AP Biology ch. 2 & 3

Describe what affect a change (denaturation) in any of the levels of structure would have on a protein?

-Involves disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process -disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape. -occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted -in the tertiary structure there are four types of bonding interactions between "side chains" including: hydrogen bonding, disulfide bonds, and non-polar hydrophobic interactions, which could be disrupted

amino

-NH2 -N attached to 2 H -compounds with NH2 = amines (amino acids) -basic -polar -positive (NH2 and C=O - polar and neutral)

hydroxyl

-OH- -organic compounds with OH = alcohols -names typically end in -ol (ethanol) -polar -hydrophilic

phosphate

-PO4 -P bonded to 4 O -acids -highly reactive -transfers energy between organic molecules (ATP, ADP)

dehydration synthesis

-a chemical reaction in which 2 molecules become covalently bonded to each other with the removal of a water molecule -one monomer donates OH- -another monomer donates H+ -together forming H2O

saturated fatty acid

-a fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds -maximizing the number of hydrogen atoms attached to the carbon skeleton -long, straight chains -most animal fats -solid at room temperature -contributes to cardio vascular disease

unsaturated fatty acid

-a fatty acid that has one or more double bonds between carbons in the hydrocarbon tail -reducing the number of hydrogen atoms attached to the carbon skeleton -plants and fish fats -vegetable oils -liquid at room temperature

cholesterol

-a steroid that forms an essential component of animal cell membranes -acts as a precursor molecule for the synthesis of other biologically important steroids -high levels in blood may contribute to cardiovascular disease

How is ice less dense than liquid water?

-as water cools below 4˚C, it expands -by 0˚C each water molecule is hydrogen-bonded to 4 other molecules creating a crystalline lattice structure that spaces molecules apart -this spacing makes ice less dense than water, so it floats

4 major classes of macromolecules

-carbohydrates -lipids -nucleic acids -proteins

sugars

-classified by number of carbons -5C and 6C sugars form rings in solution -Carbonyl (C=O) and multiple hydroxyl groups (OH-)

What contributes to the movement of water up the vessels of a tall tree?

-cohesion -hydrogen bonding -adhesion -hydrophilic cell walls

lipids

-composed of C, H, O -long hydrocarbon chains (H-C) -do not form polymers -mix poorly, if at all, with water -long term energy storage

Parts of a nucleotide in DNA

-double stranded helix -each polynucleotide strand consists of nucleotide monomers with deoxyribose sugar and nitrogen bases: adenine (A), cytosine (C), guanine (G) and thymine (T) -capable of being replicated and determining the inherited structure of a cell's proteins

carbohydrates

-energy molecules -composed of C, H, O -function: energy, raw materials, energy storage, structural materials -ex. sugars, starches, cellulose

starch

-energy storage in plants -easy to digest

Why does water absorb or release a relatively large quantity of heat as its temperature changes?

-heat must be absorbed to break hydrogen bonds before water molecules can move faster and the temperature can rise -heat is released when hydrogen bonds form as the temperature of water drops -the high proportion of water in the environment and within organisms keeps temperature fluctuations within the permits of life

Climates tend to be moderate near large bodies of water because...

-large amount of solar heat is absorbed during the gradual rise in temperature of the water -water releases heat as it cools -high specific heat of water helps to moderate air temps -heats is absorbed and released as hydrogen bonds break or form

polysaccharides

-large polymers -starch -cellulose -glycogen -chitin

phospholipid

-lipid made of glycerol, 2 fatty acids, and a phosphate group -hydrocarbon chains act as non-polar, hydrophobic tails -the rest of the molecule acts as a polar, hydrophilic head -form bilayers that function as biological membranes -define outside vs. inside

steroids

-lipids characterized by a carbon skeleton consisting of 4 fused rings with various chemical groups attached -differences created by attaching different functional groups to rings -ex. cholesterol, sex hormones

hydrocarbons

-molecules comprised of carbon and hydrogen -non polar -not soluble in water -hydrophobic

isomers

-molecules with the same molecular formula but different structures (shapes) -different chemical properties -different biological functions

long hydrocarbon chain

-non polar -hydrophobic -concentrated energy storage -cushion organs -insulates body

functional groups

-parts of organic molecules that are involved in chemical reactions -give organic molecules distinctive properties -affect reactivity -makes hydrocarbons hydrophilic -increase solubility in water

Why does water have a high heat of vaporization?

-related to the large amount of heat needed to break the hydrogen bonds holding water molecules together -water helps moderate earth's climate as solar heat absorbed by tropical seas is dissipated during evaporation, and heat is released as moist tropical air moving poleward condenses into rain

monosaccharides

-simple one monomer sugars -glucose, fructose, galactose -major nutrients for cells

Part of a nucleotide in RNA

-single stranded -type of nucleic acid consisting of a polynucleotide made up nucleotide monomers with a ribose sugar and the nitrogenous bases: adenine (A), cytosine (C), guanine (G) and uracil (U) -functions in protein synthesis, gene regulation and as the genome of some viruses

cellulose

-structure in plants -hard to digest

specific heat

-the amount of heat absorbed or lost when 1 g of a substance changes its temperature by 1˚C -water's specific heat: 1 cal/g •˚C

cohesion

-the linking together of like molecules, often by hydrogen bonds -liquid water is unusually cohesive due to the constant forming and reforming of hydrogen bonds -helps create a more structurally organized liquid and helps to be pulled upward by plants

breaking down polymers through digestion

-use water to breakdown polymers -reverse of dehydration synthesis (hydrolysis) -cleave off one monomer at a time -H2O split into H+ and OH- -H+ and OH- attach to ends -requires enzymes -releases energy

3 lipid families

1. fats 2. phospholipids 3. steroids

In an aqueous solution the product of the [H+] and the [OH-] is at a constant ____

10^-14

What is the [H+] of a NEUTRAL aqueous solution?

10^-7 M

4 levels of protein structure

Primary Structure: Amino acids on a polypeptide (can be hundreds or even thousands of amino acids long) Secondary Structure: Refers to coiled or folded polypetides, the main types of folding are alpha helix or beta pleated sheet. Hydrogen bonds hold these structure together along the backbone of the polypeptide. Tertiary Structure: side chains of amino acids in the secondary structure interact to fold up the chain into a specialized shape. Quaternary Structure: involved the folding and join ing of two or more folded polypeptides into a very specializes shape to make a properly functioning protein

ester linkage

a bond between a hydroxyl group and a carboxyl group

ionic bond

a chemical bond resulting from the attraction between oppositely charged ions

organic molecule

a chemical molecule with a carbon backbone including hydrogen atoms

hydrolysis reaction

a chemical reaction that breaks bonds between 2 molecules by the addition to water; functions in the disassembly of proteins to monomers

glycosidic linkage

a covalent bond formed between 2 monosaccharides by a dehydration reaction

polar molecule

a molecule (such as water) which an uneven distribution of charges in different regions of the molecule

acid

a substance that increases the hydrogen ion concentration of a solution

base

a substance that reduces the hydrogen ion concentration of a solution by accepting hydrogen ions or adding hydroxide ions

covalent bond

a type of strong chemical bond in which two atoms share one or more pairs of valence electrons

hydrogen bond

a type of weak chemical bond that is formed when the slightly positive hydrogen atom of polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule or in another region of the same molecule

0-6

acid

disulfide bridges

also referred to as covalent bonds form where two cysteine monomers, which have sulfhydryl groups (-SH) on their side chains are brought close together by the folding of a protein

Water is the solvent in a ______ solution.

aqueous

Why is water such an excellent solvent?

as a polar molecule, it can surround and dissolve ionic and polar molecules

R groups with carbon and hydrogen are ______

hydrophobic

A triple covalent bond would

involve the sharing of six electrons

charged amino acids form...

ionic bonds

bacteria in herbivores

live in the digestive system of herbivores and help digest cellulose rich (grass) meals

polymers

long molecules built my linking many similar or identical monomers by covalent bonds

If the H+ is higher than the OH- is ____

lower

CH4

methane

inorganic molecule

molecules that may contain either carbon or hydrogen, not both

anion

negatively charged ion that gained an electron

7

neutral

bond between H20 molecules

nonpolar covalent bonds

bond between NH3 molecules

polar covalent bonds

The V-shaped water molecule is a polar molecule with a slight _____ charge on each hydrogen atom and a slight _____ charge associated with the oxygen.

positive, negative

cation

positively charged ion that lost an electron

The polar covalent bonds of water molecules...

promote the formation of hydrogen bonds

Adding a base to a solution would...

raise the pH, decrease [H+]

macromolecules

smaller organic molecules joined together to form larger molecules

A burn from steam at 100˚C is more severe than a burn from boiling water because...

steam releases a great deal of heat as it condenses on the skin

chitin

structure in arthropods and fungi

Each element has its own characteristic atom in which

the atomic number is constant

adhesion

the clinging of one substance to another, such as water to plant cell walls, by means of hydrogen bonds

In a reaction in chemical equilibrium...

the forward and reverse reactions are occurring at the same rate

heat of vaporization

the quantity of heat that must be absorbed by 1 g of liquid to gain enough kinetic energy to overcome their attraction to other molecules in the liquid and escape into the air as a gas

What would be the probable effect of adding more product to a reaction that is in equilibrium?

the reverse reaction would increase and more reactants would be formed

monomers

the subunit that serves as the building block of a polymer

what forms between closely aligned molecules?

van der Waals interactions

All polar molecules are

hydrophilic

All non polar molecules are

hydrophobic

carboxyl

-COOH- -C double bonded to O and single bonded to OH group -compounds with COOH = acids -fatty acids -amino acids -negative

A covalent bond between two atoms is likely to be non polar if

-2 atoms are equally electronegative -2 atoms are of the same element

disaccharides

-2 monosaccharides -sucrose, maltose, lactose -joined by glycosidic linkage

polar amino acids are capable of forming...

hydrogen bonds (when hydrogen is present)

ATP/ADP Cycle

-ATP gives up its energy by breaking the phosphoanhydride bond between the last and second last phosphate groups and thereby phosphorylating (adding a phosphate to) a target molecule -When that bond is broken, the ATP loses one phosphate and becomes ADP (adenosine diphosphate), which is less energetic and infrequently used to provide additional energy for the cell -ADP must then be 'recharged' during cellular respiration or photosynthesis where energy (derived from nutrients or light) is used to add a phosphate onto ADP, recreating the phosphoanhydride bond and producing ATP

carbonyl

-C = O -O double bonded to C -hydrophilic -polar

capillary action

A process powered by adhesion that causes water molecules to move upward through a narrow tube such as the stem of a plant.

triglyceride

Circulate in the blood and are made up of three fatty acids attached to a glycerol

When acids and bases are dissolved into water the ____ and ____ balance shifts

H+ and OH-

Some archaea are able to live in lakes with pH values of 11. How does pH 11 compare with the pH 7 typical of your body cells?

It is ten thousand times more basic than pH 7

8-14

base

Which of the following is not a trace element in the human body?

calcium

identify the bonds that hold macromolecules together for peptides (proteins)

covalent bonds

identify the bonds that hold macromolecules together for phosphodiester (nucleotides)

covelent bonds

As the [H+] increases in an ACIDIC solution, the pH ____

decreases

What is the main contributor to the diversity between organic molecules?

differences in their carbon skeletons

What is one of the main changes within carbon skeletons?

double bonds varying in number and location and their interaction with different targets in the body

glycogen

energy storage in animals (liver and muscle)

A cation

has a positive charge

ice floats because...

hydrogen bonding spaces the molecules farther apart, creating a less dense structure

What is the bond between H20 and NH3 molecules?

hydrogen bonds

What type of bonds give water special properties?

hydrogen bonds