Biochemistry

What is the name for an element that is required by an organism for life?

An essential element

What is an essential element called if it is only required in very small amounts?

A trace element

What are the 4 most abundant elements found in living organisms? Also provide their chemical symbol.

Carbon - C

Oxygen - O

Hydrogen - H

Nitrogen - N

What 3 subatomic particles are found in atoms?

Protons

Neutrons

Electrons

What subatomic particles are found in the nucleus of the atom?

Protons and neutrons

What subatomic particle is found in regions that surround the nucleus?

Electrons

What subatomic particle has a negative charge?

An electron

What subatomic particle has a positive charge?

A proton

What subatomic particle has no charge?

A neutron

What is the atomic number?

It is the number of protons in an atom.

What is the mass number?

It is the number of protons plus the number of neutrons in an atom.

How are the isotopes of an element different from each other?

They are different in the number of neutrons.

What is the difference between Carbon-12 and Carbon-13?

Carbon-13 has one more neutron than Carbon-12.

What are 3 uses for radioisotopes?

1. They are used to determine the age of fossils.

2. They are used as tags to locate molecules.

3. They are used in PET-Scans.

What is an ion?

An ion is an atom or molecule with a net electric charge.

If an atom loses an electron, what kind of charge will it have?

It will be an ion with a positive charge.

If an atom gains an electron, what kind of charge will it have?

It will be an ion with a negative charge.

What types of bonds are the strongest in water?

Covalent bonds.

With respect to proteins, why are the following important in biology: ionic bonds, hydrogen bonds, van der Waals interactions, and the hydrophobic force?

1. They determine a proteins structure.

2. They allow two proteins to bind to each other when they need to interact in the cell.

3. They allow proteins to bind to each other to form larger complexes in the cell.

In what type of bond are electrons being shared?

Covalent bonds.

What is the difference between single, double, and triple covalent bonds? Explain.

The number of electrons that are shared. In a single bond one pair of electrons is shared. In a double bond two pairs of electrons are shared. In a triple bond three pairs of electrons are shared.

What type of covalent bond involves the unequal sharing of electrons?

Polar covalent bond

What happens because the electrons are shared unequally in a polar covalent bond?

One atom in the bond will have a partial negative charge and the other atom in the bond will have a partial positive charge.

What two polar covalent bonds do you need to know and what is the charge distribution?

1. O-H, oxygen will have a partial negative charge and hydrogen will have a partial positive charge.

2. N-H, nitrogen will have a partial negative charge and hydrogen will have a partial positive charge

What type of covalent bond involves the equal or fairly equal sharing of electrons?

Nonpolar covalent bond

What two nonpolar covalent bonds do you need to know?

1. C-C

2. C-H

What type of molecule has an unequal distribution of charge within the molecule? Give an example.

A polar molecule. Water is a polar molecule.

Describe the uneven distribution of charge in a water molecule.

Oxygen will have a partial negative charge and the two hydrogens will have a partial positive charge.

What type of molecule lacks an uneven distribution of charge? Give 3 examples.

A nonpolar molecule. Oxygen, carbon dioxide, and fatty acids are nonpolar molecules.

What is an amphipathic molecule? Give an example.

There are two ways you can describe and amphipathic molecule. 1. It is a molecule that has a hydrophillic part and a hydrophobic part. 2. It is a molecule that has a polar or ionized part and a nonpolar part. Phospholipid molecules are amphipathic.

How many covalent bonds can carbon form?

4

What type of bond involves the attraction between oppositely charged ions?

An ionic bond.

What type of bond involves the attraction between a partially positive hydrogen atom and a partially negative atom?

A hydrogen bond.

What do we call the force exerted by the hydrogen-bonded network of water molecules that brings two nonpolar surfaces together by excluding water between them?

Hydrophobic force.

Can water from Hydrogen bonds?

Yes, water molecules can from hydrogen bonds with other water molecules and also other polar molecules.

Describe the hydrogen bond between two water molecules.

The hydrogen bond between two water molecules would involve the the attraction between a partially negative oxygen atom and a partially positive hydrogen atom.

Is water a polar molecule?

Yes

What is the solvent in cells?

Water

What do we call the ability of water molecules to cling other water molecules?

Cohesion.

What bond is important for water's cohesion?

hydrogen bonds

What do we call the ability of water to stick to another substance (one that is not water)?

Adhesion

What bond is important for water's adhesion?

hydrogen bonds

Does water have a high or low surface tension?

High

What does it mean for water to have a high surface tension?

This means it is very difficult to stretch or break the surface of water.

Why does water have a high surface tension?

Because of its ability to form hydrogen bonds.

Does water have a high or low heat of vaporization?

High

Why does water have a high heat of vaporization?

Because of its ability to form hydrogen bonds.

What does it mean for water to have a high heat of vaporization?

This means that it takes a lot of heat to convert water from a liquid to gas. This is how sweating exerts a cooling effect.

Does water have a high or low specific heat?

High

Why does water have a high specific heat?

Because of its ability to form hydrogen bonds.

What does it mean for water to have a high specific heat?

This means that water will change its temperature less when it absorbs or loses a given amount of heat.

What is the solvent in cells?

Water

What types of molecules are generally soluble in water?

Polar molecules

What types of molecules are generally insoluble or poorly soluble in water?

Nonpolar molecules

What structure do phospholipid molecules form when placed in water?

A phospholipid bilayer

What is pH?

It is a measure of the hydrogen ion concentration in a solution.

The pH decreases

What happens to the pH if the hydrogen ion concentration increases?

What type of substance can cause the hydrogen ion concentration to increase?

An acid

What happens to the pH if the hydrogen ion concentration decreases?

The pH increases

What type of substance can cause the hydrogen ion concentration to decrease?

A base

If you wanted to increase the pH of a solution would you add an acid or a base?

Base

If you wanted to decrease the pH of a solution would you an acid or a base?

Acid

What type of substance increases the hydrogen ion concentration of a a solution?

An acid.

What type of substance decreases the hydrogen ion concentration of a solution?

A base

What type of solution has a pH equal to 7?

A neutral solution

What type of solution has a pH that is greater than 7?

A basic (or alkaline) solution

What type of solution has a pH that is less than 7?

An acidic solution

Most biological fluids fall into what range of pH?

Most biological fluids are within the range of pH 6-8.

What do we call a substance capable of resisting changes in pH?

A buffer

What do many buffers consist of?

A weak acid and a weak base that are involved in a reversible reaction.

In terms of buffers, what occurs if the pH increases?

The weak acids will release hydrogen ions to help resist the increase in pH.

In terms of buffers, what occurs if the pH decreases?

The weak bases bind hydrogen ions to help resist the decrease in pH.

What does hydrophillic mean?

It means attracted to and easily dissolved in water.

What does hydrophobic mean?

It means not attracted to and insoluble in water.

What types of molecules are generally hydrophillic?

Polar molecules

What type of molecules are generally hydrophobic?

Nonpolar molecules

What type of solvent could be used to dissolve a nonpolar molecule?

A nonpolar solvent.

Is water a polar solvent or nonpolar solvent?

It is a polar solvent.

What is an organic molecule?

It is a carbon containing molecule.

What are the 4 categories of organic molecules found in cells?

Proteins

Carbohydrates

Lipids

Nucleic Acids

Amino acids

What monomers are used to make proteins?

Monosaccharides

What monomers are used to make polysaccharides?

What monomers are used to make nucleic acids (DNA and RNA)?

Nucleotides

What type of reaction is used to build polymers by connecting monomers together?

Dehydration reaction

Hydrolysis reaction

What type of reaction is used to break polymers down by breaking off monomers?

What four things are attached to the central carbon atom of an amino acid?

1. An amino group

2. A carboxyl group

3. A hydrogen

4. A side chain

There are 20 common acids, what makes each amino acid unique?

Its side chain

Based on their side chains, there are 3 groups of amino acids. Name the 3 groups

.1. Nonpolar (these side chains are hydrophobic)

2. Polar and unharged (these side chains are hydrophillic)

3. Polar and charged (these side chains are hydrophillic)

What is name of the covalent bond that connects two amino acids together?

A peptide bond

What are the names given to each end of a protein?

The N-terminus and C-terminus.

What are the N-terminus and C-terminus?

The N-terminus is end of the protein with a free amino group. The C-terminus is the end of the protein with the free carboxyl group.

What 4 factors that we discussed determine how a protein folds in a cell?

Ionic Bonds

Hydrogen Bonds

van der Waals Interactions

Hydrophobic Force

With respect to proteins, what is the primary structure?

It is the amino acid sequence of the protein.

What determines the primary structure of a protein?

A gene (a segment of DNA)

With respect to proteins, what is a secondary structure? Give two examples.

A secondary structure is a regular local folding pattern. The examples: the alpa-helix and the beta-pleated sheet.

What type of bond is important for the folding of a alpha-helix and a beta-pleated sheet?

Hydrogen bond

With respect to proteins, what is the tertiary structure?

It is the final folded form of a single polypeptide.

With respect to proteins, what is the quaternary structure?

It is the number of polypetides that make up the final protein and how they are bound together.

What is denaturation?

It is a drastic alteration in the shape of a protein (unfolding) and usually results in a loss of function.

What are two things that can cause a protein to denature?

changes in pH and temperature