BIO 111 Exam 2 Practice

A crystal lattice is a three-dimensional arrangement of atoms, ions, or molecules in a crystalline solid

H bonds break and reform, and molecules are constantly moving even though they are densely packed.

• less dense than water

• has a crystal lattice structure

• “water-loving”

• polar molecules form H bonds with H2O (bonding onto the O)

• ions are attracted to partial charges

  • ex.) glucose and NaCl

• “water-hating”

• non-polar molecules, often Carbon and Hydrogen

• repelled by water

• cant form H bonds

  • ex.) oil

Octane

Any substance that gives up H+ (protons) during a chemical reaction.

• provide hydrogen ions (H+) and lower pH

• pH < 7

Any substance that acquires H+ (protons) during a chemical reaction.

• provide hydroxide ions (OH–) and raise pH

• pH > 7

Help maintain homeostasis

• a solution that can resist pH change upon the addition of an acidic or basic components

• 0 - 14

• a change of 1 unit of the pH scale means a 10x change in [H+]

• lower pH has a higher amount of H+ than a higher pH

A molecule that contains a Carbon and at least 1 Hydrogen.

• proteins

• nucleic acids

• carbohydrates

• lipids

• there are 6 function groups

• 5 groups are hydrophilic, 1 hydrophobic

• all behave predictably and consistently

• given unique properties to a molecule

• often the site of chemical reactions

• formula: NH2

• amino acids = compounds w/ both amino and carboxyl group

• acts as a base, tends to attract a proton to form NH3

• formula: COOH

• amino acids = compounds w/ both amino and carboxyl group

• acts as an acid, tends to lose a proton to form

  -COO-

• formula in picture

• family: aldehydes, ketones

• formula: R-OH

• family: alcohols, end in ol

• ionized: R-O^-

• highly polar; acts as a weak acid, donating a proton

• formula in picture

• formula: R-S-H

• family: thiols

• S = C in terms of electronegativity, leading to nonpolar covalent bonds; hydrophobic

• can for disulfide bonds contributing to protein structure. (S-S)

Energy is neither created nor destroyed; it just changes form.

Entropy always increases

• cells are working against this

measures the amount of energy in a physical system that is not available to do work

a chain of monomers

molecule of any of a class of compounds, mostly organic, that can react with other molecules to form very large molecules.

Monomers combine chemically to produce a very large chainlike or network molecule, called a polymer.-

• defies the second law of thermodynamics

• A reaction in which two molecules combine to form a single molecule.

• creates a peptide bond between amino acids

Water breaks polymers into monomers.

• no energy required

a sequence of amino acids linked by peptide bonds.

• N Terminus to C Terminus

A smaller and shorter chain of peptide bonds

• Primary (1°)

• Secondary (2°)

• Tertiary (3°)

• Quaternary (4°)

Unique structure of amino acids creates a polypeptide

• R groups don’t interact

Due to the number of bonds within one peptide chain, alpha(α) helices and beta(β) pleated sheets form so O and H can interact.

determined by interactions between R groups on amino acids

when two or more polypeptide chains form one more macromolecule

a molecule containing a very large number of atoms, such as a protein, nucleic acid, or synthetic polymer.

has both hydrophobic and hydrophilic parts.

• allows proteins to integrate into the lipid bilayers

proteins that act as infectious, disease-causing agents

• due to the misfolding of proteins

when hemoglobin is folded incorrectly, which can clog blood vessels

• (Glu) is usually spot 6 in the polypeptide chain but is changed to (Val) due to mutation in DNA instruction

• correct placement in the polypeptide chain

• has a (-) charge due to its side chain

• polar; hydrophilic

• incorrect placement in the polypeptide chain

• has no charge

• nonpolar; hydrophobic

the process of ribonuclease proteins being unfolded

• caused by heat, pH, [salt], solvents, and chemicals

• 1° structure still remains 2°,3°, and 4° are lost

first molecules of life and can self-replicate or synthesize using RNA

• Function 1: information storage if genetic material

  • chromosomes and genes are made of DNA

  • DNA codes the order of amino acids in the primary (1°) structure.

amino acids sticking together, making a fiber, changing the cell shape and amount of oxygen carried by the blood cells

monomers of nucleic acids

• each monomer has three parts

  • phosphate functional group

  • 5-carbon pentose

  • Nitrogenous base

• DNA:

  • cytosine (C)

  • thymine (T)

  • adenine (A)

  • guanine (G)

• RNA:

  • uracil (U)

single six-membered ring

• cytosine (C)

• thymine (T)

• uracil (U)

• nitrogenous Base

six-membered ring + five-membered ring (double)

• adenine (A)

• guanine (G)

• nitrogenous Base

TA, AT

GC, CG

AU, UA

found in ribonucleotides

• reactive

• 2’=OH

• RNA

found in deoxyribonucleotides

• stable

• 2’ = H

• DNA

3’ and 5’ of to different nucleotides react releasing a molecule of water through condensation reactions

holds nucleotides together

• creates the sugar-phosphate backbone of RNA

the portion of the DNA double helix that provides structural support to the molecule.

• hydrophobic

5’C to 3’C

N - C Terminus

• contains deoxyribose

• contains (T)

• Double-stranded

• contains ribose

• contains (U)

• The presence of the –OH group on

  the 2’ C of ribose makes RNA much

  more reactive and less stable than

  DNA.

• usually Single-stranded

• (1) The total number of purines = total # of pyrimidines in DNA

• (2) The # of Adenines = # of Thymines, and the # of Guanines = # of Cytosines in DNA

a tool used for determining the atomic and molecular structure of a crystal.

Complementary base pairing

• hydrogen bonds form between nitrogenous bases

• purine - pyrimidine

• GC = triple H bond

• AT = double H bond

• strands are antiparallel

opposite orientations of the two strands of a DNA double helix

• 1: Strands separate when H bonds between complementary base pairs are broken

• 2: base-pairing w/ template (each new strand created on the 5’ to 3’ orientation)

• 3: polymerization; the original molecule has been copied

• single RNA strand folds in on itself by H bonds

• forms a loop

(cell wall) = gives cell structure

stored in plant cells

• energy storage

• “one sugar”

  • monomer

• end is ose

• “few sugars”

  • small polymers

  • help cell-cell recognition and signaling

• “many sugars”

  • large polymers

• Storage:

  • 1. starch (plants)

  • 2. glycogen (animals)

• Structural

  • 1. cellulose (plants)

  • 2. Chitin (animals & fungi)

  • 3. peptidoglycan (bacteria)

carbonyl group at the end of a carbon chain

carbonyl group in the middle of a carbon chain

monomers of carbohydrates and monosaccharides join to form polysaccharides

hydroxyl is below the ring on the 1’C

hydroxyl is above the ring on the 1’C

Two α-glucose links through the process of a condensation reaction or dehydration synthesis

• forms an α-1,4-glycosidic linkage or β-1,4-glycosidic linkages

• α- bond is downward

• β- bond is upward

α-1,4-glycosidic linkages

• a strong bond but it is easy to hydrolyze when sugars are needed

β-1,4-glycosidic linkages

• The similar structure of these enables their function

• Strong bond, but fairly easy to hydrolyze when sugars are needed

• purple = Graham positive (+) cell wall is

  thick and holds onto dye

  • penicillin works to fight against these bacteria

• pink = Graham negative (-) less peptidoglycan

  so most dye washes away

  • erythromycin works to fight against these bacteria

high potential energy

• don’t form polymers

• are hydrophobic

• make cell membranes possible

• have no standard orientation

1. Fats - contain fatty acids

2. steroids - contain no fatty acids

3. phospholipids- contain fatty acids

   • main 3

4. waxes - contain fatty acids

make up most lipids but are not monomers b/c they can’t be built into a chain

• can be saturated or unsaturated

All carbons are single-bonded

• only one reaction can happen

Carbons are single-bonded, but at least one is double-bonded

• only one reaction can happen

• has a (kink)

ester linkages

• glycerol reacts with a fatty acid through a condensation reaction/ dehyd.

• 3 fatty acids complete the fat, forming triglycerides

formed between the oxygen molecules of glycerol and the hydroxyl molecules of fatty acids

Can become trans fatty acids when exposed to heat, then act like saturated fats.

no fatty acids, recognized by by 4 carbon rings

Hydrophilic OH piece with amphipathic properties

• 4 ring

composed of glycerol + phosphate group + 2 fatty acid tails (joined by ester linkages)

• has a polar “head” (hydrophilic)

• hydrophilic tail

• are in constant motion

saturated fats:

• lower permeability and fluidity b/c of how tightly packed it is

unsaturated fats:

• high permeability and fluidity b/c the kinks in the tails create more space between the phospholipids.

a special category of proteins that end in ose.

Function:

• acts as a catalyst that helps chemical reaction take place

• lowers the activation energy of the reaction

• increases the rate of the reaction

a molecule that an enzyme reacts with

Site where substrates bind to the enzyme

The enzyme closes around the bound substrate to make it tighter.

Regulatory molecules bind to the enzyme, blocking the true substrates from binding to the enzyme.

A regulatory molecule binds to the enzyme, changing the shape of the enzyme to make it available for the substrates to bind to the active site.

A regulatory molecule binds to the enzyme, making the enzyme change shape and making the active site unavailable to substrates.