3 Bio Chemistry

8/7/2019 3 Bio Chemistry

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CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE

1. An element is a substance that can’t be broken down into other substances by chemical reactions.

A compound is a substance w/ two or more different elements.

2. ESSENTIAL ELEMENTS OF LIFE : 25 out of 92 natural elements are essential to life.Four elements that make up 96% of living matter: C (carbon), H (hydrogen), N (nitrogen), O (oxygen).

3. Trace elements: elements required by an organism only in small quantities. Ex: Fe, I (iodine) in

vertebrates produced by thyroid. Iodine deficiency = goiter

4. Atoms: Have subatomic particles, and different # of electrons and protons.

5.Helium has an atomic mass of 4 daltons, atomic number of 2

a. Neutron: electrically neutral. Proton: positive charge. Both are found in the nucleus, and are

about the same mass. Have masses of 1 Dalton (atomic mass unit /

amu).

b. Atomic #: Number of protons in an element. Also tells

number of electrons in an electrically neutral atom. (Ex: 2He says that helium has 2 protons in its

nucleus.)

Mass number: #protons + #neutrons in nucleus of an atom. It is an approximation of the total mass

of an atom, which is the atomic mass (since protons and neutrons have mass of close to 1 dalton).

6. # of neutrons in an atom = Mass number – atomic number

7. Isotopes: Isotopic forms of an element have the same # of atoms (cuz they’re the same element). But,

they have different number of neutrons, therefore different atomic masses. (Ex: Carbon-12 has 6

neutrons and mass number of 12. Takes up 99% of carbon in nature. The rest of 1% is Carbon-13 and

has 7 neutrons. There’s also Carbon-14 which has 8 neutrons. They all have 6 protons).

8. Radioactive Isotopes: Not stable, nucleus decays spontaneously and releases particles and energy.

APPLICATIONS IN BIOLOGY ? Using measurement of radioactivity in fossils to date stuff. Can also

be used as tracers to follow atoms through chemical processes of an organism. Cells use radioactive

atoms just like nonradioactive isotopes of an element, but radioactive isotopes are easier to detect.

Also used as diagnostic tools in medicine, PET scans that monitor chemical processes (lie cancerous

growth).

9. Energy: Capacity to cause change by doing work . Potential energy: energy matter has because of its

location or structure. Matter wants to move to the lowest state of potential energy (rock goes

downhill). Electrons have potential energy due to their arrangement in relation w/ the nucleus.

Negative charged electrons are attracted to positively charged nucleus. The first electron shell is



closest to the nucleus and is under the influence of the nucleus’s pull more so it has less potential

energy.

10. CHEMICAL BONDS : attractions between atoms.

a. Covalent bond: Sharing of a pair of valence electrons. When two hydrogens come close enough for their

1s orbitals to overlap, they share electrons. 2 or more atoms held by covalent bonds are called molecules. The

more electronegative an atom, the more strongly it pulls shared electrons towards itself. In Nonpolarcovalent bonds, atoms are equally electronegative. In Polar covalent bonds, one atom is more

electronegative than another and the bond isn’t shared equally. Ex: H2O. O is a lot more electronegative.

b. Ionic Bonds: Attraction between oppositely charged ions. Two atoms are so unequal in their attraction for

valence electrons that the more electronegative atom takes the electron completely away from its partner.

ELECTRON TRANSFER takes place. Cation is positive charge (less electrons). Anion is negative (gain

electrons). Ionic compounds form salts. Yeahhh.

11. Strong covalent bonds link atoms to form a cell’s molecules. Weaker bonds also contribute to

emergent properties of life. For example, big biological molecules (proteins! Alpha helix + betasheets held by h-bonds) are held together in a functional form by weak bonds. When two molecules

make contact, they temporarily stick by weak bonds. They can come together, respond, then separate.

12. HYDROGEN BONDS: Form when hydrogen atom covalently bonded to an electronegative atom is

attracted to another electronegative atom… Electronegative partners are either Oxygen or Nitrogen.

Ex: H2O and NH3. Water molecules do hydrogen bonding!

VAN der WAALS interactions: Result of interactions of e-. Molecules w/ nonpolar covalent bonds have

+ and – regions. Forces are very weak. Occur when atoms and molecules are really close together. But

they can help gecko lizards walk up walls! There are many Van der Waals interaction between hair tip

molecules and molecules of wall’s surface that allow gecko’s to climb up walls.

13. MOLECULAR SHAPE AND FUNCTION: The shape of a molecule mirrors its function. A

molecule’s shape is determined by the position of the atom’s orbitals. When atoms form covalent

bonds, orbitals in its valence shells rearrange. Molecular shape determines how biological molecules

recognize and resond to one another. Molecules w/ complementary shapes form weak bonds and

bond w/ eachother.

14. Chemical equilibriumヽ(`д´)ﾉ is the point where reactions offset one another exactly. Reactions are

still going, but there is no net effect on the concentration of the reactants and products. (NOT thatreactants and products are equal concentration.) It means their concentrations have a stabilized ratio.

So, the forward and reverse reaction occur at the same rate and the relative concentrations of products

and reactants stop changing.



CHAPTER 3: WATER AND THE FITNESS OF THE ENVIRONMENT

15. Water is polar because oxygen is more electronegative than hydrogen, and the

electrons are pulled in towards oxygen than to the hydrogens. The slightly +

hydrogen is attracted to a slightly – oxygen of another H2O molecule. The two

molecules are held by a hydrogen bond. One hydrogen can bond to 4 neighboring

molecules (H+O-, H+O-, O-2H+)

16. Emergent properties of water that result from hydrogen bonding: cohesion, ability to

moderate temperature, expansion upon freezing, and versatility as a solvent .

17. Cohesion: Sticking of water molecules together due to h-bonding. Cohesion lets water and dissolved

nutrients travel against gravity in plants. Water from roots reach leaves through water-conducting

cells. Evaporation from leaves pulls water upward from the roots through watered conducting cells.

Adhesion: Clinging of one substance to another. Adhesion of water to cell walls by h-bonds help

counter gravity’s pull. Cohesion is related to surface tension, a measure of how hard it is to stretch or

break the surface of a liquid.

18. HEAT AND TEMPERATURE

Water moderates air temp by absorbing heat from air that is warmer and releasing the heat to cooler air. Water

is a heat bank cuz it absorbs or leases amounts of heat without changing its own temperature.

Heat: Form of energy. Measure matter’s total kinetics energy due to moving molecules. Depends on volume.

Temperature: measure of heat intensity. Average kinetic energy of molecules, doesn’t matter what volume

is.

Ex: A pot of coffee has a higher temperature than a swimming pool, but swimming pool has more heat cuz it

has bigger volume.

19. Coastal areas have milder climates than adjacent inland areas because they have large bodies of

water relatively high specific heat ! Water will change its temperature less when it absorbs or loses

an amount of heat. H2O resists changing temp, and when it does change temp, it loses a relatively

large quantity of heat for each degree of change. Oceans absorb heat during the summer. During

winters when water cools, it releases heat. Also, high specific heat of H2O stabilizes ocean

temperatures because it’s hard for H2O to change temperature and creates a favorable environment

for marine life.

Water striders can walk on the surface of a pond because of water’s high surface tension, created by the

cohesion formed by h-bonds. Water has a high heat of vaporization which means a lot of heat is needed to

break the hydrogen bonds. Evaporative cooling occurs when the molecules w/ most kinetic energy leaves, and

lets bodies of water stabilize. Evaporation of sweat in humans help us cool down like this.



Water is less dense as a solid than a liquid, so ice floats in liquid water . Water expands as it solidifies due to

hydrogen bonding. When its molecules are no longer moving vigorously enough to break hydrogen bonds,

water freezes. The ice forms a crystalline structure, and each molecule is h-bonded to 4 neighbors.

20. solute: substance that’s dissolved. Solvent: dissolving agenet of solution. Solution: homogeneous

mixture of 2 or more substancese.

21. hydrophobic: water fearing. Like nonpolar and nonionic substances. Lots in cell membrane.

Hydrophilic: water loving. Not all hydrophilic substances dissolve in water (they’d form a colloid

solution), and would suspend in aqueous liquid. Ex: cotton. And cellulose. So a towel does a good job

drying stuff, but doesn’t dissolve in the washing machine. This is cuz cellulose has regions of partial

positive and partial negative charges.

22. One molar solution of ethyl alcohol means 1 mol ethyl alcohol/L

THE DISSOCIATION OF WATER MOLECULES

23. Dissociation of water: 2H2O/ H3O+ (hydronium) + OH- (hydroxide)

In pure water, the concentration of eaech ion is 10^-7M @ 25ºC.

24/25. Acid: donate additional H+ to solution. Increases hydrogen ion concentration of solution.

HCl H+ + Cl- ….Strong acid cuz it’s not reveresable. In general for acidic solutions, [H+] > [OH-].

Base: reduses H+ concentration. Accepts H+ ions from the solution. NH3 + H+/ NH4+

Other bases indirectly reduce H+ concentration by dissociating to form hydroxide ions which combines

w/ hydrogen ions and form water. Sodium hydroxide: NaOH Na+ + OH-. The base reduces H+

solution. [OH+] > [H+].

Weak acids reversibly release and accept back H+. H2Co3/ HCO3- + H+.

26. Buffers: pH of blood is slightly basic at 7.4 Bufers minimize changes of [H+] and [OH+]. Buffers accept

hydrogene ions from solution when theye are in excess. They donate hydrogen ions to solution when

hydrogen has been depleted.

CARBONIC ACID:

If H+ concentration falls (and pH rises), rxn goes to the right and more Carbonic acid dissociates, returning

H+. When H+ rises (pH drops, more acidic) reaction proceeds to left, with HCO3- removing H+ ions from

solution and forming H2Co3.



CHAPTER 4: THE IMPORTANCE OF CARBON

1. Carbon’s electron configuration makes it able to form large, complex and diverse organic molecules.

Carbon has a tetravalence structure, and can form 4 single covalent bonds. Carbon’s e- config makes

it able to covalently bond w/ many elements. (most common are Oxygen, hydrogen, and nitrogen)

2. Carbon chains form skeletons of many organic molecules. Skeletons can be different lengths, straight,

branchd, or in rings. Some have doubl bonds in different locations. VARIATION IN CARBON

SKELETONS is an important source of molecular complexity and diversity that characterize living

matter! Also, other elements can be bonded to carbon skeletons.

3. HYDROCARBONS: organic molecules w/ only carbon and hydrogen. C-H-----… They are

hydrophobic because the bonds are nonpolar carbon to hydrogen links. Also, hydrocarbons undergo

rxns and release large amounts of energy. Example: gasoline that fuels a a car has hydrocarbons,

hydrocarbons of tails of fat molecules is stored fuel for animals, petroleum, etc.

4. ISOMERS: compounds w/ same number of atoms of the same lements, but different structures and

properties.a. Structural isomer: differ in covalent arrangemnt of atoms. Also can differ in location of

double bonds.

b. Geometric isomer: Differ in arrangement about a double bond. (cis and trans)

c. Enantiomers: Mirror images of each other.

CHEMICAL GROUPS

5. Chemical functional groups:

a. Hydroxyl –OH

Compound: alcohol Properties: Polar, due to more e- Oxygen. Can form

h-bonds w/ H2O, helps dissolvee organic compounds like sugar.

b. Carbonyl C=O

Compound: Ketones if carbonyl is in the middle, Aldehyde of carbonyl is

at the end of carbon skeleton.

Properties: Ketones and aldehydes can be structural isomers w/ different properties. Found in sugars (aldoses

and ketoses).

c. CarboxylCompound: Carboxylic acid. Properties: Acidic (source of Hydrogen ions) cuz covalent bond beterween O

and H is really polar. Found in cells in ionized form w/ charge of 1-, carboxylate ion.

d. Amino –NH2

Compound: Amine. Properties: Base. Takes H+ from solution. Is ionized under cellular conditions.

e. Sulfhydryl -SH



Compound: Thiol. Properties: 2 sulfhydryl groups form Cystein bonds in proteins. Cross-linking of cysteins

in hair protein keeps curly or straight hair. When you get a perm, you break and re-form cross-linking bonds.

f. Phosphate:

Properties: Provides backbone for phospholipids

g. Methyl -CH3

Properties: Adding Methyl to DNA or molecules bound to DNA affects gene expression. Arrangement of methyl group in male and female sex hormones affects their shape and function. Hydrophobic.

6.

ATP YEAHHHH BOII It’s an important source of energy!!!

7. When 3 phosphates are present in a series (like in ATP), one phosphate splits off when reacting with

water. This reaction releases energy that can be used by the cell.

P-P-P-Adenosine -----reacts with H2O-- Pi + P-P-Adenosine + Energy

THE MOLECULES OF LIFE.

8. Polymers are long molecules with many similar or identical units linked by covalent bonds.

Monomers are those units.

9. Condensation and Hydrolysis Reactions:

CARBOHYDRATES SERVE AS FUEL AND

BUILDING MATERIAL

10. Monosaccharide: “simple sugars”. Have a formula some multiple of CH2O. Example: Glucose

C6H12O6. Trademarks of sugar: Carbonyl group, multiple hydroxyl groups. Dpending on the

carbonyl group’s location, the sugar is an aldose or a ketose. Glucose is an aldose. Fructose, an

isomer of glucose, is a ketose.

Disaccharide: 2 monosaccharides joined by a glycosidic linkage (covalent bond formed between 2

monosaccharides by dehydration rxn). Ex: Maltose is formed by 2 glucose.



Polysaccharide: Macromolecule. Many serve as storage material, hydrolyzed when needed to provide sugar

for cells. Others are building material that protct the cell. Ex: Starch, stored in plants, is a polymer of glucose.

11. Glycosidic linkages are formed by a dehydration reaction.

12. Starch: All glucose are in alpha formation. Cellulose: Glucose monomers are all in B configuration,

so every other glucose is upside down w/ respect to its neighbor. The differing glycosidic linkages

give the molecules distinct 2D shapes. Starch is helical and cellulose is straight. Cellulose is never

branched, and hydroxyl groups on its glucose monomers are free to h-bond w/ hydroxyls of other

cellulose parallel to it. In cell walls, parallel cellulose molecules hold in units of microfibrils. This

provides strong building material.

Humans can’t digest cellulose cuz they don’t have the enzymes to do so.But cellulose can abrade walls of

digestion tract and stimulate secretion of mucus which aids in smooth passage of food through the tract.

MAKES YOU POOP!

13. Cows have cellulose-digesting prokaryotes. Prokaryotes hydrolyze cellulose and convert the glucose

to other nutrients that nourish the cow. Termites have these prokaryotes too.

LIPIDS ARE DIVERSE!

14. Lipids: All mix poorly with water. Hydrophobic, mainly consist of hydrocarbon regions.

Fat: (aka triaceylglycerol) Not a polymer butt is a large molecule. Constructed of: Glycerol and fatty acids by

dehydration synthesis. Glycerol has 3 carbons, each w/ a hydroxyl group. Fatty acid: Long carbon skeleton

with a carboxyl group at one end.

Function of fat : Storage. Also cushions vital organs like kidneys, and insulation. Phospholipids also found in

cell membranes. Stereoids make up hormones. Many steroids are produced from cholesterol. Cholesterol also

found in cell membranes.

15. Ester linkage: Bond between a hydroxyl group and a carboxyl group. Happens when fatty acid

molecules join to glycerol.

16. Saturated fat: No double bonds, thus saturated with hydrogen.

Unsaturated: Has one or more double bonds, formed by removing h-atoms from the carbon skeleton. Fatty

acid will have a kink wherever a cis double bond occurs. Kinks near cis double bonds prevent molecules from

packing togther closely, thus they remain liquid at room temp.

17. Trans Fat: IS BAD. “hydrogenated”, it is unsaturated fat (“cis fats”) synthetically converted tosaturated fat by adding a hydrogen.

18. Principal energy storages: Starch in plants. Fats/adipose in animals.

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3 Bio Chemistry