Shell must be full before moving to next shell Outermostshell is the valence shell Electrons in valence shell are valence electrons An atom has the most stable electron configuration when it has afulouter valence she 0 For most of the atoms important in biology the outer valence she target is 8 electrons C N O 0 Carbon can make 4 bonds 0 Nitrogen can make 3 bonds 0 Oxygen can make 2 bonds 7 o For hydrogen valence she can only hold 2 electrons so only forms 1 bond lone pairs of electrons unshared electron pairs Why aren39t atomic masses integers Isotopes Some elements can have diff numbers of neutrons same atomic number diff atomic mass bc of extra neutrons still the same element 0 For example carbon has several isotopes for example it can have a molecular mass of 12 13 or 14 0 The concentration of carbon14 is used for carbon dating Elements with an Ionic Charge Electrons are negatively charged When the number of electrons changes the charge ofthe atom creates an ion Positively charged ion cation has lost electrons Negatively charged ion anion has gained electrons Ionic Name Change Fluorine becomes fluoride Chlorine becomes chloride Bromine becomes bromide Iodine becomes iodide Ions Electrons are negatively charged Anions negative ions have extra electrons When the number of protons are lower than the number of electrons there is a negative charge Protons are positively charged Cations positive ions have fewer electrons When the number of protons are lower than the number of electrons there is a positive charge Molecules When atoms interact with each other they can form bonds which link them together to make molecules Definitions Atom a single unit of matter Molecule a group of linked atoms that make up one functional unit Bond the link bt atoms to make a molecule Exothermic reaction that releases energy will feel hot Endothermic reaction that absorbs energy will feel cold Types of Bonds Covalent Bonds In a covalent bond electrons are shared equally bt two atoms 0 Very strong bonds Commonly involve carbon oxygen nitrogen or hydrogen atoms 7 0 Typically between atoms of the same type of element Composed of pairs of electrons Each atom donates one electron to make a pair 0 Multiple pairs of electrons can be shared bt the same 2 atoms 0 Single bond share one pair of electrons 0 Double bond share two pairs of electrons 0 Triple bond share 3 pairs of electrons Polar Covalent Bonds n polar covalent bonds electrons spend more time orbiting one atom than the other atom in the bond 0 The larger atom pulls the electrons think gravitational pull more strongly than the smaller atom o The larger atom becomes slightly negative because the electrons spend more time orbiting it o The smaller atom becomes slightly positive because electrons spend less time orbiting it o This slight charge is called a dipole and represented by a delta and the appropriate charge 39 Water is polar which accounts for many of its lifegiving characteristics 7 0 Between atoms of different types of elements Ionic Bonds Two oppositely charged ions are attracted to each other Eg sodium chloride 7 0 Between 2 ions Hydrogen Bonds Hydrogen bonds are weak chemical bonds but are vital to biology The slight positive charge of a hydrogen atom win a polar covalent bond can form a weak attractive bond hydrogen bond wa slightly negative atom nearby in anothermoecue In water the positively charged hyd rogens are attracted to a nearby negatively charged oxygen 7 0 Between positive hydrogen atom and negative other atom Van der Waals Forces Van der Waals Forces are extremely weak 0 Result from intermittent electromagnetic interactions between resonating molecules 0 How geckos walk on walls Bonding Energy When you burn sugar in your body or around a campfire the bonds in the sugar C6H1206 break and reform to make carbon dioxide and water Bonds in sugarare weak bonds in carbon dioxide and water are strong 0 Energy is released when theless stable sugar bonds are broken to form more stable C02 bonds 0 Reactions that release energy are exothermic When plants make sugar from water and carbon dioxide they are breaking stable bonds to create less table bonds 0 The bonds in sugarare weak the bonds in carbon dioxide and water are strong 0 Breaking strong bonds requires energy plants get it from the sun 0 Energy is absorbed when the more stable C02 bonds are broken to form the less stable sugar bonds 0 Reactions that absorb energy are endothermic How to Write an Organic Molecule A bond can be drawn as a line bt element abbreviations C C single bond 1 bond CC Double bond2 bonds CthreelinesC Triple bond3 bonds A bond can be shown as two dots fortwo electrons bt element abbreviations HH Single bond composed of 2 electrons 0220 Double bond composed of4 electrons Use subscripts to show how many atoms of an element there are 0 H20 2 hydrogen 1 oxygen 0 02 two oxygen 0 CH4 one carbon 4 hydrogen CCH34 one carbon connected to 4 CH3 groups 0 So total C4C 12 H 5C 12 H When writing a structure count all the bondsfor all the atoms to make sure they have the right number Tonicity and Mixtures Monday August 24 2015 1230 PM Vocabulary Tonicity the amount of stuff in a solution Hypotonic the solute concentration is lowerin the other region compared to the reference region eg surroundings are hypertonic to cell lsotonic the solute concentration is the same in both regions Hypertonic the solute concentration is higher in the other region than the reference region Diffusion movement of stuff in a solution Cohesion and adhesion are Hydrophilic attracted to water polar bulk properties of water only occur at significant Hydrophobic repelled by water nonpolar volumes not at molecular level Cohesive sticks to self water sticks to itself Adhesive sticks to other things water sticks to surfaces Homeostasisthe tendency toward equilibrium the regulation ofa system to maintain the stable and consistent conditions Equilibriumstate where everything in balanced Equilibrationthe process of going to equilibrium remaining in equilibration Solution a mixture of solute and solvent Solute minor component in a solution dissolved in the solvent Solvent majorcomponent in a solution what the solute is dissolved in Diffusion movement of particles from one place to another down their concentration gradients Osmosis diffusion of solvent usually water Tonicity 39 T Cells are semipermeable and Tonicity is a measure of concentration blocks solute Amountofstuffperunit ofspace Tonicity and Cells In a Hypotonic solution water moved into the cell causing it to pop lyse In a hypertonic solution water moves out of the cell causing it to sh rivel Tonicity and Cells with Walls The cell wall prevents the cell from popping or shriveling too much Red Blood Cells Hypertonic solutions cause crenation sh riveling Hypotonic solutions cause hemolysis bursting Mixtures Homogeneous solution or mixture wellmixed all particles are evenly distributed Heterogeneoussolution or mixture NOT wellmixed particles are NOT evenly distributed Macromolecules Monday August 17 2015 1227 PM Overview Types of macromolecules Carbohydrates o Monosaccharides disaccharides polysaccharides Lipids o Phospholipids triglycerides steroids 0 Proteins Nucleic acids 0 DNA RNA Structures of each types of molecules and the reactions necessary to make each Why is life carbon based 0 Diversity of molecular structures 0 Chains 0 Rings 0 Branching structures 0 Can add a range offunction groups to change chemical properties Carbohydrates Contains carbon hydrogen and oxygen 121 ratio for monosaccharides Eg glucose C5H1205 0 Provides4 kcalg or4 Calg Monosaccha ride 1 ring of carbons 39 Glucose C5H1205 o Preferred energy source found in bloodstream 0 Found in grains fruits vegetables Fructose C5H1205 0 Found in honey agave nectar fruits o Digested in liver 0 Converted to glucose fat 0 Rings can open up and may be illustrated as a linear chain Chirality molecules can take different conformations o Nonsuperimposable mirrorimage Disaccha ride 2 rings of carbons Sucrose 0 Found in sugar cane sugar beets Dehydration reaction also called a condensation reaction a bond formed by elimination ofa water molecule 0 A molecule of water is created per bond formed Hydrolysis a bond is broken by addition of a water molecule 0 A molecule of water is incorporated per bond broken Oligosaccharide Multiple rings of carbons Shortchains ofcarbohydrates Polysaccharide Many many rings of carbons Glycogen 0 Long chain of glucose 0 Branching pattern 0 Stored in muscles and liver 0 Starch 0 Long chain of glucose 0 Straight chain 0 Energy stored by plants in roots tubers grains Cellulose 0 Long chain of glucose 0 Straight chain o In cell walls ofplants Lipids Long chains of carbon and hydrogen atoms Hydrophobicnot soluble in water 0 High energy content9 kcalg or 9 Calg Types oflipids o Phospholipids 1 phosphate 2 fatty acids attached to a glycerol 0 Triglycerides 3 fatty acids attached to a glycerol 0 Steroids 4 fused rings Fatty Acids Long chain of carbon and hydrogen atoms Carboxyl group from carboxylic acid at end Hydrophobic Saturated fatty acid 0 All single bonds 0 Form straight chains I Pack well together I Solid at room temperature Unsaturated fatty acid 0 Includes at least 1 double bond in chain 0 Monounsaturated fatty acid I 1 double bond 0 Polyunsaturated fatty acid I Includes multiple double bonds in chain 0 Have kin ked structure I Inhibits close packing I Liquid at room temperature 0 Cis fats double bond bends chain into a V I More likely to be liquid at room temperature 0 Trans fats double bond bends chain into a Z I Pack well and more likely to be solid at room temperature I Usually the result of hydrogenation processing 0 Hydrogenation double bonds removed increasing hydrogen bonds I May also flip cis double bonds to trans double bonds I Removes kinks allowing close packing I Makes oils solid at room temperature 0 Order of Packingfrom most likely to be solid to least likely 0 Saturated fatty acid 0 Transu nsatu rated fatty acid 0 Cisunsatu rated fatty acid 0 Polyunsaturated fatty acid Triglycerides Have 3 fatty acid tails attached to a glycerol Stored in adipose tissue Phospholipids 2 fatty acids attached to a glycerol a phosphate group 0 Makes up cell membranes Amphipathic both hydrophobicand hydrophilic parts 0 Fatty acid quottailsquot are hydrophobic o Phosphate group quotheadquot is hydrophilic Can form bilayers o 2 layers of phospholipids 0 Cell membrane Steroids Lipids that contain 4 rings 0 Cholesterol 0 Importantforcell membrane and structure Estrogen Testosterone Cortisol Essential Fatty acids Linoleic acid omega6 fatty acid We can39t make double bonds Importantforcell membranes Found in vegetable oils safflower sunflower corn oil poppy seed oil Dietary deficiency can cause mild skin scaling hair low and poor wound healing 0 Also importantfor pain sensations and other cellular signaling a Alnhalinnlpir arid nmppaR faffv Add 0000 IIVI Illlvlvlv VIVIle VIIIVDUI v IUIUU Ulvlvl r o Importantforcell membranes 0 Found in seed oils chia flaxseed nuts vegetable oils 0 Helps all kinds of things Proteins Roles Structure of cells 0 Movement of cells 0 Communication wand bt cells Localization of molecules win cells 0 Transportation of molecules within cells Metabolism break down and build up molecules Immune response 0 Cell death Overview 0 Fold up into active proteins 0 Great structural diversity built from o 20 amino acid quotbuilding blocksquot 0 Two possible strand bendsfor local bending Amino Acids Amino acids side group R carboxyl group 0 R group is differentchanges Proteins composed ofamino acids linked by peptide bonds to form a polypeptide 0 Form by dehydration reaction 0 Count amino acids by 0 Numberof R groups 0 Numberof nitrogen o Numberof double bonds 0 Each amino acid has a unique chemical identity 0 The uniqueness of each amino acid is due to a distinct R group 0 There are 20 R groups so 39 4 categories D Polar hydrophilic ll IUIJUIdI IIYUIUPIIUUIL III Acidic hydrophilic The R groups ofthe 2 acidic amino acids dissociate in solution to their most stable form Carboxyl OH group lose H lowering pH making the solution more acidic III Basic hydrophilic The R groups ofthe 3 basic amino acids dissociate in solution n solution the nitrogens attract H raising the pH making the solution more basic 0 All amino acids dissociate in solution 0 O In solution it will dissociate into its most stable forms Carboxyl OH group lose H and amino groupsNHz attracts H Protein Structure 4 Levels of Structure 0 Primary sequence of amino acid residues 0 Secondary local folding of polypeptide O Polypeptide strand adopts local secondary structure 0 Alpha helices O 39 Corkscrew shape 39 Tu ms of helix held together by hydrogen bonds between turns beta strands beta sheet 39 Pleated flat shape 39 Strands held together by hydrogen bonds 39 Can be parallel or antiparallel to other strands III Ifantiparallel quotnicequot hydrogen bondsform between strands III If parallel quotbentquot hydrogen bondsform between strands Tertiary 3 D structure of protein 0 O O O Globular orfibrous This is the active form ofa polypeptide At this stage a polypeptide is called a protein Proteins can be 39 Globular D Roundbh I Fibrous D elongated Quaternary multiple polypeptides fold together to make one functional unit 0 Multiple folded polypeptide strands associate to form one active complex multiple polypeptide strands form one structure and work together to perform a function 0 Not all proteins form a quaternary structure Protein Modifications The amino acids can have chemical modifications after the protein is made 0 Over 200 known modifications alters what protein does Lipoprotein proteins that have lipids attached 0 Cholesterol triglycerides and phospholipids 0 Found circulating in the blood Glycoproteins proteins that have oligosaccharides attached 0 Sugars added 0 Founds on the surface of cells Enzymes Enzymes proteins that catalyze chemical reactions 0 Some proteins are enzymes 0 Cause reactions to happen more quickly 0 Enzymes catalyze reactions Enzymes cause reactions to happen faster because they 0 Hold pieces together 0 Activate reacting pieces 0 Some enzymes are RNA molecules ribosomes Nucleic Acids Role ofDNA Deoxyribose Nucleic Acid 0 Store genetic information 0 Longterm storage DNA Structure Composed of nucleotides 0 Sugar o Nitrogenous base I Atoms in nitrogenous base are numbered 39 Atoms in the sugar are numbered with 39 primes 39 So you can tell if an atom position is in the base in the sugar by whether it has a 39 or not 39 4 possible basesin DNA III Thymine III Adenine III Cytosine III Guanine D Pyrimidines Have 1 ring Thymine Cytosine Uracil D Purines Have 2 rings Guanine and Adenine o Phosphate groups Nucleotides linked together by phoshodiester bonds to make a polynucleotide strand 0 Formed by dehydration reaction 0 Formed bt the 539 sugar position ofone nucleotide and the 339 sugar position on the next nucleotide 39 The directionality of a nucleotide strand can be determined by identifying the 539 and 339 carbon atoms that are linked by a phosphodiester bond 39 The phosphodiester linkages of the two polypeptide strands in the alpha helix are antiparallel Two antiparallel nucleotide strands are held together by hydrogen bonds bt bases Two strands wrap around each other to make double helix structure o In the double helix the phosphate sugar backbone is on the outside 0 Hydrogenbonded base pairs on the inside 0 Bases 39 Adenine and thymine always pair together in DNA 7 III There are 2 hydrogen bonds bt A and T 39 Guanine and cytosine always base pair together in DNA III There are 3 hydrogen bonds bt C and G Roles of RNA Ribose Nucleic Acid 0 mRNA messenger RNA 0 Transcript of DNA encodes info for making a protein rRNA ribosomal RNA 0 RNA that folds up to make the major components ofthe ribosome tRNA transfer RNA 0 the decoder fortranslating mRNA into protein 0 Base pairs to mRNA and delivers the corresponding amino acid DNAVSRNA Ribose sugar instead ofdeoxyribose 0 Changes stability ofthe polynucleotide Uracil base instead ofthymine RNA is single stranded Like DNA RNA is composed of nucleotides linked by phosphodiester bonds 0 Like DNA there are 4 RNA bases 3 from DNA and 1 different tRNA Transfer RNA carries amino acids to ribosomes to make protein Folds up into an active form to do this 0 Levels of Structure 0 Primary structure nucleotide sequence 0 Secondary structure cloverleaf loops 0 Tertiary structure Lshaped ATP Adenosinetriphosphate Contain53 phosphategroups The bonds between phosphate groups are broken to release energy to do endothermic reactions in the cell 0 Good energy source because 0 Fast access to energy 0 Readily available 0 Reversible


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