Study Guide for Chapter 5

Hydrophobic and hydrophilic molecules

Be able to give examples of hydrophobic and hydrophilic molecules and explain why they are hydrophobic or hydrophilic. Include a discussion of electronegativity, bond type, and hydrogen bonding. Be able to give examples of hydrophobic and hydrophilic molecules. Be able to pick hydrophobic and hydrophilic molecules out of a molecule “lineup”. Recognize that for many molecules it may not be easy to classify them as hydrophobic or hydrophilic. That is fine. Just be able to logically justify your answer.

Four major groups of macromolecules?

1)Carbohydrates

2)Lipids

3)______

4)______

Carbohydrates

What is the ratio of carbon:hydrogen: oxygen for carbohydrates.

Are most carbohydrates hydrophobic or hydrophilic? Explain

Be able to recognize carbohydrates as monosaccharides, disaccharides, or polysaccharides.

Know the following table:

Function / Plants / Animals
Carbohydrate most frequently found in cells not related to storage or transport. / Glucose / Glucose
Transport carbohydrate / ______/ ______
Storage carbohydrate / Starch / ______
Structural carbohydrate / Cellulose / ------

Way I abbreviate the structure of carbohydrates

Glucose ______

Sucrose

Starch and ______

Cellulose

Lipids

All lipids have the following characteristic: mix poorly with water (hydrophobic).

Also, they are the only group that do not form true polymers.

There are three major types of lipids:

1)Fats

2)______

3)Steroids

Fats

Fats are made up of 3 fatty acid molecules and one ______molecule.

Below is a fat molecule

The following functional groups are found in fatty acids: hydrogens and ______

Human fatty acids are generally 16-18 carbons long.

Fatty acids can be:

1)______– no carbon-carbon double bonds (known to contribute to antherosclerosis)

2)Monounsaturated- at least one carbon-carbon double bond

3)Polyunsaturated- two or more carbon-carbon double bonds

Hydrogenated vegetable oils means that the mono or polyunsaturated fats have been synthetically converted to saturated fats.

Double bonds in fatty acids can be:

1)Cis C-H

C-H

2) _____ H-C

C-H

Trans fatty acids are not found in nature but can be man made. Trans fats have been found to contribute to diseases such as antherosclerosis.

Fats rich in saturated fatty acids tend to be solid at room temperature. The lack of double bonds allows the tails to be flexible and pack together tightly. Butter and lard are examples.

Fats rich in unsaturated fatty acids tend to be liquid at room temperature and are called oils. The double bonds cause ‘kinks’ in the tails and keep them from packing tightly.

Phospholipids

Phospholipids have similarities to fat molecules. They are made of glycerol and fatty acids.

However, they are different from fats in that they have just ___ fatty acid ‘tails’ NOT three. Instead of a third fatty acid bonding to the glycerol, a phosphate and choline group are attached instead. See below

Notice that the phosphocholine ‘head’ makes that part of the molecule is very polar (hydrophilic) an the hydrocarbon tails make that part of the molecule very nonpolar (hydrophobic). This is the only ‘true’ aphipathic molecule that you will have to identify as such for the test.

Phospholipids make up most of our membranes. When phospholipids are put into water they naturally form a bilayer.

The ______heads point out to watery medium while the hydrophobic tails point inward making a hydrophobic zone in the middle of the membrane.

Steroids

Steroids are lipids that are characterized by four-fused rings as shown below:

Cholesterol is a steroid that plays an important role in cell membranes.

Many hormones (e.g. animal sex hormones) are steroids.

Proteins

Proteins are polymers made up of amino acids (the monomers)

There are ____different amino acids. Below are examples of some amino acids:

Notice that they all have a central carbon with what is called an amino group ( notice new functional group!) on one side of the central carbon and a ______group the other side. A hydrogen atom is also bonded to all central carbons. The only thing that differs among all 20 amino acid is the fourth group that is attached to the central carbon. Notice that this fourth group (called “R group” ) can be very different from each other.

Amino acids can bond together to form long chains (polymer) usually between 100 and 300 amino acids long. A carboxyl group of one amino acid always bonds with an ______group of another amino acid. The covalent bond that is formed has a special name called a ______bond. This a special type of dehydration synthesis reaction. See below:

Notice that the amino acids have a ______charged carboxyl group on one end and a positively charged amino group on the other (see previous diagram of amino acids). When the acid group and amino group bond, the combination (peptide bond) no longer has a net charge. The only acid group (not counting R groups) is at one end of the long chain, and the only amino group (not counting R groups) is a the other end of the long chain.

If you don’t count the R groups there are still parts of the chain that could potentially form hydrogen bonds with water or other hydrophilic molecules. These are the ______group and the ______atoms bonded to the N atoms. Notice also these carbonyls and Hs attached to Ns occur at regular intervals along the chain (every fourth atom)..

Four Levels of Protein Structure

Remember proteins are very cool! They do lots of things. A major reason they can do so much is that they are:

1)made of 20 different building blocks

2)have relatively large and complex shapes.

Primary Structure

The first level of structure of the protein is its primary structure. This is basically just the sequence of amino acids of the protein chain.

Once the protein has formed its primary structure it will naturally fold into its other levels.

Secondary Structure

Most protein chains (also called polypeptide chains) fold into segments that are either

1)______

or

2)beta pleated sheets

Notice that both these structures are held together by hydrogen bonding among the carbonyls and hydrogens attached to nitrogen along the original chain. R groups are NOT involved. R groups may determine if a segment can form a beta pleated sheet or alpha helix, but it is NOT involved in any bonding.

Tertiary Structure

Superimposed on the secondary structure is the tertiary structure. It is the tertiary structure that give the molecule its main three-dimensional shape.

It is the tertiary structure where the R groups play an important role in determining the ultimate three dimensional shape. Depending on the kind and location of the various R groups, different bonds can form.

1)______

2)hydrophobic interactions and van der Waals interactions

3)______

4)______

This is a good time to go back and look at the amino acids. They can be grouped into three types: nonpolar, ______, and electrically charged. Be able to name and draw the structure of at least one of each of the types of amino acids. Notice nonpolar amino acids can form can form hydrophobic interactions and van der Waals interactions. ______amino acids can form hydrogen bonds. ______can form ionic bonds.

Cysteine is of particular importance because it can form a disulfide bridge with another ______amino acid. This is a very strong covalent bond compared to the other weaker type of bonds. (Sulfhydryl is another functional group: -SH).

Remember amino acids are grouped by their R groups. All amino acids have charges on them in water because the carboxyls lose a H+ and the nitrogen atoms gain an H+. Remember also that these carboxyls and amino groups become part of peptide bonds when they form polypeptides and therefore cannot ionize.

Notice also that when proteins take on a three-dimensional shape that they can form small grooves. These grooves can actually be the active sites of proteins such as enzymes. The physiochemical nature of the inside of the grooves will be determined by the type and orientation of R groups facing into the groove.

Quaternary Level

If two or more polypeptide chains are held together to form the protein (see three figures above) then a quaternary structure can form. Not all proteins have a quaternary structure.

These quaternary structures can form rope like structures with great tensile strength like collagen or they can form more globular aggregations like hemoglobin. See below.

Because the three-dimensional shape is held together by relatively weak bonds, the three dimensional shape can be disturbed by changes in the chemical make-up of the cell or by temperature. Often times these changes in the chemistry or temperature affect the 2nd , 3rd and 4th levels of structure but not the primary. When the three-dimensional shape is altered to the point the protein loses its function, we say that it is denatured. Many times the shape and therefore the function can be restored by restoring the chemical environment or temperature back to the right levels for the protein.

Sometimes proteins need the help to fold into their three dimensional shape. This help comes from special proteins called chaporonins.

Function of Proteins

Most important functions of proteins for this class are:

1)Enzymes

2)Transport proteins

3)Receptor proteins

Other less important functions of proteins for this class are:

1)Structure 4) Contractile and motor

2)______5) ______

3)Hormones

Other Concepts

Also know the seven functional groups on pgs. 64-65. Know names and be able to draw their structures.

Know that the large molecules that we consume in food get broken down into building blocks in our digestive tract.

Primary Large Biomolecules in Food / Building Blocks / Function in cell when formed again into large biomolecules within the cell.
Carbohydrates:
e.g. starch, glycogen / ______/ Storage (energy)
Proteins / ______/ Many (see above)
Fats / ______and ______/ Storage (energy)