AP bio unit 1

Aqueous solutions

Those in which are solvent in water

Polar covalent Bond

between oxygen and hydrogen in the same water molecule

hydrogen bond

between adjacent water molecules

Polar molecule

Uneven distribution of charge

Cohesion

the attraction between water molecules

• Responsible for surface tension

• Due to hydrogen bonds

Surface tension

the elastic tendency of a liquid surface making it resist external force and shrink into the minimum possible surface area

Adhesion

attraction between water molecules and other polar molecules

Capillary Action

ability of water to move up small tubes

• Combination of cohesion and adhesion

• Important for plant transport

Specfic heat

the amount of energy required to change the temperature by 1^o C

• Water has high specific heat: It takes more energy to heat/cool water than most other substances

• Due to hydrogen bonds

• Importance: Moderates temperatures on Earth and in organisms- you are 50-65% water!

Heat of Vaporization

it takes a lot of energy to convert 1 g of liquid water to gas

• As a liquid evaporates, its remaining surface cools, a process called evaporative cooling

• Prevents bodies of water from evaporating

• Temperature regulation in animals and transpiration in plants

Expansion upon Freezing

Happens because water molecules form a rigid, open hexagonal crystal lattice linked by hydrogen bonds, which holds the molecules farther apart than they are in a loose liquid state

Versatile Solvent

Water is the universal solvent because it dissolves more substances than any other substance

Hydration Shell

When an ionic substance is dissolved in water, each ion is surrounded by a sphere of water

• This allows for water to dissolve and transport ionic and polar substances

Ionization of H2O

• is the process of converting electrically neutral atoms or molecules into charged particles (ions) by adding or removing electrons

• Water is capable of transferring a proton from one water molecule to another

Bicarbonate Buffer

a vital chemical mechanism that keeps the pH of human blood stable between 7.35 and 7.45

pH

• measures how acidic or basic a water based solution is

• Measures the concentrations of H+ ions

Organic Compounds

Living things

• Organic compounds contain carbon (and usually hydrogen)

Hydrocarbons

lengths of covalently-bonded carbons, bonded to hydrogens

• non-polar

Isomer

are these alternate arrangements and have different properties

Structural Isomer

a molecule that has the same exact molecular formula as another, but a different physical connection of its atoms

Cis-Trans Isomer

two elements are on the same side

Trans Isomer

Two elements on opposite sides

Hydroxyl

Chemical Formula: -OH

Structural Formula: -OH

Carboxyl

Chemical Formula: -COOH

Structural Formula: -C=O(OH)

Sulfhydryl

Chemical Formula: -SH

Structural Formula: -SH

Amino

Chemical Formula: -NH2

Structural Formula: -N-H(H)

Phosphate

Chemical Formula: PO4

Structural Formula: O=P-O-O

Carbonyl (Aldehyde)

Chemical Formula: -COH

Structural Formula: -C=O(H)

Carbonyl (Ketone)

Chemical Formula: -CO

Structural Formula: -C=O

Monomer

One Subunit

Polymer

Chain of repeating monomers

Polymerization

Formation of polymer from monomers

Dehydration synthesis

joins monomers together by removing a hydrogen atom from one and a hydroxyl group from the other - creating a new covalent bond and a water molecule

Hydrolysis

separates monomers by adding a molecule of water to break a covalent bond

Control group

Treatment in which the independent variable is either eliminated or is set at a standard value  

Experimental Group

Treatment(s) in which the independent variable is manipulated

Positive Control

• Exposed to a treatment level that is known to produce the expected effect

• Ensures that there is an effect when there should be an effect

• If the positive control does not produce the expected result, there may be something wrong with the experimental procedure 

Negative Control

• Not exposed to the experimental treatment or to any other treatment that is expected to have an effect.

• Ensures that there is no effect when there should be no effect (aka NOTHING SHOULD HAPPEN)

Constants

Variables that are kept equal in all treatments

Dependent Variable

• The variable measured or observed during the experiment

• Responds to the change in the independent variable

Independent Variable

• The variable changed by the researcher during the experiment

Monosaccharide

Monmers of Carbohydrates

Carbohydrates

• Molecules with CHO

• Functional groups: hydroxyl, carbonyl (aldehyde OR ketone)

• Functions: Energy, building blocks of other organic molecules, Structure

Polysaccharides

Polymers of carbohydrates

Disaccharide

Dimers of carbohydrates

Glycosidic linkage

Covalent bond between carbohydrates

Glycogen

Storage carbohydrate of animals

• branched structure makes it easier for energy release

Starch

Storage carbohydrate of plants

Cellulose

A structural carbohydrate used in plant cell walls, due to its linear nature

• indigestible by humans because we don’t have the enzymes

Chitin

a polysaccharide, is found in the exoskeleton of arthropods and the cell walls of many fungi.

Peptidoglycan

A polysaccharide that makes up bacterial cell walls

Lipids

• CHO and sometimes P

• Functional Groups: carboxyl, methyl, and sometimes phosphate

Ester Linkage

Covlent bond for glycerol to fatty acids

glycerol

Three carbon alcohol

Saturated fatty acids

possess single bonds in the hydrocarbon chain, and have linear structure

• Solid @ room temp

Unsaturted fatty acids

at least one double bond in the hydrocarbon chain, which creates a kinked structure

• Liquid @ room temp

Trans fat

artificially, partially hydrogenated to be solid at room temperature.

• Helps keep food shelf-stable (last longer)

• Double bond but still relatively straight → pack tightly together

Triglycerides

Made of 3 fatty acids attached to a glycerol molecule

• If at least ONE fatty acid is unsaturated it is classified as an unsaturated triglyceride

Functions - stored energy, cushion, insulation

Ester linkages bond fatty acids to glycerol backbone

Phosolipids

The main component of cells membranes 

• Two fatty acid tails and a phosphate head bound to a glycerol backbone

• The phosphate head is polar while the fatty acid tails are nonpolar

Steriods

Nonpolar molecules consisting of four fused carbon rings

• Some have hormonal properties and are used in cell-to-cell communication

Cholesterol

Found in cell membranes (helps keep it fluid and flexible); low density type (LDL) can build up in blood vessels

Waxes

• Formed when fatty acids are reacted with alcohol

• Diverse in structure but all have long, nonpolar hydrocarbon chains

• Water is polar and waxes are nonpolar so waxes are good barriers

Lipid Functions

• Storage of energy for long-term use (e.g. triglycerides)

• Hormonal roles (e.g. steroids such as estrogen and testosterone)

• Insulation – thermal (triglycerides) 

• Protection of internal organs through insulation and cushioning (e.g. triglycerides and waxes)

• Structural components of cells (e.g. phospholipids and cholesterol)

Nucleic acids

• Store and transmit genetic information

• Comprised of a 5-carbon sugar, a phosphate, and a nitrogenous base

• Elements - C, H, O, N, P

• Functional Groups - phosphate, hydroxyl

Nucleotides

Are monomers of nucleic acids

Pentose sugar

• Ribose

• Deoxyribose

Ribose

found in RNA nucleotides.

Deoxyribose

found in DNA nucleotides.

Nitrogenouse bases

• Purines

• Pyrimidines

Purines

Bases with TWO rings; adenine and guanine

Pyrimidines

Bases with ONE ring; cytosine, thymine, and uracil

Nitrogen base pairings

Hydrogen bonds form between complementary nitrogenous bases

• A bonds to T (or U) with 2 bonds 

• C bonds to G with 3 bonds

Phosphodiester bonds

Covalent bonds between nucleotides

• These links create a backbone of sugar-phosphate units

• In DNA the backbones run in opposite (antiparallel) 5′ → 3′ directions from each other

DNA

• Functions to store genetic information

• Two strands form a double helix

• Bases are adenine, guanine, cytosine, and thymine

• Larger and more stable

RNA

• Functions to carry genetic information from the DNA

• Single stranded

• Bases are adenine, guanine, cytosine, and uracil

• Smaller and less stable

Proteins

• Composed of amino acids

• Elements - C, H, O, N, sometimes S

• Functional Groups - amino, carboxyl, various others depending on the amino acid

• Have diverse structures and functions:

  • Enzymes

  • Structure

  • Carrier/transport proteins

  • Cell communication signals and receptors

  • Defense/immunity

  • Movement 

Peptide bond

Covalent bond between proteins

Amino acid

proteins monomers

• contains a central carbon atom covalently bonded to an amine functional group, a hydrogen atom, a carboxyl group and an R-group

Dipeptide

Dimer of proteins

Polypeptide

Chain of amino acids

Carboxyl group

R group

A variable group that differs in each of the 20 amino acids 

• Decides if the amino acids are polar, nonpolar or charged/ionic

Central carbon

Carbon in the middle of amino acid

C-terminus

the end of a protein or polypeptide chain that has a free carboxyl group

N-terminus

the starting end of a protein or polypeptide chain that features a free amine group (-NH₂)

Primary structure

Hydrophobic/Nonpolar amino acids

amino acids have R groups tend to hide away from water molecules in the folded polypeptide

Hydrophillic/Polar amino acids

R groups tend to stick to each other by hydrogen bonding; often found on the outside of the folded polypeptide to interact with water molecules

Acidic R group

negative charge

Basic R group

Postive charge

Primary structure

the amino acid sequence (specified by an mRNA sequence)

• AKA just the polypeptide chain - no folding yet! 

Secondary structure

In the backbone of the polypeptide chain the oxygen atoms  (in carboxyl) can hydrogen-bond with the H of the amino group.

• Forms alpha helices or beta-pleated sheets.

• No R group interactions

Tertiary structure

functional groups of R-groups interact, forming a three-dimensional, globular structure

Possible bonds between R-groups:

• Hydrophobic interactions

• Hydrogen bonds 

• Ionic bonds 

• Covalent bonds (disulfide bridges)

Quaternary Structure

more than one tertiary structure binds to another polypeptide, forming a multi-unit complex

• The polypeptides are held together by: hydrophobic interactions, hydrogen bonds, ionic bonds, covalent bonds (disulfide bridges) between R groups

• ALL proteins have a primary, secondary, and tertiary structure. Many also have a quaternary structure.

Denaturation

• Means a protein unfolds or loses its shape. 

• High temperatures or pH disrupts bonds between the R groups and H bonds in backbone (alpha helices and beta pleated sheets)

• The protein will lose all folding EXCEPT the primary structure. 

• The primary structure is never lost!!!! 

Hydrophobic interactions

the natural tendency of nonpolar, water-fearing molecules to clump together in water instead of mixing

• In tertiary structure

Disulfide bridge

strong covalent chemical linkages (represented as –S–S–) formed between the thiol groups of two cysteine amino acid residues