BIO 111 Exam 2 Practice

Crystal Lattice

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

Liquid Water

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

Solid Water (Ice)

• less dense than water

• has a crystal lattice structure

Hydrophillic

• “water-loving”

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

• ions are attracted to partial charges

  • ex.) glucose and NaCl

Hydrophobic

• “water-hating”

• non-polar molecules, often Carbon and Hydrogen

• repelled by water

• cant form H bonds

  • ex.) oil

Octane

Acids

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

• provide hydrogen ions (H+) and lower pH

• pH < 7

Bases

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

• provide hydroxide ions (OH–) and raise pH

• pH > 7

Buffers

Help maintain homeostasis

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

pH Scale

• 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

Organic Molecules

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

4 Major Categories of Organic Molecules Important to Life

• proteins

• nucleic acids

• carbohydrates

• lipids

Functional Groups

• 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

Amino Group

• family: amines

• formula: NH2

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

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

Carboxyl Group

• family: carboxyl acids

• formula: COOH

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

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

  -COO-

Carbonyl Group

• formula in picture

• family: aldehydes, ketones

Hydroxyl Group

• formula: R-OH

• family: alcohols, end in ol

• ionized: R-O^-

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

Phosphate Group

• family: Organic phosphates

• formula in picture

Sulfhydryl Group

• 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)

First Law of Thermodynamics

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

Second Law of Thermodynamics

Entropy always increases

• cells are working against this

Entropy

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

polymer

a chain of monomers

monomer

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

polymerization

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

• defies the second law of thermodynamics

Condensation Reactions/ Dehydration Synthesis

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

• creates a peptide bond between amino acids

Hydrolysis

Water breaks polymers into monomers.

• no energy required

Polypeptide chains

a sequence of amino acids linked by peptide bonds.

• N Terminus to C Terminus

Oligopeptide

A smaller and shorter chain of peptide bonds

4 Levels of Protein Structure

• Primary (1°)

• Secondary (2°)

• Tertiary (3°)

• Quaternary (4°)

Primary (1°) Structure

Unique structure of amino acids creates a polypeptide

• R groups don’t interact

Secondary (2°) Structure

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.

Tertiary (3°) Structure

determined by interactions between R groups on amino acids

Quaternary (4°) Structure

when two or more polypeptide chains form one more macromolecule

macromelcule

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

anthropatic

has both hydrophobic and hydrophilic parts.

• allows proteins to integrate into the lipid bilayers

prions

proteins that act as infectious, disease-causing agents

• due to the misfolding of proteins

sickle-shaped red blood cells

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

Glutamate (Glu)

• correct placement in the polypeptide chain

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

• polar; hydrophilic

Valine (Val)

• incorrect placement in the polypeptide chain

• has no charge

• nonpolar; hydrophobic

Denaturation

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

Nucleic Acids

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.

Sickle sell results in….

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

Nucleotides

monomers of nucleic acids

• each monomer has three parts

  • phosphate functional group

  • 5-carbon pentose

  • Nitrogenous base

Nitrogenous Bases

• DNA:

  • cytosine (C)

  • thymine (T)

  • adenine (A)

  • guanine (G)

• RNA:

  • uracil (U)

Pyrimidines

single six-membered ring

• cytosine (C)

• thymine (T)

• uracil (U)

• nitrogenous Base

Purines

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

• adenine (A)

• guanine (G)

• nitrogenous Base

Nitrogenous Base Pairings

TA, AT

GC, CG

AU, UA

Ribose

found in ribonucleotides

• reactive

• 2’=OH

• RNA

Deoxyribose

found in deoxyribonucleotides

• stable

• 2’ = H

• DNA

How to build a nucleic acid:

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

phosphodiester linkage

holds nucleotides together

• creates the sugar-phosphate backbone of RNA

sugar-phosphate backbone

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

• hydrophobic

Standard Orientation of Nucleic Acids

5’C to 3’C

Standard Orientation of Proteins

N - C Terminus

1º Structure of DNA within nucleic acids

• contains deoxyribose

• contains (T)

• Double-stranded

1º Structure of RNA within nucleic acids

• 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

(Erwin) Chargaff’s Rules:

• (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

X-ray crystallography

• Franklin & Wilkins

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

Watson and Crick Model

Complementary base pairing

• hydrogen bonds form between nitrogenous bases

• purine - pyrimidine

• GC = triple H bond

• AT = double H bond

• strands are antiparallel

Antiparallel

opposite orientations of the two strands of a DNA double helix

DNA Replication

• 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

Stem-and-Loop Hairpin

• single RNA strand folds in on itself by H bonds

• forms a loop

Cellulose

(cell wall) = gives cell structure

Starch

stored in plant cells

• energy storage

monosaccharides

• “one sugar”

  • monomer

• end is ose

oligosaccharides

• “few sugars”

  • small polymers

  • help cell-cell recognition and signaling

polysaccharides

• “many sugars”

  • large polymers

• Storage:

  • 1. starch (plants)

  • 2. glycogen (animals)

• Structural

  • 1. cellulose (plants)

  • 2. Chitin (animals & fungi)

  • 3. peptidoglycan (bacteria)

aldose

carbonyl group at the end of a carbon chain

ketose

carbonyl group in the middle of a carbon chain

Glycosidic Linkages

monomers of carbohydrates and monosaccharides join to form polysaccharides

α-glucose

hydroxyl is below the ring on the 1’C

β-glucose

hydroxyl is above the ring on the 1’C

α-glycosidic linkages/ β-glycosidic linkages

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

Storage polysaccharide linkage

α-1,4-glycosidic linkages

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

Structural polysaccharide linkage

β-1,4-glycosidic linkages

• The similar structure of these enables their function

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

Graham Stain in Bacteria Cell Wall structure

• 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

Organic molecules such as carbohydrates, lipids, and proteins contain relatively weak covalent bonds and thus have

high potential energy

Lipids

• don’t form polymers

• are hydrophobic

• make cell membranes possible

• have no standard orientation

Types of Lipids

1. Fats - contain fatty acids

2. steroids - contain no fatty acids

3. phospholipids- contain fatty acids

   • main 3

4. waxes - contain fatty acids

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

Saturated Fatty Acids

All carbons are single-bonded

• only one reaction can happen

Unsaturated Fatty Acids

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

• only one reaction can happen

• has a (kink)

Fats form via?

ester linkages

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

• 3 fatty acids complete the fat, forming triglycerides

Ester linkages

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

Unsaturated Fat Heat Exposure

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

Steroids

no fatty acids, recognized by by 4 carbon rings

Cholesterol

Hydrophilic OH piece with amphipathic properties

• 4 ring

Phospholipids

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

• has a polar “head” (hydrophilic)

• hydrophilic tail

• are in constant motion

Fatty Acids Affect on Cell Membranes

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.

Enzymes

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

Substrate

a molecule that an enzyme reacts with

Active Site

Site where substrates bind to the enzyme

Induced Fit

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

Competitive Inhibition

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

Allosteric Attraction

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.

Allosteric Inhibition

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