AP Biology Flash Cards: Unit 2.5 and Unit 3

Define a covalent bond

A bond where atoms share e-

O is more electronegative compared to H, resulting in. . .

An unequal sharing of e-

Covalent bonding can result in. . .

Polarity when there is a difference between atomic electronegativity

Define hydrogen bond

A weak bond between the negative and positive region of two separate molecules

H2O can form Hydrogen bonds with:

Other water molecules and other charged molecules

Define cohesion

Two of the same molecules form a hydrogen bond

Define adhesion

Two different molecules form a hydrogen bond

Define surface tension

The result of increased hydrogen bonding forces between water molecules at the surface

Water’s cohesive property allows:

• For unique hydrogen bond intractions to occu when water is solid

  • It to absorb a lot of thermal energy before changing chemical states, resisting sudden changes in temperature

What is a result of both the adhesive and cohesive properties of water

Capillary Action

Define acid

Any substnce that increases the [H+] of the solution

Define base

Any substance that decreases the [H+] of the solution

What is a buffer and why is it important in living systems?

Chemical systems that can accept extra H+ and OH- and help regulate the pH

• Carbonic acid (in blood)

What is an organic compound?

A compound containing carbon

What are the four main categories of molecules of living things?

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids

An atom’s electron configuration determines. . .

The kinds and number of bond the atom will form with other atoms

How many valence electrons do H, C, N, and O have?

H - 1 / C - 4 / N - 5 / O - 6

Define the duet rule and octet rule

Octet rule: eight electrons needed for stability

Duet rule: two electrons needed for stability (Hydrogen)

Carbon chains form. . .

The skeletons of most organic molecules

Hydrocarbons are organic molecules consisting of. . .

Only carbon and hydrogen and can undergo reactions that release a large amount of energy

Functional groups are:

The conponents of organic molecules that are mostly involved in chemical reactions

• The # and arrangement of functional groups give each molecule its unique properties

The seven functional groups:

• Hydroxyl (-OH)

• Carbonyl (C—O)

• Carboxyl (C—O-OH)

• Amino (-NH2)

• Sulfhydral (-SH)

• Phosphate (-OPO3^-2)

• Methyl (-CH3)

What is the primary energy-transferring molecule in a cell?

ATP

Define polymer

A long molecule consisting of many similar building blocks

Define monomer

The small building block molecules of a polymer

What occurs when two monomers bond together through the loss of a water molecule?

Dehydration synthesis

Define hydrolysis

How polymers are disassembled to monomers, a reaction that is essentially the reverse of the dehydration reaction

What facilitates hyrdolysis and dehydration reactions?

Enzymes

What are the simplest carbohydrates?

Monosacchaides or simple sugars

Monosaccharides have molecular formulas that are usually multiples of:

CH2O

Facts about monosaccharides:

• Monosaccharides are classifieid by the number of Carbons in the skeleton and the placements of the carbonyl group

• Though often drawn as linear skeleons, in aqueous solutions many sugar form rings

  • Monosaccharides serve as a major fuel for cells and as raw building materials to make molecules

A disaccharide is formed when:

A dehydration reaction joins two monosaccharides where the covalent bond is called the glycosidic linkage

Polysaccharides, the polumers of sugars, have storage and structural roles, how are they determined?

Structure and function of a polysaccharides are determined by its sugar monomers and the positions of glycosidic linkage

Storage polysaccharide:

• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers

  • Surplus starch = granules

• Glycogen is a storage polysaccaride in animals

  • Humans and other vertebraes store it mainly in the liver and muscle cells

Structural polysaccharides:

• Cellulose is a major component of the tough wall of plant cells

  • A polymer of glucose, byt glycos. link. differs

  • Based on two rig forms for glucose

Examples of polysaccharides arranged in beta pleated sheet and alpha conformation

• Starch, glucose molecules are arranged in the alpha conformation

• In cellulose, the monomers are arranged in the beta conformation

Extra notes:

• Enzymes that digest starch by hydralizing alpha linkages cant hydrolyze beta linkages in cellulose

Lipids Notes

• Lipids do not form true polymers

  • A unifying feature of lipids is having little of no affinity for water

  • They are hyrdrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds

• The most biologically important lipids are fats, phospholipids, and steroids

Fats Notes:

Fats are constructed from two trypes of smaller molecules: glycerol and fatty acids

• Glycerol is a three carbon alchol with a hydroxyl group attached to each carbon

A fatty acid consists of:

A carboxyl group attached to a long carbon skeleton

Why do fats seperate from water?

Because water molecules hydrogen bond to each other and exclude the fats

• Three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol

Saturated Fatty Acids and Fats

• SFA have the maximum number of hydrogen atoms possible and no double bonds

• Fat made from saturated fatty acids and are solid at room temperature; mostly animal fats

Unsaturated fatty acids and fats

• Have one or more double bonds

• Fat that is liquid at room temp.

• Plant and fish fats

What is the major function of fats?

Energy storage

Phospholipid Notes:

• In a phospholipid, two fatty acids and a phosphate group are attatched to glycerol

  • Two fatty acid tail are hydrophobic

  • Phosphate group and attachments creates a hydrophilic head

  • They are major constituents of cell membranes

• When they are added to water, they self assemble into a bilayer

Steroid Notes:

Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

• Cholesterol, an important steroid, is a component in animal cell membranes

  • Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease

Protein Notes:

Proteins account for more than 50% of the dry mass of cells

• Protein is a biologically functional molecules that consists of one or more polypeptides

Enzymatic Proteins

• Function : selective acceleratiion of chemical reactions

• Example: digestive enzymes cataluze the hydrolysis of bonds in food molecules

Defense Proteins

• Function: protection against disease

• Example: Antibodies inactive and help destroy viruses and bacteria

Storage Proteins

• Function: storage of amino acids

• Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals ; Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo

Transport Protein

• Function: Transport of substances

• Examples: Hemoglobin, the iron-containing protein of verterbrae blood, transports oxygen from the lung to other parts of the body

Hormone Proteins

• Function: Coordination of an organism’s activities

  • Examples: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration

Receptor Proteins

• Function: Response of cell to chemical stimuli

• Examples: receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells

Contractile and Motor Proteins

• Function: Movement

• Examples: motor proteins are responsible for the undulations of cilia and flagella ; actin and myosin proteins are responsible for the contraction of muscles

Structural Proteins

• Function : support

• Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages ; insects and spiders use silk fibers to make their cocoons and webs ; collagen and elastin proteins provide a fiborous framework in animal connective tissues

Enzyme Notes

• Life would not be possible without enzymes

• Enzymatic proteins act as catalysts, to speed up chemical reactions without being consumed by the reaction

Polypeptide Notes

• Polypeptides are unbranching polymers built from the same set of twenty amino acids

• Range in length from a few to more than a thousand monomers

• Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end and an amino end

What kind of bonds are amino acids linked together by?

Peptide bonds

Protein Structure Notes

• A functional protein consists of one or more polypeptides precisely twisted, folded, coiled into a unique structure

  • ribbon model vs. space filling model

• The sequence of amino acids, determined genetically, leads to a protein’s 3D structure

• A protein’s structure determines its function

When does a protein get to the fourth level of structure?

When a protein consists of more than one polypeptide chain

Primary Structure

A protein’s unique sequence of amino acids determined by inherent genetic information

Secondary Structure

The folding or coiling of the polypeptide into a repeating configuration

• Results from hydrogen bonds between repeating constituents of the polypeptide backbone

Includes the alpha helix (coiled) and the beta pleated sheet (folded)

Tertiary Structure

Is the overall 3D shape of a polypeptide

• Results from interactions between amino acids and R groups

• These interactions btween R groups include hydrogen bonds, ionic bonds, hydrophobic bonds, and Van Der Waals interactions (ie slfhydral bridge)

Quaternary Structure

Is the overall protein structure that results from the aggregation of two or more polypeptide subunits

• Collagen is a fiborous protein consisting of three polypeptides coiled like a rope

• Hemoglobin is a globular protein consisting of four polypeptides

Denaturation Notes

In addition to primary structure, physical and chemical conditions can affect structures

• Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

Denaturation: Loss of proteins native structure

Chaperone Notes

• Protein synthesis begins in the ribosome

• As the polypeptide is released from the ribosome, chaperone proteins assist in their folding

  • Also a protective mechanism seen in cells that are under stress, they attempt to help proteins refold

• If proteins cannot maintain their structure, they should be destroyed by the proteasome

• Many diseases are the result of misfolded proteins

Nucleic Acid Notes

The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

• Genes are made of DNA, a nuclic acid made of moomers called nucleotides

DNA vs RNA

DNA - a double helix

1. 5-carbon sugar (deoxyribose)

2. Adenine, Thymine, Guanine, Cytosine

3. Phosphate group

RNA - single strand

1. 5-carbon sugar (ribose)

2. Adenine, Uracil, Guanine, Cytosine

3. Phosphate Group