consider the amino acid alanine. an amino acid has both a weak acid and a weak base. what is the...

Bio 5A Lec 2

Consider the amino acid alanine. An amino acid has both a weak acid and a weak base.What is the weak baseWhat is the weak acidBy lowering or raising the pH you can change

both the protonation state and the charge on this molecule. Sketch the three possible forms of alanine as you go from low pH to high pH and indicate overall charge on the molecule.

Below is one form of alanine

Answer to Core Question 5

Amino acids such as alanine, are also buffers. In one minute, write down a definition of a buffer.

Core Question 6

A buffer is a substance that resists ph change, and a buffer consists of a weak acid or a weak base. Buffers are substances that minimize changes in concentrations of H+ and OH- in a solution.

Answer to Core Question 6

EnantiomerOne of two compounds that are mirror images

of each other

Draw the Enantiomer

Enantiomers

Is it an Enantiomer?

One of several compounds that have the same molecular formula but differ in the covalent arrangements of their atoms

Structural Isomer

Is it an Enantiomer?

YES!

Is it an Enantiomer?

One of several compounds that have the same molecular formula and covalent arrangements but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds

Geometric Isomers

Is it an Enantiomer?

Structural Isomers

Is it an Enantiomer?

Geometric Isomers

Is it an Enantiomer?

YES!

Functional GroupA specific configuration of atoms commonly

attached to the carbon skeletons of organic molecules and usually involved in chemical reactions

Seven main functional groups

Functional Groups!

Draw the Hydroxyl GroupAlcoholsEnd in –olEx. ethanol

Functional Groups!

Draw the Carbonyl groupKetones and AldehydesDouble bond to oxygen

Functional Groups!

Draw the Carboxyl GroupCarboxylic acids or organic saltsEx. Acetic acid

Functional Groups!

Draw the Amino groupAminesEx. Glycine

Functional Groups!

Draw the Sulfhydryl GroupThiolsEx. Cysteine

Functional Groups!

Draw the Phosphate groupOrganic phosphatesEx. Glycerol phosphate

Functional Groups!

Draw the Methyl GroupMethylated compounds

Functional Groups!

An organic molecule possessing both carboxyl and amino groups, Amino acids serve as the monomers of polypeptides

PolypeptideA polymer (chain) of many amino acids linked together by

a peptide bondPeptide Bond

The covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction

Amino Acids

A chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule

Dehydration Reaction

Draw four amino acids with the following R groups

-H-CH3-CH2COOH-CH2NH2

Identify polar (including acidic and basic) and nonpolar groups

Identify the amino acids that can form enantiomers Form a tetrapeptide showing the loss of water and

the formation of three peptide bonds. Identify the amino and carboxyl termini.Put a box around the 3 peptide bonds

Core Question 3

Hydrogen bonds are formed when a hydrogen atom covalently bonded to one electronegative is also attracted to another electronegative atom.

What is the maximum number of hydrogen bonds that can form between water molecules?4 Hydrogen bonds

When are hydrogen bonds formed?

Snowflakes The water molecules in an ice crystal form a

hexagonal lattice, there are 2 hydrogen's for each oxygen so the chemical formula is H2O

Hydrogen and Oxygen connect with covalent bonds. The bonds between H2O in the snowflake connect with hydrogen bonds.

The hexagonal pattern at the molecular level carries right on through to the snowflake structure. Hence the six points.

Hydrogen Bonds Snowflakes

Draw it, where are the H-bonds?

Where are the H-Bonds

Emergent properties of waterCohesive behaviorAbility to moderate temperatureExpansion upon FreezingVersatility as a solvent

H2O

CohesionHydrogen bonds hold water molecules togetherTransport water against gravity in plantsThe Celery Experiment

http://www.youtube.com/watch?v=_Mn_AoDm3wE&feature=related

As water evaporates from a leaf hydrogen bonds pull on the water molecules further down in the vein.

H2O

Ability to moderate temperatureWaters high specific heat

Minimize temperature fluctuationsEvaporation

Due to hydrogen bonds which must be broken for water to evaporate, high boiling point.

Remember water is the only molecule which can form 4 hydrogen bonds other molecules can not form this many.

H2O

Expansion upon freezingWater when cooled contracts down to 4

degrees C then expands.Hydrogen bonds in ice are more ordered,

snowflake.The molecules in ice are more ordered and less

dense which is why ice floats in liquid water

H2O

H2O

Versatility as a solventSolvent – the dissolving agent of a solutionWater is an effective solvent because

It readily forms hydrogen bondsDissolve ionic compounds, nonionic polar

molecules, and larger polar molecules like proteins with ionic and polar regions

H2O

Carbohydrates, simplest form of sugarNames for sugars end in -ose

Building blocks of disacchaarides such as sucrose and polysaccharides (cellulose, starch)

KEY POINTSEach carbon supports a hydroxyl groupChemical formula Cx(H2O)y

Can contain either a ketone or aldehyde depends on where the carbonyl group is

Monosaccharides

KEY POINTSEach carbon supports a hydroxyl groupChemical formula Cx(H2O)y

Can contain either a ketone or aldehyde depends on where the carbonyl group is

Monosaccharides

Consists of two monosaccharides joined by a glycosidic linkage.A covalent bond formed between two

monosaccharides by a dehydration reaction.Maltose is a disaccharide formed by the linking of

two molecules of glucoseWhat type of bond is formed in a dehydration

reaction between two amino acids?Peptide bond – to form polypeptide

Disaccharide

Draw two monosaccharides with 4 carbonsOne of these should be an aldose and the other

a ketoseIdentify the asymmetric carbons in each.How many different stereoisomers can be

formed for the aldose and the ketose?Identify the key functional groups that identify

these as carbohydrates.

Core Question 4-1a

What is an asymmetric carbon?Is a carbon atom that is attached to four

different atoms or four different groups of atoms

Knowing the number of asymmetric carbon atoms you can calculate The maximum possible number of stereoisomers

for any given molecule

Max # Stereoisomers = 2n

n = the # of asymmetric carbon atoms

Asymmetric Carbons