Exam 1 MAIN Study Guide

8/13/2019 Exam 1 MAIN Study Guide

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Exam 1 MAIN Study Guide..Detailed Page by Page Version (Also try to look at other exam 1 filesbelow))

BSC1010 Exam 1 Detailed Page by page ……. Study Guide.

Chapter 1

IN ADDITION TO THIS VERY DETAILED STUDY GUIDE ALSO LOOK OVER THE OTHER GENERAL STUDYGUIDES IN THIS SAME FOLDER (BELOW) FOR EACH CHAPTER 1-4 and 5 WHICH HAVE 10-20 OBJECTIVEQUESTIONS AND VOCABULARY LISTS.

Page 1. Be able to define the terms biology and evolution. Be able to distinguish what is alive or livingversus that which is not based on the seven properties of life.

Page 2. Know figure 1.3 in detail ; know each property of life and it’s description.

Page 3. Know what is meant by “emergent properties” what are they? How do they come to be.

Page 4-5. Be able to list the 10 levels of biological organization in correct sequence and be able to

describe/define what each level represents. For example ecosystems fall between the higher biospherelevel and the lower communities level. By definition we can describe an ecosystems as all the livingthings in a particular area as well as the non-living components and the interactions between living andliving non-living and living and non-living with non living. The sun a nonliving component of mostecosystems can interact with organisms termed producers such as plants leading to the synthesis oforganic compounds which are used by the plant and also by consumers which eat plants (page 6) . Theorganic compounds serve as fuels for the plants and consumers. Utilization of the fuels produces heatwhich is released back into the ecosystem. When consumers and producers die they return nutrients tothe soil a nonliving component. The soil will in turn provide these nutrients to the next generation ofproducers and consumers. Scientists who study such interactions within ecosystems arecalled ecologists .

The above was an example of one level of biological organization along with a complete description ofthe level and examples of events occurring at the level. You should know all the remaining 9 levels ofbiological organization at this level of detail.


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Page 7 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 8 Know that the cell is the smallest simplest form of life capable of exhibiting the 7 properties oflife. Know all cells are surrounded by a membrane that regulates passage of materials between the celland its surrounding. Know cells are classified into 2 groups eukaryotes and prokaryotes. Know thedifferences between the 2 types. For example prokaryotic cells are smaller, they are older, they cameinto existence 3.8 billion years ago whereas eukaryotes first came into existence 2.1 billion years ago.Prokaryotes lack a nucleus, lack a nuclear envelope, lack nuclear pores, lack any nuclear proteins such asthe lamin proteins or histones. Most prokaryotes lack any internal membranes such as golgi or vacuolesor endoplasmic reticulum, a few like cyanobacter have some in-folds of their plasma membrane but noseparate membrane enclosed organelles. Only eukaryotes have a nucleus and only they have internalseparate membrane enclosed organelles like vacuoles and lysosomes and rough ER smooth ER etc...

Page 8 Know about DNA and its function (Also covered in end of chapter 5)

Know that DNA is found in structures called chromosomes in association with proteins. Know that eachchromosome consists of a linear or circular strand of DNA which is in turn composed of chains ofbuilding blocks called nucleotides. Know that there are 4 nucleotides used in DNA described by theletters A,C G and T (page 9) . Linking these 4 nucleotides together in variable sequences creates longchains of nucleotides also known as a DNA chain . To form DNA requires that 2 chains of nucleotides beinterwoven as a double helix. Very long chains of connected nucleotides create chromosomes. Knowthat along the length of a chromosome’s long chains of nucleotides ( DNA strands ) are small units calledgenes. Each gene codes or contains instructions or the blueprint on how to build a specific protein. Achromosome may be 1-200 million nucleotides long, but each gene is only about 10,000 nucleotideslong. So a chromosome may have from 100-10,000 genes each coding for a specific protein. When anorganism grows and develops from a single fertilized egg it is the creation and actions of thesethousands of proteins coded for by the genes that actually carry out the building events and

maintenance activities of the cell that will make that single cell become thousands of cells and that willorchestrate the formation of the various bodily structures. The 4 nucleotides of DNA when chained insequences create words or instructions for the cell on how to build these proteins. Like an alphabet ofonly four letters words like ACCGGTTGCCCATG which don’t mean much to us, such words have veryspecific meanings to a cell engaged in protein synthesis, just as words created from our 26 letteralphabet have specific meanings for us.


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Page 10 Know what the term genome means.


Page 12 Know that “Diversity” is a hallmark of life. Know that there are currently 1.8 million differentspecies of life. Know that taxonomy is the branch of biology that names and classifies species, thatgroups diverse organisms according to their similarities and their relationships to each other. It alsoorders them into groups of increasing breadth spanning from the most specific and least inclusivegrouping to the broadest and almost all inclusive grouping ie from a species to a domain.

Know the 8 taxon levels of taxonomic grouping in ascending and or descending order. Ie species, genus,family, order, class, phylum, kingdom, domain….

Page 13 know the three domains of life and their descriptions be able to distinguish between the 3,bacteria, archaea, eukarya. Also know the 4 eukaryotic kingdoms and their descriptions, plantae,animalia, fungi, protista (figure 1.15)


Page 15 Know what “natural selection” means Page 16-17 know how new species arise according to theDarwinian model of descent with modification


Page 19 Read (BUT MATERIAL WILL NOT BE ON TEST).......... Except for figure 1.24 know this figure andknow the steps of the scientific method



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Chapter 2


Page 31 Know the section 2.1…Matter consists of chemical elements in pure form and in

combinations…..

Know that chemistry is the study of matter in all of its three states solid, liquid and gas. Knowthat matter is anything that occupies space and has mass. Know that living organisms are composed ofmatter. Know that matter can be divided into pure substances and mixtures. Know that pure formsof matter include : elements and compounds . Know that an element is a pure form of matter that

cannot be broken down to other substances by chemical reaction. Know that compounds are also pureforms of matter created by the bonding of two or more different elements in a fixed ratio. The bondingcan be ionic or covalent and requires chemical reactivity between valence electrons.

Note: Compounds are newly formed pure substances and have new novel physical properties andchemical properties that differ from the parental elements from which the compound was formed.


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Know what a physical property of matter is? (ie boiling point, taste, solubility.

Know what a chemical property of matter is

Know that mixtures of matter may be homogenous (air) or heterogenous

Page 32 Know the elements of life. Study Table 2.1. Know all the elements and trace elements found inthe human body. Know the effects of trace element deficiencies such as iron (Fe) zinc (Zn) andiodine(I) deficiency.

Page 32 The case study on toxic elements. Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 33. Know atomic structure including the definition and location of protons neutrons, electrons ,quarks, and neutrinos.

Know what the atomic number , and mass number are. Know how these numbers are representedsymbolically on an Element Letter as super or sub scripts.

Given a graphical description with atomic number, and mass number be able to find the number of

neutrons, protons and electrons.

Know what a “ cation ” and an “anion” are and how they are f ormed.

Page 34. Know what an isotope is? Know what a radioactive isotope is. Know some uses in medicine andresearch for radioactive isotopes.

Page 35-36 and PowerPoint and class notes and via Google search. Be familiar with N iels Bohr ; who hewas; what his contribution to the field of chemistry was.

Know that electrons around the atoms nucleus have potential energy. The ones closest to the nucleushave the least the ones in the outer or valence shells have the most energy. Know that electrons can


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only occupy specific energy levels or shells ranging from J -K-L-M-N…. or levels 1 -5 or higher. As electronsmove from outer shells to inner shells they lose energy which is emitted as released energy like light orheat or fluorescence. As electrons move from inner to outer shells they gain or absorb energy which thesurrounding environment loses. The electrons on the outer shells (the valence electrons in the valenceshell ) have the most energy and the most potential to react or form bonds. On the periodic table the

rows or periods correspond to the number of energy shells that have electrons in their orbits. So H andHe on row 1 or period 1 have only one energy shell with 1 or 2 electrons respectively. Row 2 or period 2includes Lithium through Neon all of the atoms of these elements have two (2) energy shells. Row 3 orperiod 3 includes sodium (Na) – Argon (Ar) all of the atoms of these elements have 3 energy shells withelectrons in orbit. The third shell in this case is the valence she ll. The columns on the period tablerepresent groups of atoms of similar size with regard to the radius of the nucleus and similar in theirchemical properties. The group number also tells us how many Valence electrons are in the valanceshell . For example carbon is in group 4a so carbon has 4 valence electrons available for sharing incovalent bonds. Oxygen has six valence electrons in its valence shell or group 6A so 2 electrons aremissing and needed to fill its octet or we say oxygen has a valence of 2; which represents its bondingcapacity; it can form 2 bonds by sharing 2 electrons from another atom or atom. Note the number ofvalence electrons is different then an atoms “valence”< span> Oxygen has 6 valence electrons but avalence of 2. In the third period phosphorus which is in group 5A does not have a valence of 3 asexpected but rather 5 due to hybrid sp orbitation. Hence phosphorous can form 3 single bonds andoften forms also a double bond. Arsenic can also do this and in some bacteria arsenic may replacephosphorous in the formation of molecules such as DNA that usually has phosphate groups.

Also know the following:

Page 36-37 Know that electrons have specific configurations within the energy levels they occupy andmay be positioned on sublevels or orbitals. On energy level 1 there is one sublevel s which can hold 2electrons often written as 1s 2. On the second energy level further out from the nucleus or the K shell wehave s and p sublevels or orbitals. 2 electrons can be found in the s and 6 electrons can be found in thex,y,z, planes of the 3 p orbitals. Or energy level 2 can hold a maximum of 8 electrons. Sometimes fillingthe s and p of the valence shell is called completing the octet . All stable elements such as the inert

gases have complete octets in their valence shells, with all s and p orbitals filled. On energy level 3 whichis even further away from the nucleus we have 3 sublevels s, p, and, also d. 2 electrons can occupy thelevel 3 s orbital or sublevel; 6 electrons can occupy the level 3 p …. x-y-z orbitals and 10 can occupy the5 d orbitals or a total of 18 electrons on level 3 or the L shell.


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Also know the following:

There are 2 ways to represent electron configurations either by an alphanumeric descriptioni.e [1s 22s 2 2p x

22 p y22p z

23s 2 or 1s 22s 2 2p 63s 2] or by drawing concentric circles and showing via dots thenumber of total electrons found within that energy shell. Similar to a bullseye with orbiting electrons on

each ring. The second way does not tell us which specific orbitals have electrons but we can guessbased on the fact that the s only fits 2 electrons and p orbitals only hold 2 electrons on each axis or 6total; d orbitals hold 10 electrons and f orbitals at the 4 th energy level hold 14 electrons. Also Levelone only has s orbitals Level 2 has sand p Levl 3 has s p and d, level 4 has spdf orbitals.

One additional representation is called Lewis dot structure. A letter representing the atom is written anddots representing the paired or unpaired valence electrons are drawn around the written letter. ie

:C:

Concentric circles or bullseye drawings don’t give us the true picture of electron orbit shape; the s

orbits for example are really spheres and the p orbits are dumbbell-shaped.

Atoms with unpaired electrons in their valence shell; usually found when an octet of electrons in the sand p orbitals is incomplete, are chemically active and want to form bonds to become stable bycompleting their octet and leaving no unpaired electrons. Only the inert gases like neon and argon arechemically inert or non reactive.

Because of this most atoms want to form ionic or covalent bonds with other atoms via the valenceelectrons. The purpose is so that after bonding the atoms involved in the bond will have filled valenceshells or complete octets and will become stable compounds or molecules like the inert gases.

Page 38 Know what covalent bonds are.

Top of page 38 …know what a molecule is.

Know that compounds can form via ionic or covalent bonds but molecules all form via covalent bonds.

Know that covalent bonds can be polar or non-polar. (page 39) Polar covalent bonds form when thedifference in the electrotronegativity values of the atoms attempting to bond is > 0.5 and less than1.9. If this value is 1.9 then theatoms will form an ionic association.


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Know that water H2O forms a polar covalent bond leaving partial charges or dipoles that are positive onthe 2 hydrogens and dipoles that are negatively charged on the single oxygen. Oxygen which has astrong electronegativity value shares hydrogen’s electrons unequally holding them >80% of the time. By

gaining Hydrogen ‘s electrons the oxygen in water takes on 2 negatively charged electrons and hencetakes on a slight negative charge. Each of the two Hydrogen’s which had their single electron rippedaway from heir 1s orbitals; leaving only its nucleus carries a slight positive charge due to the positivecharge of the single proton in the nucleus.

In your power points I have a periodic table with electronegativity values that you can look at to predictthese types of bonds

A single pair of shared electrons yields a single bond represented graphically by a single line betweenatoms in the structural formula of the molecule. Ie H 3-C-C-H3. Two (2) pair of shared electrons yields adouble bond represented graphically by two lines between atoms in the structural formula of themolecule i.e H 3-C=C-H3

(Know the difference between structural and molecular formulas)

Page 39 know what ionic bonds are and how they are formed. Be able to show the formation of anionic bond (this question will be on the tests 100% ) and represent it graphically (this question will beon the tests 100% ). ( Graphically means: Drawing the electron orbitals around the atomic nucleus andshowing the transfer of electron from the valence shell of one atom to the receiving valence shell of theother atom and the resulting creations of anion and cation that then attract and from the bond) Seefigure 2.14 also PAGE 40 AT BOTTOM the text which describes Mg which loses two electrons one gainedby one Chlorine and the second gained a second chlorine to form MgCl 2. (hthat is one Mg+2 cationbonding with two Chlorine anions Cl- …. Cl-

Know ionic compounds unlike covalently bonded molecules, do not have definite size and number of

atoms but rather form aggregates of ions that form growing crystal lattices of variable dimension.

Page 40 Know what “weak chemical bonds are” . For e xample what is a hydrogen bond how is itformed. What is a dipole dipole bond? What is a van der Waal force? In living organisms many weakbonds are used to give biological macromolecules their specific three dimensional shape. DNA strandsare held together via hydrogen bonds. Water molecules stick to each other using hydrogen bonds.


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Boiling point and melting points are affected by the strength of inter molecular interactions. Twomolecules held together via van der Waals forces wil boil at a much lower temperature than two watermolecules held together via hydrogen bonds. The backbone of the alpha helix shape of proteins dependson hydrogen bonds to keep that spiral staircase shape

Page 40-41 Know that even a molecule with non-polar covalent bonds may have very very very weakpositive and negative charged regions due to the electrons surrounding each atom and the protons inthe nucleus of each atom. Non-polar molecules may interact via these weak electrostaic forces if theyare close together and no energy exists in the system to push them apart. These weak interactions arecalled van der Waals forces or aka London dispersion forces. Molecules like lipids, fats fatty acids oils,waxes all stick to one another using this type of weak force. This type of force is easily disrupted byslight elevations in temperature, which will melt solid forms or boil liquid forms of these non-polarhydrophobic molecules.

Page 41 Know about molecular shape . Know that repulsions from the electrons in the orbitals of theatoms that are bonded into molecules create molecular shape and geometry. Hybrid orbitals of theinteracting orbitals of each atom create shapes such as t etrahedral or pyramidal or trigonal or linearforms.

Page 42 Know about the importance of molecular shape to biology and fields such as pharmacy basedon the example in figure 2.18 concerning morphine and endorphins.

Page 43 Know that chemical reactions involve reactants and products . The atoms of the reactants areconserved in the production of products. We say that chemical reactions do not create or destroymatter; reactions rearrange matter and bond associations. Reactants appear on the left hand side of achemical equation followed a right proceeding arrow -> which leads to products on the right hand sideof the chemical equation. A reaction may be in equlibrium having an equal likilihood to proceed to theleft or to the right.

Chapter 3

Three fourths of the earths surface is covered by water.


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Page 46 Know why water is important to life here on earth as well as on other planets.

Page 47. Know about the relationship between polar covalent bonds found in water and the dipolesformed on the molecule and how these dipole charges make hydrogen bonding between watermolecules possible ( see figure 3.2 page 47).

Know that 4 four hydrogen bonds can form with any single water molecule occurring in approximately atetrahedral shape in the solid form of water. This arrangement means water molecules are typicallyalways tethered to one another preventing their free kinetic movement and preventing changes instates of water unless significant energy is invested to break all four hydrogen bonds. We say that waterhas great cohesion , it is held together by its self associations, it sticks easily to itself. Water also sticks toother polar molecules or we say it has good adhesion to polar molecules. These two features makes it

possible for water to travel from the roots of a plant to its leaves against gravity. Breaking cohesivewater molecules apart along the surface of water is difficult compared to other liquids water has a highsurface tension.

Page 48 know the definition of kinetic energy, heat, temperature, calorie, joule, kilocalorie.

Know how water moderates global temperatures (see what follows below):

Know what the term specific heat means. Know that compared to other liquids water has a very highspecific heat. It is because of this that the oceans and seas on our planet can absorb extreme levels ofsolar energy daily absorbing massive amounts of heat but with very little shift in temperature. Whatgives water this property are the four hydrogen bonds that keep each water molecule tethered so theydo not move. In other words the average kinetic energy does not increase much when water is exposedto solar energy because the suns energy may break a hydrogen bond on a water molecule but since thatmolecule is tethered to three other water molecules it does not move or we say it is not put into motionhence does not gain kinetic energy. A gain in kinetic energy shifts temperatures upward but water which

resists kinetic motion due to its four tethers shifts very little in temperature in spite of absorbing a greatdeal of heat energy from the sun. This makes it possible for the planet to be exposed to solar energy butnot have drastic increases in global temperature. Water moderates daily temperatures by absorbing thesuns heat but water does not shift much in temperature. The absorbed daytime heat of solar energy isstored in the bodies of water during the day. At night when hydrogen bonds reform in the waters of theworld; that stored energy is released back into atmosphere keeping evening temperatures moderate.


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In a desert environment where no water is around there are broad shifts in temperature; in the day 130C ; in the evening 30 C. But in coastal areas near water the range is much narrower with day time tempsaround 80 and night time temps around 55 C. Water in tose areas absorbs heat in the day so it doesn’tgo much above 80 . then at night the wate releases the absorbed energy back into the night sonighttime temps stay above 50.

Page 49 know the principles behind evaporative cooling. (the idea that the fastest molecules leave asthey evaporate bringing the average kninetic motion down and hence temperatures lower)

Page 50 know why water in its solid from “ice” is less dense then water in its liquid form

Know exactly how much less dense ice is than liquid water (page 50 1 st paragraph in left column ofpage) 10% less dense for a given volume. We say that in liquid water at the higher temp, watermolecules break bonds and “slip” closer together making them more densely packed. In ice the bondsare rigid no “slipping “ occurs so molecules are held at greater distances from one another as comp aredto the situation in a liquid sample.

Page 50 know that water is the solvent of life. Know the terms: solvent, solute, solution, aqueoussolution

Page 51 be able to explain how a solute such as NaCl dissolves when placed in water. In yourexplanation talk about water’s polar covalent bonds, its partial dipole charges and how these chargesinteract with the Na cation and the Cl anion.

Know the terms hydrophobic and hydrophilic? Can a hydrophobic solute be dissolved in a polar solvent?Why? or Why not?

Molar Concentrations

Know about molarity and how to determine solute concentrations. Know the example on page51 bottom right hand column where they calculate the number of grams of sucrose that are needed tomake a 1 molar solution in 1 liter.


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In this regard first be able to calculate the molecular mass of sucrose C 12H22O11 . In the book this comesout to 342 daltons or 342 grams per mole. (there are 6.02 x 10 23daltons in 1 gram)

Know where on a periodic table to find the molar mass

Know that a mole is equal to 6.02 x 10 23 atoms or molecules

So 342 grams of sucrose weighed out is the same as 1 one mole or 6.02 x 10 23 molecules of sucrose.

A 1 molar solution is defined as 1 mole of solute in 1 liter of solvent.

Calculating molarity

Part 1 : Calculating molar mass of a molecule is often required to do some molarity problems. The videobelow shows you how to calculate molar mass

http://www.youtube.com/watch?v=F9NkYSKJifs

Part 2 : Many times molar mass is given and other things are varied. Below are some videos thatdemonstrate how to solve different molarity problems where the molar mass is given but numbers ofmoles are sought ; or special volumes are used in the problem

http://www.youtube.com/watch?v=raq2Y1yBQrQ

http://www.youtube.com/watch?v=8oTqwBAvbnY

http://www.youtube.com/watch?v=S12wa4oe1fE

Based on these examples then:

342 grams of sucrose put in a liter of water will create a 1 Molar sucrose solution. (1 mole in a liter)

If we wanted to make a 0.5 liter at 1 molar we would add ½ of 342 grams in 500 ml

http://www.youtube.com/watch?v=F9NkYSKJifshttp://www.youtube.com/watch?v=F9NkYSKJifshttp://www.youtube.com/watch?v=raq2Y1yBQrQhttp://www.youtube.com/watch?v=raq2Y1yBQrQhttp://www.youtube.com/watch?v=8oTqwBAvbnYhttp://www.youtube.com/watch?v=8oTqwBAvbnYhttp://www.youtube.com/watch?v=S12wa4oe1fEhttp://www.youtube.com/watch?v=S12wa4oe1fEhttp://www.youtube.com/watch?v=S12wa4oe1fEhttp://www.youtube.com/watch?v=8oTqwBAvbnYhttp://www.youtube.com/watch?v=raq2Y1yBQrQhttp://www.youtube.com/watch?v=F9NkYSKJifs


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If we wanted to make 2.5 liters @ 1 molar, we would add 2 x 342 grams plus ½ 342 grams of sucrose in2.5 liters of water. To make a 2 Molar solution we would need 2 moles of sucrose in a liter of water.Hence we would add 2 x 342 grams in a liter of water

Page 53 Know what acids and bases are. Know that when acids dissolve in water they donate additionalH+ to the solution that joins with water to form H 3O+ ions. Acids increase the H+ akaH3O+ concentration such that there are more H+ than OH- ions

A substance that reduces the H+ or H 3O+ concentration by accepting protons is known as a base .

In pure water the H+ concentration is 10-7 molar and the OH- is perfectly balanced at 10-7 molar. Acids

will increase the H+ let say up to 10-2 when this occurs the OH- will correspondingly go down 5units to 10-12

Instead of using actual concentration we can refer to H+ concentration via a logarithm expressiontermed the pH or potential hydrogen value

pH = -Log[H+]= negative log of the H+ concentration

Low pH values represent high H+ concentrations because 10 -1 is actually greater than 10 -6 . The -Log[10 -1]= 1 -Log[10 -6]=6 So pH 1 equals 0.1 Molar H+ but pH 6 equals .000001 Molar H+

Also every pH value change is based on Log base 10 so each pH change is a 10 fold change.

Page 54 Know Figure 3.10 thoroughly including all examples and their pH values.

Page 54 Know what a buffer is.


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Be familiar with amino acids and H2CO3 carbonic acid as natural buffers of the blood stream


Chapter 4

Page 58 Know that living organisms are made up of chemicals based mostly on the element carbon . Thiscarbon originates in the atmosphere as CO2. Plants take it in and integrate this atmospheric carbon intoorganic chemicals such as carbohydrates, ie sugars. Animals eat these Carbon products when they eatthe plants. Animals restore Carbon to the atmosphere when they respire out CO2. Plants can also do thisat the cellular level via cell respiration which produces CO2 which the plant can either release to theenvironment or use in the synthesis of more sugars. These events represent the carbon cycle.

Page 58 Know that organic chemistry is the branch of chemistry that specializes in the study of carboncompounds such as the sugars produced by plants and metabolized by both animals and plants. CO2 isconsidered inorganic even though it contains carbon. This is based mostly on the historic principleof vitalism , which assumes organic compounds can only be produced within living organisms and not viaartificial synthesis in the lab. Since CO2 can be produced artificially it was and is still consideredinorganic. We now know that most organic compounds can also be produced in the lab artificially so bytoday’s stan dard we would need to alter our definition of what is organic if we wish to not consider CO2organic. After all CO2 does contain carbon. But the majority of “organic “ compounds also contain

hydrogen. These range from hydrocarbons like gasoline to biopolymers such as proteins and lipids.


Page 60 Know how to write the molecular formula for hydrocarbons such as methane (CH 4), Ethane(C2H6) and ethene (C 2H4) (see figure 4.3)

Page 60 Know how to write the stuctural formula for hydrocarbons such as methane (H2-C-H2),Ethane and ethaene (see figure 4.3 for actual drawn structures))


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Page 60 Know the difference between a structural formula and a molecular formula.

Page 60 Know that all molecules including hydrocarbons form definite shapes such as tetrahedrons,trigonal planar and linear arrangements. The shapes and isomeric forms of molecules play a role in theirbiological functionality.

Page 60 know that carbon which has a valence of 4 can form 4 bonds. When it shares these electrons itform s covalent bonds. It is this reason that carbon can from large branched complex molecules. Carbonchains form the skeletons of most organic molecules. These chains are not always linear;some formrings and are called cyclical.

Page 60-63 Know the characteristics of hydrocarbons as an organic compound group.

a) Hydrocarbons are all non-polar hydrophobic compounds (page 61)

b) Hydrocarbons all have low melting points and boiling points and low solubility in water. (SeePowerPoints and class notes not in textbook) Lacking polar or ionic dipoles or charges these compoundscan only interact via van der Waals forces which are weak and easy to break. Hence very low

temperatures provide sufficient energy to break these molecules apart and shift them from the liquidstate to the vapor state. Also lacking polar or ionic dipoles or charges means no way to interact withwater molecules which carry positive and negative partial charges. Hence these hydrocarbons can notinteract with water, they can not dissolve in it.

c) Hydrocarbons are major components of petroleum or fossil fuel. All hydrocarbons are good fuels . iebutane, propane, octane which serve as lighter fluid, fuel for cook outs; and gasoline respectively (page61)

d) Page 61 ….Living organisms have molecules which contain segments that are 100% identical tohydrocarbons like octane (gasoline). The molecules known as FATS or adipose have long hydrocarbontails attached to a non-hydrocarbon region. Neither petroleum or FAT dissolve in water. FAT is used inliving organism as stored fuel. Petroleum likewise functions as a fuel. (See figure 4.6)

e) Many biological organic compounds are converted hydrocarbons having a carbon chain skeleton but

substituting other atoms for the hydrogen’ � � � � � � � � � s on the hydrocarbon chain withOxygen, and Nitrogen. Usually this is in the form of functional groups (page 64). These substitutionschange the physical and chemical properties of the hydrocarbon. They become less non-polar and gain


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water solubility along with increased Boiling and Melting points and may become less flammable.Example Octanoic acid a fatty organic acid and octane are very different, the latter being 100 timesmore flammable than the former.

f) Page 62 Figure 4.7 and the text on this page: Know the three different types of isomers. Be able to

draw examples of each type. Be able to define and compare each type

g) Page 63 figure 4.8 know the relationship between eantiomer shape and pharmaceutical efficacy.Example Ibprofen Only the “S”or “L” eantimoer is effective for pain treatment. The “D”< span> or “R”form has no effect. Example 2 Allbuterol: only the “R” enantiomer form aka “D” form is effective againstAsthma; the “S” or “L” form does nothing to help asthma.

Page 64- 65 Know all the organic functional groups. Be able to draw all the functional groups or torecognize a functional group from a drawing.

Be able to list examples of molecules that are representative examples of molecules that have aspecific functional groups. For example on page 64 in figure 4.9 under Hydroxyl. Ethanol a alcohol islisted as a representative example that contains a hydroxyl group. Ethanol = CH 3CH2OH.

Be able to distinguish between aldehydes and ketones (page 64) and give examples of molecules thathave these functional groups.

Know any organic molecule that gains a carboxyl group automatically becomes an “Organic acid)Carboxyl groups donate the H+ from their OH portion leaving hydrogen’s electron behind with the C= Oand Oxygen. This is written as COO- and H+ anions and cations.

Know any organic molecule that gains an AMINO functional automatically becomes an “ Organicbase) Amino groups accept H+ protons becoming NH3+ or NH4+

Know that sulhydryl groups are seen frequently in protein structures where disulfide bonds formbetween different protein segments to fold the protein into its 3D shape.


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Know that any organic molecule that gains a phosphate group automatically becomes a ACID”<span> The phosphate has 3 OH hydroxyls. In solution the H of the OH groups ionizes as a proton intosolution leaving the electron behind and makes the phosphate carry a negative charge. Phosphates areimportant parts of DNA and RNA molecules and of the cell energy molecule known as ATP. Cellmembranes are made up of phospholipids. Phosphate groups are important to membrane function

providing the hydrophilic part of a membrane that faces out or inside a cell where water is located.

Know that methyl groups are important to the expression of genes. DNA which is methylated does notexpress genes which means those regions will not be able to code for new proteins.

Page 66 Know about ATP, what it does , and how it works as a cell energy molecule.

Chapter 5

Page 68 Know the 4 classes of critically important large moleculesare carbohydrates , lipids , proteins and nucleic acids . The largest are the carbohydrates, proteins and

nucleic acids which are called macromolecules . Lipids are smaller and not relatively as large as theothers.

Page 68-69 Know that: macromolecules are polymers built from momomers . Know that a polymer : is along molecule consisting of many identical building blocks (aka monomers) linked by covalentbonds. Analogy is a train which is a chain of identical cars linked together.

Page 69 Know that: The Monomers of large macro molecular polymers are representedby small molecules like amino acids or nucleotides or monosaccharides which are the repeating unitsthat serve as the identical building blocks that are to be linked together to build themacromolecule/polymer.


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Page 69 Know that: To connect one monomer to a second monomer chemically requires a processknown as a dehydration or condensation reaction. This process removes a water molecule and formsa new covalent bond linking/chaining them together. If this occurs again then the chain will have 3monomers linked together; if another dehydration occurs then 4 monmers will be linked together viacovalent bonds. In this way polymers which may have 100’s of su ch links can be formed. The bonds

formed by dehydration that link monomers have many names; in carbohydrates the link betweenmonosaccharides are called glycosidic bonds; in proteins the link between amino acids are calledpeptide bonds, in nucleic acids the link between nucleotides are called phospoester bonds. All of theseare created via dehydration

Page 69 Know that: To disconnect a monomer from a polymer; to remove it off the polymer chainrequires the opposite to dehydration ; a reaction called a hydrolysis reaction. In this reaction water isadded across a bond restoring the functional groups to the molecules and breaking the covalent bondthat links one monemer to a second monomer. When you eat a steak for dinner you are eating protein amacromolecule; apolymer. When that protein reaches your stomach enzymes like pepsin begin to“hydrolyze” or chemically digest that protein by adding water across the bonds that link amino acidstogether in the protein. After hydrolysis the only thing that remains are the individual amino acidmonomers the polymer is completely disassembled.

Know that is the sequence of monomers that creates macromolecular diversity. Proteins are only builtfrom 20 different monomers but occurring in infinite distinct sequences.

Carbohydrates:

Know/Learn all that follows about Carbohydrates:


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Page 69 Know that Carbohydrates consist of sugars and polymers of sugars. The termCarbohydrates means hydrates of carbon indicating that Carbohydrates are combinations of water andcarbon. Also in chemistry Carbohydrates are often called polyhydroxy aldehydes and ketones whichindicates that sugars the building blocks of Carbohydrate polymers structurally have many Hydroxylgroups and also have atleast one aldehyde group (a carbonyl at the chain terminus) or atleast one

ketone group (a carbonyl within the chain)

There are three classifications of Carbohydrates

Page 70

a) Monosaccharides: or simple Sugars (CH 2O)n ………Examples include:

Glucose C6H12O6 …… glucose is main fue l for all cells

Galactose C6H12O6 …> > > > > > > > > > > > > > > > > > > > > > …& lt; span> is a part of lactose can be usedas fuel

Fructose C6H12O6 …> > > > > > > > > > > > > > > > > > > > > > …& lt; span> is used to make sucrose it also isvery sweet and can be used as fuel

Ribose C5H10O4 …> > > > > > > > > > > > > > > > > > > > > > …& lt; span> is used to make RNA and ATP the

energy molecule …. also comes as deoxyribose which is used to make DNA.

Other terms to know:

Triose : 3 carbon sugar, example: glyceraldehyde

Tetrose : 4 carbon sugar, example: Threose, Erythrose

Pentose : 5 carbon sugar, example: ribose, ribulose

Hexose : 6 carbon sugar example: galactose, glucose, fructose

Aldose : sugar with aldehyde group, Example: glucose, galactose

Ketose : sugar with ketone group, Example: fructose, ribulose, dihydroxyacetone

Page 71 figure 5.5


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b) Disaccharides: 2 monosaccharides linked together via a dehydration reaction forming glycosidic bondsbetween them. Examples include:

Sucrose …… is made o f glucose and fructose linked via alpha 1-2 glycosidic bond. Aka table sugar. Sweettaste. Plants transport sugar from leaves to roots as sucrose.

Lactose …… is made of galactose and glucose linked via a beta 1-4 glycosidic bond. Known as milk sugar.Many peolple who are lactose intolerant can not digest the beta glycosidic bond between the galactoseand glucose sugars. Does not taste very sweet

Maltose …… is made of glucose and glucose linked via an alpha 1-4 glycosidic bond. Aka grain or maltsugar. Found in wheat or barley grains used to make “Malt” liquor and beer..

Page 71-74

c) Polysaccharides: many monosaccharides linked together via a dehydration

reaction forming glycosidic bonds between them. Examples include:

Cellulose : Plants use cellulose in their cell walls for support and stability. Cellulose is a simple moleculeconsisting of, simple linear chains of glucose monomers held via beta glycosidic linkages; it isundigestable in many organisms. Some organisms carry bacteria or protists in gut that allows digestionof cellulose because these organisms make cellulase the enzyme that can digest cellulose. Humans lackenzymes like cellulase and also lack the microorganisms that make cellulase and hence can not digestcellulose Cellulose represents a structural polysaccharide . It is NOT used for fuel or energy by theorganism that synthesizes it but rather it uses it as a structural support for cell walls. Microfibers arecreated from intertwined cellulose chains which are straight and never branched and make strong

building materials. paper and cotton are strengthened by cellulose fibrils.

Amylose- simple form of starch, simple linear chains of glucose monomers held via alpha glycosidiclinkages. Stored in plastids, used as a stored form of energy. Amylose representsa storage polysaccharide . It is used for fuel or energy by the organism that synthesizes it. Plants storesugar for later use as amylose or amylopectin. Animals can eat amylose and amylopectin and digest thealpha glycosidic bonds releasing glucose for use as fuel


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Amyolpectin - complex branch/chained form of starch found only in plants. Uses alpha glycosidic links ofmonomers and alpha 1-6 links. Stored in plastids, used as a stored form of energy.Amylopectin represents a storage polysaccharide . It is used for fuel or energy by the organism thatsynthesizes it.

Chitin - found in fungi cell walls ….uses amino sugars such as glucosamine. Glucosamine monemers arelinked to one another via 1-4 beta glycosidic bond Also used for sutures and also used as supportmolecule in an insects exoskeleton/outer skin. Chitin represents a structural polysaccharide . It is NOTused for fuel or energy by the organism that synthesizes it.

Glycogen, Stored in liver and muscle; found only in animals, used as a stored form of energy. Highlybtanched with alpha 1-4 and alpha 1-6 glycosidic links. Glycogen represents a storage polysaccharide . Itis used for fuel or energy by the organism that synthesize it. Animals store sugar for later use asglycogen

Lipids

Page 74

Know the following

Know that lipids all share two important traits: 1) all lipids are nonpolar, 2) all lipids are hydrophobic,(they all mix poorly or not at all with water). They are mostly hydrocarbons but may have some polarbonds with oxygen..

Examples of Lipids include;

Fat or Adipose- Triglycerides

Oils or Fatty acids- Long hydrocarbon with carboxyl group, ex. Palm Oil; Coconut Oil

Waxes- Bees Wax, Car Wax

Pigments- sudan IV, chromolipids, lipofuscins…. found in liver c ells

Anionic detergents, Soaps


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Phospholipids- membrane structures

Steroids: Cholesterol, Estrogen/Estradiol Testosterone

A. Know that fats are constructed from a glycerol molecule which is an alcohol with three hydroxylgroups and also from 3 fatty acids or oil molecules. The fatty acids are mostly hydrocarbons with 14- 20carbons in the carbon chain (similar to gasoline or petroleum) but with a carboxyl group on one end. TheC-H bonds are non polar along the main axis of each fatty acid and hence water molecules can not formhydrogen bonds with the fatty acids on the fat molecule and so water and fats separate from eachother if mixed. To chemically form a fat molecule a dehydration reaction between one of the hydroxyls(OH) on the glycerol and the OH on the carboxyl of the fatty acid occurs removing water and createsan ester bond . This must occur two more times between the other OH groups on glycerol and the other2 fatty acids. The final fat molecule has 3 fatty acids ester linked to glycerol. It is because of this thatFATs carry the chemical name “Triacylglycerol” or “Triglyceride”< /b>

Functions of Fat:

Energy Fuel in stored form

Insulation for body

Protection of organ systems from blunt trauma

Page 75

Know that the fatty acids attached to glycerol on a fat molecule may be saturated orunsaturated. Solitary Fatty acids (oils) also may be saturated or unsaturated

Know that a saturated fatty acid has no carbon carbon double bonds and has as many hydrogen atomsas possible bonded to the carbons in t he fatty acid’s hydrocarbon chain.

Know that an unsaturated fatty acid has one or more carbon carbon double bonds. i.e. C=C with onefewer hydrogen atoms on each double bonded carbon.

Most naturally produced unsaturated fatty acids fats form cis double bonds with the remaininghydrogens appearing on the same side of the double bond and creating a kink or bend in the molecule.It is this bend that keeps the fatty acid molecules from getting very close to one another and thus


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keeps unsaturated fats and fatty acids as liquids at room temperature . Saturated fatty acids don’t havethis bend or kink so they lay flat on top of each other , very tightly associated and hence saturated fatsor fatty acids will form solids at room temperature

Know that fats made from saturated fatty acids are called saturated fats. Animal fat is usuallysaturated. Lard and Butter are examples. They are solid at room temperature

Page 76

Know that:

Plant and Fish FAT is liquid at room temperature due to the fact that the fatty acids in the triglyceridesare unsaturated. Examples: olive oil, cod liver oil. Fish oils contain essential fatty acids for humans and

also are less likely to cause the cardiovascular problems like saturated and trans fatty acids cause. i.e.Omega 3 fish ol which is unsaturated at carbon 3 position, it is essential for humans and it has all cisconfigurations around its double bonds.

Hydrogenation puts hydrogen atoms back on to the unsaturated fats’ fatty acids removing the doublebonds. If a plant fat is hydrogenated it becomes solid at room temperature. Example: Peanut butter orMargarine.

In making solid margarine and peanut butter and other hydrogenated vegetable fats, the hydrogenationprocess is sometimes incomplete creating mostly solid hydrogenated fat but also someincomplete trans rather than natural cis unsaturated fats. The trans fats are difficult to metabolize andcan become incorporated easily in atheromas leading to vascular stenosis (blockage) and cardiovascularcomplications such as stroke and heart attack.

Page 76

Phospholipids

Know the following about phospholipids


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Know that cells depend on phospholipids as the basis for their membrane structure. Know that eachphospholipid consists of a diglyceride with a negatively charged phosphate group and a positivelycharged base called choline. Glycerol is the backbone of these molecules. Two rather than 3 fatty acidsare attached via ester links to glycerol. The third position on glycerol is bonded to a phosphate group viadehydration reaction and a phosphoester link/bond.

Know that the two (2) phospholipid fatty acid tails are nonpolar and hydrophobic but the phosphate andcholine base at position 3 are charged and polar and hydrophilic.

This arrangement creates a dual nature that fits perfectly with membrane function.

Know that Cell membranes consist of a bilayer of phosphoplipids. The charged phosphate and cholineparts of these phospholipids face outside or inside the cell where polar water is located. Since thephosphate and choline are charged and hydrophilic they interact naturally with this aqueous

environment. The tails of the phospholipids face the interior of the membrane and since they arehydrophobic they exclude water and other polar molecules. In essence, the core of the phospholipidbilayer is like a layer of wax in the middle of the membrane which prevents any large polar moleculesand water, to an extent, from passing in or out of the cell. These represent the basic functions of amembrane, which is to regulate passage of materials between the cell and its surrounding. Cells couldnot exist without phospholipids which creates this boundary between a cell and its environment.

Page 77

Steroids:

In class we watched a video about a pregnant man. In reality this was a pregnant woman who wastransgender. By taking steroid hormones like testosterone she was able to make her body express malesecondary characteristics such as a deeper voice, hair on the chest and face and legs, breast reduction,shoulder br oadening, hip straightening etc….

Page 77

Know that: Testosterone and other steroids like estrogen and the molecule they both are derivedfrom cholesterol , all represent lipids because these molecules are hydrophobic and nonpolar. Knowthat: Cholesterol and all its derivatives have a 4 ring system with 3 fused six membered rings fused to asingle five membered ring. Cholesterol also has a hydrocarbon tail that allows it to insert into the


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phospholipid bilayer of animal membranes. Know that: Cholesterol plays a role in animal membranefluidity and function. Its derivatives estrogen and testosterone are sex hormones that influencedevelopment of male or female characteristics. Anabolic steroids which are not natural may lead toheart disease and other health complications. High levels of cholesterol in blood may contribute toatherosclerosis and heart disease. Saturated fats and trans fats elevate cholesterol levels. The liver

usually produces cholesterol but we also obtain it from the foods we eat.

Page 77

Proteins

Every dynamic of a living being depends on proteins. All cellular activities are carried out by proteins.Every metabolic reaction is catalyzed by Enzymatic proteins . Genes code for proteins; genes contain theblueprint to build all cellular proteins. But it is the proteins themselves that do the actual work of growthdevelopment reproduction and energy utilization. Every cell builds thousands of different proteinsbased on genetic instructions; each with a unique structure and functional purpose.

Page 77 Be able to define what a protein is and how it is distinct from a polypeptide

Know that proteins are polymers built from amino acid monomers. Such polymers are referred to aspolypeptides. If the polypeptide by itself has a specific cellular function it is then referred to as a“protein” Some polypeptides need other polypeptides to join together with them for them to be “functional” proteins.

Know that all proteins use the same pool of 20 amino acids for their construction

Page 78 figure 5.15 Be able to list and or describe 3 organismal functions that proteins typically carryout: i.e. Transport proteins like Hemoglobin which carry oxygen in red blood cells. Or Defensive

proteins such as antibodies that tag foreign invaders found in bodily fluids.

Be able to draw the basic structural formula for an amino acid (bottom of page 78 left column). Be ableto identify the parts of a drawing of an amino acid with unlabled arrows pointing to its structures.


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Page 79 Know the three major classifications of amino acids (below) which are based on the “R” groupor side chains chemistry.

a) 1) Nonpolar – hydrophobic non polar side chains, Examples: Valine proline

b) 2) Polar - side chains have atoms with partial charges(dipoles) Example: Serine

c) 3) Electrically charged - side group carries a full +/- electric charge Example: Aspartate(-) or Lysine(+)

Page 80

Peptide Bonds: Forming polypeptides/proteins

Be able to describe the chemical process required to join/link amino acids together (figure5.17). A dehydration reaction occurring between the Amino end of one amino acid and the OH on thecarboxyl end of a second amino acid produces a peptide bond with water as a byproduct. Peptide bondsare really amide links which all have a carbonyl covalently linked to an amine group (R-H 2N-C=O).

When many peptide bonds are formed between 10 or more amino acids we producea polypeptide . Every polypeptide has an amino terminus and a carboxy terminus at opposite ends.Polypeptides can be as short as 10 and as long as 1000 amino acids chained together. The portions ofthe linked amino acid chain that includes the amino group; the alpha carbon and the carboxyl groupsbut NOT THE R OR SIDE CHAIN is called the polypeptide backbone (see page 80 figure 5.17). Thebackbone is very important to forming the secondary level of protein structure via hydrogenbonding between atoms in the backbone (see page 82 right hand column figure 5.20)

Page 80

Levels of protein structure


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A proteins shape/structure determines its functions. Chains of polypeptides which are linear sequencesof amino acids must fold into globular or fibrous 3 dimensional proteins of very specificshapes/structures that fit the functions they must perform.

Know all the details of each of the levels of protein structure which follow below:

Primary

Page 80-82

Every polypeptide/protein has its own unique sequence of amino acids. Frederick Sanger was the firstscientist to figure out the exact amino acid sequence of insulin.

The alpha chain of insulin’s sequence based on Sanger’s work:

H2N-Gly-ile-Val-Glu-Gln_Cys-Cys-Ala_Ser-Val-Cys-Ser-Leu-Tyr-Gln_Leu-Asn-Tyr-Cys-Asn-COOH

We say that the above represents the Primary Structure of insulin; its exact amino acid sequence; itshows which amino acid is 1 st 2nd 3 rd 4 th etc… in the specific sequence that represents insulin and onlyinsulin. No other protein in the world has this exact sequence of amino acids.

In 1958 Sanger won the Nobel Prize in Chemistry for his work.

Know that the primary level of protein structure can be critical to normal cell function. Even switchingone amino acid in the sequence of a protein can have grave consequences. For example in sickle cell


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disease (Page 84 figure 5.21) switching glutamate which is the 6 th amino acid in the sequence of the betaglobin protein to valine results in causing the final protein (hemoglobin) to stick to itself forming stiffrod like fibers in the red blood cells that stretch the cell making it bend into a sickled shape andsometimes causing the red blood cells to burst.

Secondary

Page 82

To reach the secondary level of protein structure, the atoms in the amino acid chain that include theamino group; the alpha carbon and the carboxyl groups but NOT THE R OR SIDE CHAIN (the

polypeptide backbone ) (see page 80 figure 5.17) form hydrogen bonds between other atoms inthe same backbone (see page 82 right hand column figure 5.20) These are intra molecular weakbond associations. Typically this results in two main structural forms:

a) 1) alpha helices

b) 2) beta pleated sheets

Polypeptide chains are variable in their numbers of regions that are alpha helices versus non-helical orsheeted regions. Collagen’s polypeptides are 100% alpha helix with no beta sheets. Transerythrin (page83 top illustration) has only one small stretch with a helix and two major sections of beta sheets.

Tertiary

Page 83

In tertiary structure polypeptides fold into a unique 3 dimensional shape


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To reach the tertiary level of protein structure the polypeptide in its primary forms and secondarystructural regions must interact with one another via amino acid side group interactions . An amino acidon the left side of the polypeptide chain with a positively charged R group/side chain may interact withan amino acid located further down on the right side of the polypeptide chain with a negativelycharged R group/side chain (page 83 bottom left illustration). This type of intra molecular interaction is

termed an 1) “ionic” interaction. The other three possible side chain interactions are 2) disulfide bonds -a covalent bond created between thiol groups on opposing amino acid side chains; 3) Polar/dipole-dipole interactions such as hydrogen bonds; 4) hydrophobic interactions between non-polar sidechains- these interactions usually occur in the interior (core) of a protein away from water or the polarenvironment of the cells cytoplasm. These interactions are weak bonds such as van der Waals forces akaLondon Dispersion forces.

Quaternary

Page 83

To reach the Quaternary level of protein structure requires two or more polypeptides interacting toform a functional protein. Each polypeptide by itself is non functional but when joined together in aspecific conformation form a functional whole. Examples include Hemoglobin which consist of fourpolypeptides two alpha chains and two beta chains that when put together in the presence of ironFe creates a functional protein that can carry oxygen. Collagen is perhaps the second best knownexample of quaternary protein structure. 3 chains , each completely an alpha helix intertwine to formthis important protein which is found as the girders of connective tissue of skin, bone, tendons, andligaments. The forces that hold the polypeptides to each other are the same as seen in tertiarystructure; 1) ionic 2) disulfide bonds ; 3) Polar/dipole-dipole interactions such as hydrogenbonds; 4) hydrophobic interactions between non-polar side chains

Page 84

Denaturation

Proteins only function when they are folded into their correct shape. If we heat a protein or expose itto high or low pH we will disrupt the hydrogen bonds and other polar and ionic interactions and van derWaals forces that hold the protein its unique three dimensional shape. The H+ and OH- cations and


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anions found in acidic solutions and basic/alkaline solutions strongly disrupt the ionic interactionsbetween +/- charged side chains that hold proteins together in their proper shape.

Placing a protein in acid will cause it to unfold/denature exposing its hydrophobic core and making itseparate out of solution as a precipitant. If you place a raw egg in lemon juice the proteins will denature

and precipitate out as a solid precipitant. This is the same principle as oil separating from water. The nonpolar (oil like) side chains are exposed in the unfolded/denatured protein. When they contact the polaraqueous solution it causes them to separate and cluster together away from the water as a solid mass ofprecipitant.

Page 85 Know that in cells proteins often require “chaperones” to fold correctly in to the proper shape(see figure 5.23)

Page 86 know that X-Ray diffraction is a tool used by chemist to figure out the specific shape of a foldedprotein

Nucleic acids

Page 87

Know that DNA and RNA are the major nucleic acids found in cells

Know that DNA a nucleic acid is found in structures called chromosomes in association withproteins. Know that each chromosome consists of a linear or circular strand of DNA which is in turncomposed of chains of building blocks called nucleotides . Know that there are 4 nucleotides used inDNA described by the letters A,C G and T .


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Know that each nucleotide consists of a pentose sugar ( 5 carbon sugar); a phosphate group; anda nitrogenous base. The sugars are either deoxyribose which is missing an oxygen atom on its secondcarbon, or ribose which has a OH hydroxyl on its second carbon. The basesare adenine,guanine cytosine and thymine in DNA or adenine, guanine cytosine and uracil in RNA.

Know that Adenine and Guanine are Purines —two ringed structures (PuGA)

Know that Cytosine Uracil and Thymine are Pyrimidines- one ring structures (PyCUT)

Linking these nucleotides together in variable sequences creates long chains of nucleotides or akanucleic acids such as a DNA/RNA chains . To form DNA requires that 2 chains of nucleotides beinterwoven as a double helix.

When interwoven the two DNA chains pair A’s with T’s and G’s with C’s

Hence if we know one chains sequence we can infer the second chains sequence.

i.e. if one chain is 5’G CCCCATTGCTTA3’ then the second chain must be

……………………..3’CGGGGTAACGAAT5’& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp;amp; amp; amp; amp; amp; amp; lt; /p>

note: the chains run in anti- parallel/opposite directions

When an A from one chain pairs with a T from a second chain it does so by hydrogen bonding

Very long chains of connected nucleotides create chromosomes. Know that along the length of achromosome’s long chains of nucleotides ( DNA strands ) are small units called genes. Each gene codesor contains instructions or the blueprint on how to build a specific protein. A chromosome may be 1-200million nucleotides long, but each gene is only about 10,000 nucleotides long. So a chromosome mayhave from 100-10,000 genes each coding for a specific protein. When an organism grows and developsfrom a single fertilized egg it is the creation and actions of these thousands of proteins coded for by the


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genes that actually carry out the building events and maintenance activities of the cell that will makethat single cell become thousands of cells and that will orchestrate the formation of the various bodilystructures. The 4 nucleotides of DNA when chained in sequences create words or instructions for thecell on how to build these proteins. Like an alphabet of only four letters words like ACCGGTTGCCCATGwhich don’t mean much to us, such words have very specific meanings to a cell engaged in p rotein

synthesis, just as words created from our 26 letter alphabet have specific meanings for us.

..

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Exam 1 MAIN Study Guide

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