Biology exam 4

compound

A compound is usually a molecule as well. To be a compound, it has to have two different types of atoms, such as H2O.

Some compounds like NaCl are not molecules because they are linked together in a crystalline structure, rather than being molecularly bonded.

molecule

Chemical bond = molecule
crystalline structure or atom by itself -- not a molecule

A molecule consists of two more atoms, which can be the same or different types of atom, that are linked by a chemical bond. A molecule of H2 or O2 is still a molecule, but not a compound.

mass number

Mass number is the total number of protons and neutrons in the most common isotope of an atom

atomic number

Atomic number is only the number of protons in the nucleus of the atom, giving the atom it's identity as a particular element

Identify the four elements that make up 96% of living matter

CHNO -- Carbon, Hydrogen, Nitrogen, Oxygen

Draw and label a simplified model of an atom. Explain how this model misrepresents our understanding of atomic structure

The electrons don't actually go around in a circular orbit, but rather they appear in places around the nucleus that can be predicted with probability.

Distinguish between each of the following pairs of terms:
a. Neutron and proton

A neutron has a neutral charge and a proton has a positive charge. A neutron has slightly more mass than a proton.

Neutron

neutral charge

Proton

proton has a positive charge

Distinguish between each of the following pairs of terms Atomic number and mass number

Mass number is the total number of protons and neutrons in the most common isotope of an atom
Atomic number is only the number of protons in the nucleus of the atom, giving the atom it's identity as a particular element

Atomic number

Atomic number is only the number of protons in the nucleus of the atom, giving the atom it's identity as a particular element

mass number

Mass number is the total number of protons and neutrons in the most common isotope of an atom

Distinguish between each of the following pairs of terms
Atomic weight and mass number

Mass number is an absolute -- it is the total number of protons and neutrons in an atom
Atomic weight is the ratio of the average mass of the atom relative to 1/12 of the weight of a carbon atom.

Atomic weight

Mass number is an absolute -- it is the total number of protons and neutrons in an atom

mass number

Atomic weight is the ratio of the average mass of the atom relative to 1/12 of the weight of a carbon atom.

Explain how the atomic number and mass number of an atom can be used to
determine the number of neutrons

Subtract atomic number from mass number and you will have the number of neutrons

Explain how two isotopes of an element are similar. Explain how they are different.

The two isotopes of an element have the same number of protons but different numbers of neutrons

What is the significance of an atoms valence in the construction of molecules and compounds?

If the valence shell of an atom is filled, the element is stable and less likely to form a chemical bond with another atom. If the valence (outer) shell of an atom is missing one or more electrons, it is likely to fill those shells by sharing electrons with other atoms that also have unfilled valence shells.

Define electronegativity.

A chemical property that describes the tendency of an atom or a functional group to attract electrons (or electron density) towards itself.[1] An atom's electronegativity is affected by both its atomic number and the distance that its valence electrons reside from the charged nucleus. The higher the associated electronegativity number, the more an element or compound attracts electrons towards it.

Distinguish between nonpolar covalent, polar covalent and ionic bonds.

A nonpolar covalent bond is a bond where electrons are shared equally between two atoms.
A polar covalent bond is a chemical bond where the shared electrons spend more time closer to the nucleus of the more electronegative atom.
In an ionic bond, the electrons are completely transferred from one atom to another rather than shared.

How Many Bonds Can an Atom Have?

Atoms with more than one unpaired electron can form multiple single bonds with multiple atoms or double or triple bonds with a single atom.

Describe the electron-sharing continuum

The degree to which electrons are shared in chemical bonds forms a continuum, from equal sharing in nonpolar covalent bonds, to unequal sharing in polar covalent bonds, to the transfer of electrons in ionic bonds.

Explain why strong covalent bonds and weak bonds are both essential in living
organisms.

Strong covalent bonds are needed for living organisms so that organism bodies can form and hold together and not fall apart.
Water is made of weak hydrogen bonds, which make it a solvent, and water is needed for life to dissolve nutrients for ingestion or wastes for excretion, to transport important chemicals or even be used as one.

Explain how you would make up a one molar (1M) solution of ethyl alcohol.C2H6O.

2 carbons - 24 grams, 6 hydrogens, 6 grams, 1 oxygen, 14 grams, 24 + 14 + 6 = ethanol has a molar weight of 44. Ethanol is 0.789 grams per milliliter, so 55.8 milliliters of ethanol in 1 liter of water will create a 1 molar solution of ethanol.

With the use of a diagram or diagrams, explain why water molecules are polar

The water molecule is polar because the shared electrons are closer to the oxygen atom rather than the hydrogen atoms.

With the use of a diagram or diagrams, explain why water molecules are capable of hydrogen bonding with 4 neighboring water molecules

The oxygen atom is charged as 2- .And the two hydrogen atoms are charged as 1+ each.Therefore the oxygen atom can attract two hydrogen atoms of other two water molecules and the two hydrogen atoms can attrat two oxygen atoms of another two water molecules

List four characteristics of water that are emergent properties resulting from
hydrogen bonding.

1. Cohesive
   2 Adhesive
2. Denser as a liquid than as a solid
3. Able to absorb large amounts of energy

Define cohesion as regards to water

Water is attracted to other water. This is cohesion

Define adhesion as regards to water

Water is attracted to other materials besides water. This is adhesion

How does water's cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree.

The cohesion of water allows a long string of water molecules to be hydrogen bonded to all the way from the roots to the leaves in a long train of water molecules. Adhesion helps this process with capillary action, where the water that is attracted to the side of the of the xylem vessels, which allows other water molecules to move further up. Finally, transpiration acts as a water "pump" against gravity, by having water molecules evaporate out through the stomata on the leaves of plants, and this evaporation action pulls the chain of water molecules up behind it.

What is the difference between "heat" and "temperature?" Give examples.

Temperature is an intensive property, measured in degrees, while heat is an extensive property measured in BTU's. An intensive property is not dependent on the amount of substance present -- water boils at a temperature of 100 degrees, whether it's a gallon or a million gallons.
Heat is an extensive property, measured in BTU's. it is the amount of heat energy required to increase the temperature of 1 pound of water from 3.8 degrees to 4.4 degrees Celsius.

Temperature

Intensive property, measured in degrees, while heat is an extensive property measured in BTU's. An intensive property is not dependent on the amount of substance present -- water boils at a temperature of 100 degrees, whether it's a gallon or a million gallons.

Heat

extensive property, measured in BTU's. it is the amount of heat energy required to increase the temperature of 1 pound of water from 3.8 degrees to 4.4 degrees Celsius.

Explain the following observations by referring to the properties of water Coastal areas have milder climates than adjacent inland areas.

Water is able to absorb large amounts of energy, including heat. So the ocean absorbs heat in the summer because the water is cooler than the air, sucking the heat out of the air, thus cooling the air in summer. In the winter, the air is cooler than water, so the heat moves from the water to the air, warming the air in winter.

Intensive property

not dependent on the amount of substance present -- water boils at a temperature of 100 degrees, whether it's a gallon or a million gallons.

Define specific heat

specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.

Define heat of vaporization

the amount of heat required to convert unit mass of a liquid into the vapor without a change in temperature.

Explain the following observations by referring to the properties of water. Ocean temperatures fluctuate much less than temperatures on land.

Water is able to absorb large amounts of energy, including heat, and is denser as a liquid than a solid. Therefore, it takes a lot of energy to heat water, and water does not give up it's heat as quickly as air does -- high specific heat and high heat of vaporization

Insects like water striders can walk on the surface of a pond without breaking the surface.

The cohesive property of water -- the tendency of water to be attracted to water, makes the top layer of water molecules that don't have any water above them are pulled inward to other molecules, so when a water strider steps on water, the force of the top layer of water coheres to itself and resists the foot of the water strider from separating water molecules from each other.

If you slightly overfill a water glass, the water will form a convex surface
above the top of the glass.

The cohesive property of water -- the water at the top of the overfilled glass is more attracted to the the water than to the side of the glass, creating a convex meniscus.

If you place a paper towel so that it touches spilled water, the towel will draw
in the water.

Adhesion

Ice floats on water.

Water expands as it changes from a liquid to a solid, becoming less dense rather than more dense.

Humans sweat and dogs pant to cool themselves on hot days.

High specific heat Water absorbs latent heat in order to evaporate, and this absorption of heat causes a cooling for sweating humans and panting dogs.

Name the products of the dissociation of water and give their concentration in
pure water.

2 H2O OH− + H3O+
H3O^+1 = hydronium ion
OH^-1 = hydroxide ion
Concentration in pure water 1x10^-7 mol/L

Define acid

A solution in which the concentration of hydronium ions is greater than 10^-7 moles per liter. pH less than 7
Gives away protons

Define a base

A solution in which the concentration of hydronium atoms is less than 10^-7 moles per liter. pH more than 7
Takes protons

Define pH

The measure of concentration and activity of hydronium atoms in a solution

Explain how acids and bases may directly or indirectly alter the hydrogen ion concentration of a solution.

When an acid interacts with a solution, it can donate protons. When an alkaline interacts with a solution, it can accept protons.

What is a buffer? In your explanation, use as a model acetic acid and acetate in solution.

Acetic acid and acetate maintain a pH equilibrium. Acetic acid is an acid and acetate is a base. The two function together as a buffering system.
CH3COOH

Explain the role of catabolic and anabolic pathways in cellular metabolism.

Reactions that break down molecules and produce ATP are called catabolic pathways. Reactions that synthesize larger molecules from smaller components are called anabolic pathways.

Anabolic pathways.

Reactions that synthesize larger molecules from smaller components

Catabolic pathways

Reactions that break down molecules and produce ATP

Distinguish between kinetic and potential energy

Potential energy is stored energy

kinetic energy is energy in motion that is doing work.

Kinetic

energy in motion that is doing work

Potential energy

stored energy

Distinguish between an isolated and an open system. Explain why an organism is considered an open system.

An isolated system is a physical system without any external exchange. It's total energy and mass stay constant. An open system is a system which continuously interacts with its environment. The interaction can take the form of information, energy, or material transfers into or out of the system boundary, depending on the discipline which defines the concept (see below). An open system should be contrasted with the concept of an isolated system which exchanges neither energy, matter,nor information with its environment.

Isolated system

physical system without any external exchange. It's total energy and mass stay constant, isolated system which exchanges neither energy, matter,nor information with its environment.

Open system

system which continuously interacts with its environment. The interaction can take the form of information, energy, or material transfers into or out of the system boundary, depending on the discipline which defines the concept.

What three things can an open system exchange with the environment?

1. Information
2. Energy
3. Materials

Explain the first and second laws of thermodynamics in your own words.

First -- energy cannot be created or destroyed, but can be transformed from a more useful form to a less useful form, such as from wood to smoke and ashes
Second -- Energy moves towards entropy -- the potential energy of a system will be less than the initial energy, if there are no inputs of energy.

First law of thermodynamics

energy cannot be created or destroyed, but can be transformed from a more useful form to a less useful form, such as from wood to smoke and ashes

2nd law of thermodynamics

Energy moves towards entropy -- the potential energy of a system will be less than the initial energy, if there are no inputs of energy. Entropy is always increasing.

Explain why highly ordered living organisms do not violate the second law of thermodynamics.

this increase in organization over time in no way violates the second law. The entropy of a particular system, such as an organism, may actually decrease, so long as the total entropy of the universe-the system plus its surroundings-increases. Thus, organisms are islands of low entropy in an increasingly random universe. The evolution of biological order is perfectly consistent with the laws of thermodynamics.

Write and define each component of the equation for Gibbs free-energy change.

ΔG = ΔH - TΔS
Gibbs free energy equation determines if a chemical equation will be spontaneous or not. If ΔG comes out negative, it is spontaneous, if positive, it's not spontaneous. ΔH is change in enthalpy, or energy in a system, and TΔS is difference in entropy multiplied by temperature, and entropy is the energy that is not used for work and accumulates as waste heat. So if difference in enthalpy is greater than difference in entropy times temperature, that means that energy was added to the system, and if difference in enthalpy is less than difference in temperature times difference in entropy, that means that energy left the system.

What does ΔG stand for?

How much energy, both mechanical and heat, that was either added to or subtracted from a system.

What does ΔH stand for?

Change in enthalpy, or change in energy in the system.

What is enthalpy?

measure of the total energy of a thermodynamic system

What two things does energy have to do to be a thermodynamic system?

1. The thermodynamic system uses energy to create itself
2. The thermodynamic system must make room for itself by displacing it's environment and establishing its volume and pressure.

ΔH < 0 in other words, change in enthalpy is negative. Is reaction endothermic or exothermic

Exothermic, because it lost energy, therefore the energy was given off.

ΔH > 0 or change in enthalpy is positive, is reaction endothermic or exothermic?

Endothermic, because it gained energy, energy was put into it.

What does ΔS stand for?

change in entropy

What happens with energy when electrons go from a higher potential to a more stable configuration?

energy is released

exothermic

Distinguish between exergonic and endergonic reactions in terms of free energy change.

In an exergonic reaction, energy leaves the system and the reaction is spontaneous, ΔG is negative. In an endergonic reaction, ΔG is positive -- energy was added to the system and it is not spontaneous. If ΔG is zero, the equation is in equilibrium

Exergonic

reaction, energy leaves the system and the reaction is spontaneous, ΔG is negative.

Endergonic

Reaction, ΔG is positive -- energy was added to the system and it is not spontaneous.

Explain why metabolic disequilibrium is one of the defining features of life.

If there was metabolic equilibrium, no work would be able to be performed, no energy would be transferred, and life would not be possible. Thus metabolic disequilibrium. This can be expressed as a ΔG of zero

Explain how carbon's electron configuration explains its ability to form large,complex and diverse organic molecules.

It has four valence electrons which can form many covalent bonds, of different combinations of single and double bonds,and multiple carbon atoms can form long chains such as gasoline.

Describe 4 ways carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules.

Covalent bonds link carbon atoms together in long chains that form the skeletal framework for organic molecules. These carbon skeletons may vary in:
-Length
-Shape
-Number and Location of double bonds
-Other elements covalently bonded to available sites

Do amino functional groups function as acids or bases? Do amino functional groups attract or drop a proton?

bases, and they attract a proton

Do carboxyl functional groups function as acids or bases? Do carboxyl functional groups tend to attract or drop a proton?

acids and they tend to drop a proton

Name the 6 major functional groups found in organic molecules. ACCHPS

Amino, Carbonyl, Carboxyl, Hydroxyl, Phosphate, Sulfhydryl

Describe and draw the basic structure of the Amino functional group and outline the chemical properties of the organic molecules in which they occur.

Amines act as a base, they tend to attract a proton in solution, form with carboxyls to make amino acids

Describe and draw the basic structure of the Carboxyl functional group and outline the chemical properties of the organic molecules in which they occur.

acidic, tends to drop a proton, forms with amines to make amino acids Amino acids are linked together by covalent bonds that are formed between amino and carboxyl containing groups

Describe and draw the basic structure of the Carbonyl functional group and outline the chemical properties of the organic molecules in which they occur.

acts as an acid, tends to lose a proton in solution. found on aldehyde and ketone molecules. The carbonyl functional group is the site of reactions that link these molecules into more complex compounds like ribose

Describe and draw the basic structure of the Hydroxyl functional group and outline the chemical properties of the organic molecules in which they occur.

Hydroxyl groups act as weak acids. Highly polar, molecules with hydroxyl groups are soluble. Defining functional group of alcohols such as ethanol and methanol

Describe the basic structure of the Phosphate functional group and outline the chemical properties of the organic molecules in which they occur.

Phosphate groups carry two negative charges and they go from one molecule to another, the two negative charges often greatly affects the receiving molecule
When several phosphate groups are linked together, breaking O-P bonds between them releases large amounts of energy.

Describe and draw the basic structure of the Sulfhydryl functional group and outline the chemical properties of the organic molecules in which they occur.

Sulfhydryl groups are a sulfur atom bonded to a hydron atom, they link up with disulfides S-S bonds. In proteins, they form disulfide bonds that contribute to protein structure

Distinguish between a protein and a polypeptide.

1. A polypeptide is a linear polymer of amino acids, linked together by peptide bonds.
2. Proteins are functional entities composed primarily of one or more polypeptides and often non-polypeptide cofactors. A protein without its co-factors is known as an apoprotein.

Explain how a peptide bond forms between two amino acids.

An amino acid links with another amino acid through a condensation reaction to form a peptide bond
A peptide bond (amide bond) is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, causing the release of a molecule of water (H2O), hence the process is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acid

List and describe the four major components of an amino acid. Explain how amino acids may be grouped into 4 groups according to the physical and chemical properties of the R group.

1. amino group,
2. hydrogen
3. R group
4. carboxyl group
   (1) non-polar and neutral,
   (2) polar and neutral,
   (3) acidic and polar,
   (4) basic and polar.

Explain what determines protein structure and why it is important.

Protein structure is determined first by the gene that codes for that protein, and then by non-covalent interactions such as hydrogen bonding, ionic interactions, Van Der Waals forces, and hydrophobic packing.
Proteins serve many different functions because they are diverse in size and shape -- form follows function.

Explain how the primary structure of a protein is determined.

The primary structure refers to amino acid sequence of the polypeptide chain. The primary structure is held together by covalent or peptide bonds, which are made during the process of protein biosynthesis or translation. The two ends of the polypeptide chain are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end (NH2-group), which is the end where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation. The sequence of a protein is unique to that protein, and defines the structure and function of the protein.

Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary structure.

Hydrogen bonding between the carbonyl oxygen of one amino acid residue and the hydrogen on the amino group of another. Two types are:

1. ά-helix
   Formed from Hydrogen Bonds

There are 3.6 amino acid residues per turn of the helix.

Notice the regular helix shape.

This is drawn as a helix that follows the -N-C-C-N-C- backbone of the polymer

Alpha helices are often the basis of fibrous polymers (see below).

The Alpha helix was first discovered by Linus Pauling.

Right handed helix.

Second type of secondary protein structure

beta pleated sheet
Beta-pleated sheets are so called because of the 'pleated' or folds when view form the side.

The polypeptide chain is much more stretched out in comparison to the alpha helix.

This Beta-pleated sheet was discovered by Pauling and Corey.

This 'sheet' often has twists that increase the strength and rigidity of the structure. (Try twisting a sheet of paper to see this effect).

Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.

As you know that hydrogen bonding aids the formation of the secondary structures. Once these structures are formed (ie alpha helix, beta-sheet, beta-turn), the R groups now can interact with other R groups. In the tertiary structure, the weak interactions (ie hydrogen bonding, ionic bonding, van der waals interactions) aid in the 3D structure of the protein. Disulfide bonds form in the tertiary structure which add extra stability to the overall 3D shape of the protein.

List four conditions under which proteins may be denatured.

1 Extreme heat

2. high or low pH
3. ionization of liquid medium
4. A change in environment. The last one needs a little more explanation. If a protein is meant for a liquid-liquid environment, and it is brought into an air-liquid environment, it may denature. Proteins form because of the folds created from hydrophilic and hydrophobic folding. If there is no water in which these bonds form, the protein will denature.

Explain how molecular chaperones may assist in proper folding of proteins.

Molecular chaperones are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the structures are performing their normal biological functions having completed the processes of folding and/or assembly

Describe the function of enzymes in biological systems

they act as catalysts to reactions, thus lowering the energy required for a reaction to proceed to formation of product.