Chapter 2 The Molecules of Cells

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1 Chemistry is the science dealing with the properties & the transformations (chemical reactions) of all forms of matter Matter is any substance: solid, liquid, gas, plasma All matter is composed of elements a substance that cannot be broken down into substances with different properties; composed of only one type of atom Atom Smallest unit of matter that cannot be divided by chemical means Structure of an atom Composed of three subatomic (SA) particles Protons positively charged SA particles; mass of 1 Dalton (mass of a hydrogen atom) Neutrons zero or null charged SA particles; mass of 1 Dalton Electrons negatively charged SA particles; mass = 1/2000 of 1 Dalton (= zero for mass determination of an atom) Mass the amount of matter in something; similar to weight, but weight takes into account gravity; a person weighs 150 lbs on Earth and zero in space, but his mass remains constant

2 Protons & neutrons are located in a central mass called the nucleus Electrons move around the nucleus in energy shells and the number of electrons orbiting the nucleus is equal to the number of protons in the atom Elements are arranged on the periodic table by increasing atomic number (# of protons) the number of protons defines the atom

3 Atomic weight (mass) = number of protons & neutrons in the nucleus of the atom Given that the atomic mass of carbon is 12 and the atomic number is 6, how many neutrons are in a carbon atom s nucleus? ow many electrons are orbiting this carbon nucleus?

4 Isotopes alternative forms of an atom that differ in their number of neutrons Carbon-12 & Carbon-14 are isotopes of one another What is Carbon-14 used for? What is the atomic number for Carbon-12? Carbon-14? ow many electrons are orbiting each one? If Carbon-12 has a mass of 12 Daltons and Carbon-14 has a mass of 14 Daltons, how many neutrons are in each respective isotope? Molecules & Compounds Molecule the linking or bonding of like atoms together Compound the linking or bonding of different atoms together Is oxygen gas (O2) a molecule or compound? Is liquid water (2O) a molecule or compound? ow are atoms linked together? Why would they want to link together?

5 Why would atoms link up with one another? Most atoms are not stable by themselves due to the number of electrons that they carry Remember, electrons are located in energy shells with the following basic configuration: 1. First energy shell can contain a maximum of 2 electrons 2. All other shells can contain a maximum of 8 electrons (there are exceptions) An atom is most stable when the outer shell contains a full 8 electrons = OCTET RULE

6 Go back to the periodic table, and determine how many elements are stable in their isolated condition? So what do the roman numerals in the columns represent?

7 Given the octet rule, atoms will interact with one another to obtain a full outer shell of electrons ow will atoms interact with one another to fulfill the octet rule? Via bonding: Ionic or Covalent! Ionic bonding Atoms transfer or accept electrons from one another Look at the following diagram with regards to sodium (Na) and chloride (Cl) What must each do to fulfill the octet rule?

8 Sodium really wants to give up an electron so that its third energy shell goes away, leaving it with a full outer (second) shell Chloride really wants to accept an electron so that its third energy shell is full When sodium gives up an electron it becomes a postively charged ion called a cation When chloride accepts an electron it becomes a negatively charge ion called an anion Ion a charged atom Count up the respective protons & electrons in the both sodium & chloride before & after the movement of an electron to see the generation of the +1 charge on sodium & the 1 charge on chloride!

9 Since sodium & chloride have the same need, but go about in different ways, they will form an ionic bond in the process The resulting ionic bond is due to the attractive forces between the now positively charged sodium & the negatively charged chloride

10 The force or term that describes the degree to which an atom will take away or give up an electron is electronegativity Those elements with more electrons in their valence shell have higher electronegativity than those elements with fewer electrons in their valence shell Look at the periodic table & determine which elements have higher electronegativity

11 Covalent bonding Atoms share electrons Take these 2 chlorines. Will either of them want to just give up an electron to the other? NO! But they are perfectly willing to share them. So a single bond between 2 atoms involves the sharing of a pair of electrons, one from each atom

12 Additional representations of single covalent bonds Each bond equals an electron pair being shared; one from each atom Cl Cl Cl Cl I like to modify mine just a bit! Cl Cl

13 ow many covalent bonds can exist between 2 atoms? Let s take carbon as an example ow many electrons does carbon need to fulfill the octet rule? Where will it get the 4 electrons & how?

14 Let s introduce a great Filler atom - ydrogen ydrogen is different from the other atoms due to its single energy shell This shell can hold a maximum of 2 electrons thus hydrogen s octet rule is really a duet rule

15 Let s combine 1 carbon + 4 hydrogens & see what we get Carbon 4 single bonds develop between each of the hydrogens & carbon; each involve an electron pair

16 Let s look at some other types of bonds Chapter 2 The Molecules of Cells C C C C Double bond Triple bond Do you think that the following bond is possible? Does it obey the octet rule? C C Even though the octet rule is obeyed, this quadruple bond DOES NOT exist do to the 3D arrangement of the electrons orbiting the nucleus. The fourth electron is always out of position!

17 Different types of covalent bonds Non-polar covalent equal sharing of electrons Polar covalent unequal sharing of electrons The bond between a carbon & a hydrogen is an example of a non-polar covalent bond What does the word polar mean? Or what is polarity? Well, in a non-polar covalent bond there is no charge across the bond! Pay attention to the relative shape of the shells C Each atom retains ownership of their respective electrons ence, the protons in each nuclei null out their respective electrons No charge development between the two bonded atoms

18 ow does this differ from a polar covalent bond? Since a non-polar covalent bond does not have a charge develop between the two bonded atoms, a polar covalent bond must have a charge develop across the bond with one end being POSITIVE & the other end NEGATIVE. Let s see how this polarity develops O If the location of the letters indicates the position of the respective nuclei, what have I done to the position of each atoms electrons with respect to their nuclei? Compare this to how I drew methane (C4) in the previous slide!

19 O So, are the electrons hovering closer to the oxygen nucleus or to each of the hydrogen s nuclei? ow many protons does oxygen have in its nucleus? So, with regards to oxygen, is oxygen neutral, have more negative charges, or have more positive charges?

20 O ow does this differ from an ionic bond? All atoms retains ownership, but they just spend more time around the other atom No transfer of electrons so full charges cannot be used as a notation Partial charge notation is used instead: δ+ & δ

21 δ+ δ+ O δ δ Why does the oxygen pull on the hydrogen s electrons? Oxygen has higher electronegativity than hydrogen!

22 This interaction between two atoms via their electrons introduces us to a new term! Oxidation & Reduction Reactions or REDOX reactions Oxidation loss of electrons Reduction gain of electrons We can see this easily in ionic bonds! Both atoms go through their changes simultaneously & are thus COUPLED

23 For covalent bonds, there is no transfer of electrons, but we can still describe the bonding using REDOX reactions Oxidation the loss of a hydrogen atom Reduction the gain of a hydrogen atom O O O C C C C O Succinic acid Reduced state 2 Will be used to reduce another molecule O O O C C C C O Fumaric acid Oxidized state

24 Other types of bonds or interactions don t involve electrons ydrogen bonding occurs when a covalently bonded hydrogen is δ+ & is attracted to a δ - atom some distance away

25 Water interactions the interaction between polar compounds (water loving or hydrophilic) vs non-polar compounds (water hating or hydrophobic) What happens when you place salt (sodium chloride NaCl) in a glass of water? What happens when you place oil (a molecule with a lot of non-polar covalent carbon hydrogen bonds) in a glass of water? Thus: 1) ydrophilic molecules interact with one another 2) ydrophobic molecules interact with one another 3) ydrophilic & hydrophobic molecules repel each other

26 Water The solvent of Life Chapter 2 The Molecules of Cells Solute substance dissolved in a solvent to form a solution Solvent fluid that dissolves solutes Think about all of the substances that your body s water must dissolve on a daily basis Characteristics of water 1) Adhesion The tendency of water to hydrogen bond to other compounds 2) Cohesion The strong attraction of water to each other 3) igh eat Capacity Water can absorb a great deal of heat (energy) before a change in temperature will occur 4) igh eat of Vaporization Water requires a lot of heat (energy) to be evaporated The last two are keys to regulating temperature Chemical reactions in your body generate a lot of heat need water to regulate temperature changes associated with chemical reactions

27 Water, Acids, & Bases Chapter 2 The Molecules of Cells Water just doesn t exist as water in a solution. It can dissociate into two ions! + - ydrogen ions O- - ydroxide ions

28 Why is this important? Chapter 2 The Molecules of Cells The level of free + ions determines the overall p of a solution p deals with how acidic or basic a solution is Can acidic or basic solutions be harmful? Acidic solutions have a high concentration of free + or a low p number (0 6.99) Basic solutions have a low concentration of free + or a high p number ( ). You can also think of this as having a high concentration of O- Pure water is neutral = O- null out +; p is 7

29 Changing pure water from a neutral solution to an acidic or basic one

30 ow does your body maintain a constant p? Buffers Compounds that are used to maintain proper p by binding with free + or O- 2 CO CO 3 - Carbonic acid hydrogen ion bicarbonate ion When + or O- are added to your blood the following reactions occur to maintain your normal blood p + + CO 3-2 CO 3 2 CO 3 + O - 2 O + CO 3 -

31 p Scale & some common solutions Chapter 2 The Molecules of Cells

32 Organic molecules Any molecule or compound that contains carbon Inorganic molecules Any molecule or compound that does not contain carbon Molecules of life 1) Carbohydrates 2) Lipids 3) Nucleic acids 4) Proteins All of these molecules exist as small, single units generally called monomers, which can then be combined to form larger units called polymers Molecule Monomer Polymer Carbohydrates Monosaccharide Polysaccharide or Carbohydrate Protein Amino Acid Polypeptide or Protein Nucleic Acid Nucleotide Nucleic Acid

33 Common characteristics between biomolecules (biologically important molecules) Functional groups parts of a molecule that impart a specific characteristic to the molecule R - N2 amino group R - O hydroxyl group R COO carboxyl or carboxylic acid group R = the rest of the molecule

34 See how changing the functional group changes the characteristics of a molecule! O C C C C O Ethane (natural gas) Acetic acid (vinegar) C C O Ethanol C C N Aminoethane (rotting food)

35 Common characteristics between biomolecules (biologically important molecules) ow are polymers formed from monomers? ow are monomers formed from a polymer? Dehydration synthesis Removal of a water molecule between two reacting molecules forming a new covalent bond in the process ydrolysis Addition of a water molecule to a polymer to break a bond within a polymer to form the monomers

36 Carbohydrates Functions 1. Quick energy source 2. Structural support Characteristics Chapter 2 The Molecules of Cells 1. Only contains Carbon, ydrogen, and Oxygen 2. ydrogen and Oxygen exist in a 2:1 ratio Given that glucose has a chemical formula of C 6 12 O 6, what would be the chemical formula for maltose which is two glucoses linked (bonded) together? C O 11 Remember, you have to remove a water molecule whenever you join two molecules together!

37 Types of carbohydrates Chapter 2 The Molecules of Cells Do you see anything similar or different between these three polysaccharides? They are all made of glucose But they are linked together differently Do you think that these different linkages will change their characteristics or function?

38 Types of carbohydrates Glucose basic monomer that we love Chapter 2 The Molecules of Cells Starch polymer of glucose found in plants; storable form Glycogen polymer of glucose found in animals; storable form Cellulose polymer of glucose found in plants; forms the cell wall in plants; indigestible by us As you can see, all made up of glucose, but with different functions or found in different organisms Do you happen to know what kind of molecule makes up the exoskeleton of a crab or lobster? Carbohydrate

39 Lipids Functions 1. Long term energy storage 2. Insulation 3. Protective cushion 4. Forms the cell membrane phospholipids/cholesterol important 5. ormones Characteristics 1. They do not dissolve in water, but some can interact with water 2. NO simple monomer pattern, like carbohydrates, nucleic acids, or proteins

40 Types of lipids 1. Fats & Oils 2. Phospholipids 3. Steroids Fats & Oils Chapter 2 The Molecules of Cells As you can see the completed TRIGLYCERIDE is made up of predominantly non-polar covalent (hydrophobic) carbon-hydrogen bonds

41 Do you see anything different between the fatty acid tails in this phospholipid? Saturated fats no double bonds exist in the fatty acid tails Unsaturated fats have at least one (mono) carbon carbon double bond in any of their fatty acid tails What does this do to the shape of the molecule? ow does this contribute to the liquid nature of an oil & the solid nature of butter?

42 What makes a phospholipid different from a triglyceride? It s missing a fatty acid tail It has a phosphate group to replace this missing tail Based on the elements making up this phosphate group, would you say that this phosphate group is hydrophobic or hydrophilic? Are the fatty acid tails hydrophobic or hydrophilic? A phospholipid can interact with both hydrophobic & hydrophilic molecules This is the key molecule that makes up the plasma membrane which surrounds a cell just like your skin surrounds, covers, & protects you

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44 Steroids are lipids which possess a ringed structure When looking at cholesterol or testosterone below, what would tell you that they fall into the lipid category? Cholesterol is a major component of the cell s plasma membrane (structural function), but it is also the precursor for the key hormones testosterone & estrogen

45 Nucleic acids Functions Chapter 2 The Molecules of Cells 1. Make up the genes which store all of the information about an organism both structural & behavioral 2. Convert the information stored on your genes that contribute to the growth & development of the organism both structural & behavioral 3. Energy currency of the cell Characteristics 1. The monomer form is referred to as a nucleotide, which is formed from the following parts: A. 1 five carbon sugar either deoxyribose or ribose B. 1 phosphate group C. 1 of 5 different nitrogenous bases adenine, guanine, thymine, cytosine, uracil 2. Individual nucleotides are linked together via dehydration synthesis to form larger polymers

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49 Types of nucleic acids DNA deoxyribonucleic acid 1. Deoxyribose 2. Phosphate group 3. Adenine, guanine, thymine, cytosine 4. Double-stranded structure, strands are intertwined in a helical form (double helix) RNA ribonucleic acid 1. Ribose 2. Phosphate group 3. Adenine, guanine, uracil, cytosine 4. Single-stranded linear structure

50 ATP adenosine triphosphate Ribose Chapter 2 The Molecules of Cells 3 phosphate groups - the terminal or last phosphate is held on by a high energy but weak bond when this bond is broken energy is released Adenine

51 Proteins Functions Chapter 2 The Molecules of Cells 1. Structural bones, muscles, collagen 2. Enzymes proteins which speed up chemical reactions necessary for life 3. Transportation hemoglobin within your red blood cells transports oxygen to all parts of your body 4. Protection antibodies enable you to fight off infections 5. Identification cells have protein markers to identify those cells as yours MC (major histocompatibility) proteins 6. A LOT MORE!

52 Characteristics Chapter 2 The Molecules of Cells The monomer form is referred to as an amino acid, which has the following structure A. A central or alpha carbon which is connected to the following: B. An amino group C. A carboxylic acid group D. A hydrogen E. A R-group

53 Characteristics Chapter 2 The Molecules of Cells 2. There are 20 different amino acids based on their R groups 3. R groups vary in length & in their functional groups; some are hydrophobic, others hydriohilic, some positively charged & others negatively charged 4. The R group establish the distinctive properties of each amino acid & the properties of the resulting polypeptide

54 Proteins are folded into complex 3 dimensional structures

55 Proteins are folded into complex 3 dimensional structures

56 Proteins are folded into complex 3 dimensional structures

57 Proteins are folded into complex 3 dimensional structures

58 Proteins are folded into complex 3 dimensional structures Levels of protein organization 1. Primary structure linear sequence of amino acids joined by peptide bonds constructed via dehydration synthesis 2. Secondary structure hydrogen bonding between amino acids in the polypeptide causes the formation of the alpha helix & beta pleated sheet 3. Tertiary structure Interaction between R groups can fold the polypeptide into elaborate 3 dimensional shapes 4. Quaternary structure A combination of 2 or more of the above structures Why are these structures & shapes important for a protein? Think back to the structure of the polysaccharides that are all made from only glucose! STRUCTURE = FUNCTION!

59 PRACTICE QUESTIONS 1. Define the terms atomic number & atomic mass 2. Where would you find protons & neutrons within an atom? 3. What is an isotope? 4. What is the OCTET rule? 5. What is the difference between an ionic bond & a covalent bond? 6. ow can a covalent bond be polar or non-polar? 7. Define oxidation & reduction 8. What are the four charcteristics of water? 9. What are buffers? 10. ow are monomers linked together to form polymers? 11. What is the differences between a saturated fat & unsaturated fat? 12. What are the parts of a nucleotide?

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