Unit 1: Chemistry of Life

What is a hydrogen bond?

noncovalent attraction between a hydrogen atom bonded to an electronegative atom (O,N,F) and another electronegative atom; usually nitrogen or oxygen (maybe fluorine)

Where are hydrogen bonds found in water?

Hydrogen bonds are found between a hydrogen atom of one water molecule and an oxygen atom of another. One water molecule can form 4 hydrogen bonds at one time.

Where are hydrogen bonds found in DNA?

Hydrogen bonds are responsible for specific base-pair formation in the DNA double helix. They are also integral to the stability of the structure.

How many hydrogen bonds are found between complementary base pairing?

Between adenine and thymine there are two; there are three between guanine and cytosine.

What is the structure of an amino acid?

At the center of the amino acid is a carbon atom called alpha carbon. Bonded to it is an amino group, carboxyl group, hydrogen atom, and a variable (R) group- a.k.a side chain- which determines the unique characteristics of the amino acid.

What are the three options for the R group? For each R group option, describe the polarity and justify your reasoning.

Nonpolar R groups are hydrophobic and typically have a nonpolar bond of Carbon - Hydrogen. Polar R groups are hydrophilic and are identified by a bond of oxygen to hydrogen or sulfur to hydrogen. Finally, electrically charged R groups are hydrophilic and possess a carboxyl - carbon double bonded to oxygen making it acidic (-) - or amino (NH2/3) making it basic (+)

What are three properties of water?

There are four properties of water: cohesive behavior, ability to moderate temperature, expansion upon freezing, and versatility as a solvent.

How does hydrogen-bonding allow for the cohesive behavior of water?

The cohesive behavior of water occurs within water as hydrogen bonds between neighboring water molecules keep the substance together

How does hydrogen-bonding allow for the ability of water to moderate temperature?

Water has a high specific heat due to hydrogen bonds as energy (heat) is required to break the bonds between water molecules before speeding up water molecules and increasing temperature

How does hydrogen-bonding allow for water to expand upon freezing?

At temperature at 4ºC and higher, water behaves like any other liquid. From temperatures at 4ºC to 0ºC water molecules begin to move too slow to break the hydrogen bonds between water molecules and it forms ice. Because the hydrogen bonds keep other water molecules "arms-length" apart, this forms a crystalline lattice, enabling ice to be 10% lighter than water. This is why ice floats above the water, preserving aquatic life below it.

How does hydrogen-bonding allow for water's versatility as a solvent?

Because water is a polar molecule it has partially positive and partially negative parts. These partially charged parts of water molecules can bond to, separate, and isolate the partially positive and partially negative parts of the solute.

Describe why water is considered a polar molecule.

Water is considered a polar molecule because its overall charge is unevenly distributed. Therefore, the oxygen region is partially negative and each hydrogen is partially positive. The polarity of this molecule is also indicative of its bent shape.

Using the properties of water, describe how water can move up a capillary tube to move from the roots to the leaves in a plant.

As water evaporates from the leaf, hydrogen bonds cause the water molecules leaving the veins to tug on the molecules further down- pulling the water up through the plant. This is made possible by cohesion as the water attempts to stick together, and also adhesion as adhesion of water to cell walls by hydrogen bonds helps counter the downward pull of gravity as water moves up the capillary tube.

Using the properties of water, describe how a water strider can walk on water.

Due to hydrogen bonds allowing water to exhibit cohesive behavior, water has high surface tension. Surface tension measures how difficult it is to stretch/break the surface of a liquid. Because eater has a high surface tension, it allows a water strider to walk on it without breaking

What are the four macromolecules?

Carbohydrates- include sugars and polymers of sugars (monosaccharides, polysaccharids, etc.)

Lipids- fats, steroids

Proteins- enzymes (transport proteins etc.)

Nucleic Acids- DNA, RNA

What are the elements found in a carbohydrate?

Carbon, Hydrogen, Oxygen

What are three functions of carbohydrates in living organisms?

Remember- Storage/Structure

Plants store starch- a polymer of glucose monomers. Synthesizing starch allows them to stockpile glucose and glucose=energy
Animals store glycogen in mainly liver and muscle cells. Breakdown of glycogen in these cells release glucose when the demand for energy increases

Cellulose is a major component of the tough walls that enclose plant cells (alternating orientation of glucose molecules provides stability compared to starch)
Chitin is used by arthropods to build their exoskeleton. Fungi also use it to build their cell wall. (similar to cellulose except glucose monomer has N-containing attachments)

What are the elements found in a protein?

carbon, hydrogen, oxygen, nitrogen (most contain sulfur)

What are the functional groups found in all amino acids?

The functional groups found in all amino acids are the amino (NH2) and carboxyl (COOH-) as well as an R group

What are three functions of proteins in living organisms?

Nearly every dynamic function of a living being depends on proteins
1) Enzymes- Catalyze chemical reactions in body (digestive enzymes catalyze hydrolysis of bonds in food molecules)
2) Transport proteins - Transports substances across phospholipid bilayer
3) Contractile and motor proteins - movement such as contractions of muscle
(for all see page 58)

What are the elements found in nucleic acids?

Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus

What are parts found in all nucleotides?

phosphate group bonded to a five carbon sugar bonded to nitrogenous base

What are three functions of nucleic acids in living organisms?

There are two types of nucleic acid:
Deoxyribonucleic acid- genetic code- all necessary to build organism
Ribonucleic acid- essential for coding, decoding, regulating/expressing genes

Storage and transmit hereditary and genetic information

What are the elements found in a lipid?

carbon, hydrogen, oxygen (sometimes sulfur, phosphorus, nitrogen)

How are the three different types of lipids different?

What are three functions of lipids in living organisms?

Which macromolecule(s) contain nitrogen?

Which macromolecule(s) contain phosphorus?

Which macromolecule(s) contain sulfur?

How does the R group affect the folding of the protein? (include polar and nonpolar R groups)

What is dehydration synthesis?

join two monomers together into a polymer and a water molecule is removed.

Provide an example of dehydration.

What is hydrolysis reaction?

add a water molecule to cleave the covalent bond between two monomers in a polymer

Provide an example of hydrolysis.

What is the hydrolysis? Identify inputs and outputs using a specific example.

What is the dehydration? Identify inputs and outputs using a specific example.

What type of bond is found in carbohydrates? Specifically, where is this bond located?

What type of bond is found between protein monomers? Specifically, where is this bond located?

What type of bond is found between nucleic acid monomers? Specifically, where is this bond located?

What is the monomer of a carbohydrate? Identify the components of the monomer.

Saccharides- monosaccharides- chains or rings most often 5-6C

What is the monomer of a protein? Identify the components of the monomer.

What is the monomer of a nucleic acid? Identify the components of the monomer.

Nucleotides

Identify the components of a phospholipid.

What type of bond is found in starch?

What type of bond is found in cellulose?

Which bond can be broken by animals?

Does DNA and/or RNA have a pentose sugar?

Does DNA and/or RNA have nitrogenous bases?

What is the traditional strandedness of DNA? of RNA?

look at doc for hydrophobic/hydrophilic/charged practice

ok

How does a saturated and unsaturated fatty acid differ? How does the level of saturation affect the function of the lipid?

Describe how a nonpolar to polar R group substitution changes the structure and function of a protein.

Describe how a cytosine to thymine substitution changes the structure and function of DNA. Note this is a pyrimidine-to-pyrimidine substitution

Describe how a cytosine to guanine substitution changes the structure and function of DNA. Note this is a pyrimidine-to-purine substitution

Describe how a deoxyribose to ribose changes the structure and function of a nucleic acid.

Describe the structure of the nucleic acid polymer. What are the ends called and what is found at each end? Which end is the location of the growing nucleic acid strand?

What are the complementary base pairings found in nucleic acids? Identify the number of hydrogen bonds found between these two nitrogenous bases.

Describe and give the types of bonds in the Primary level of folding in proteins.

Describe and give the types of bonds in the Secondary level of folding in proteins.

Describe and give the types of bonds in the Tertiary level of folding in proteins.

Describe and give the types of bonds in the Quaternary level of folding in proteins.

What are the ends of a protein called and what is found at each end? Which end is the location of the growing polypeptide strand?

Describe the structure of a carbohydrate polymer.

What are the components of a fat molecule?

Three fatty acids + glycerol

What are the components of a phospholipid?

Two fatty acids + glycerol + phosphate group

Describe the structure of a steroid.

Four fused carbon rings (the last looks like a dog house)

What are the three components of a DNA or RNA molecule?

What is the directionality of DNA?

what type of molecule is a water molecule?

Polar covalent

What is evaporative cooling?

The highest energy molecules will evaporate first, cooling the surface of remaining liquid

What are the significant characteristics of glucose?

Aldehyde group (C branching to bond with hydrogen and double bond with oxygen), 6 carbons,

What are the significant characteristics of glycerol?

3 carbons, hydroxyl group, no aldehyde

What are the significant characteristics of fatty acids?

Carboxylic acid group on end (C double bonded to Oxygen and single bonded to OH), the rest is hydrogen and carbon

Do pyrimidines have one or two rings?

one

What is denaturation?

a structural change in a protein that results in a loss of its biological properties

What leads to denaturation?

Temperature, pH, salinity changes

What is at the 3' end of DNA?

hydroxyl group

What is at the 5' end of DNA?

phosphate group