Unit 1 - Chemistry of Life

Question 1

What is an element?

Answer 1

Substances that can’t be broken down into simpler substances by chemical means

Question 2

What is an atom?

Answer 2

The smallest unit of an element that retains its characteristic properties (subatomic particles like electrons are not unique anymore)

Question 3

Why is water polar?

Answer 3

Water is made up of two partially positive hydrogen atoms and one partially negative oxygen atom. First of all water had polar covalent bonds because the electrons are shared unequally between oxygen and hydrogen due to differing electronegativities. The molecule also has a polar structure as witnessed by its bent shape. This is due to the lone pairs on oxygen. Polar bonds and a polar structure constitute a polar molecule.

Question 4

What are the properties of water? (8)

Answer 4

Cohesion and adhesion

High surface tension (bugs can walk on water, water forms raindrops)

High heat capacity/specific heat

High melting/boiling points

Expansion on freezing

Ice is less dense than water so it floats

Good polar solvent that dissolves other polar or charged substances

Neutral pH of 7 (concentration of H+ and OH- are equal)

Question 5

What is cohesion?

Answer 5

Attraction to molecules of the same substance

Question 6

What is adhesion?

Answer 6

Attraction to molecules of a different substance

Question 7

What is transpiration and how does cohesion affect it?

Answer 7

Transpiration is when water evaporates off a leaf.

Cohesion, or attraction between water molecules in this case, pulls neighboring water molecules upwards until eventually they all move into the air

Question 8

What is capillary action and how does cohesion/adhesion affect it?

Answer 8

Capillary action is when water rises up thin vessels such as plant roots, stems, or trunks. Through adhesion, water molecules stick to other polar substances - the vessel. Through cohesion, water molecules stick to each other. These attractive forces draw up water molecules in a chain like fashion that enables water to move upwards.

Question 9

What does it mean to have a high heat capacity/specific heat? Why does water have this property?

Answer 9

Water can absorb a lot of heat without experiencing a substantial raise in temperature.

Heat capacity depends on both mass and type of substance. Specific heat only depends on type of substance

This property arises from water’s strong hydrogen bonds which take a lot of heat to break before the molecules can start moving faster to increase the temperature

Question 10

What are the effects of water’s high heat capacity? (3)

Answer 10

Oceans/bodies of water maintain a stable temperature so they can sustain marine organisms on hot or cold days. Water absorbs heat during the day and releases it at night

Water is essential for cellular structures so it’s important that it doesn’t boil away on hot days

Water makes up the bodies of many organisms so its high heat capacity enables them to keep a constant body temperature

Question 11

What is significant about the density of water? What are the environmental effects of this property?

Answer 11

Solid water is less dense than liquid water unlike most substances. This is because ice has a crystalline structure that keeps molecules far apart. When ice melts, the molecules slip closer together

Water is most dense at 4 C - 1.0 g/mL

Ice floats on the surface of bodies of water, allowing animals to live underneath. If ice was denser than water, it would sink to the bottom and freeze the water solid which would kill aquatic life.

Question 12

What are the essential elements to life?

Answer 12

C, H, O, N

Question 13

What are hydrophobic substances?

Answer 13

Substances that are insoluble/can’t dissolve in water because they don’t form hydrogen bonds.

EX: nonpolar substances like oils

Question 14

What are hydrophilic substances?

Answer 14

Substances that are soluble in water because they form hydrogen bonds

EX: ionic compounds, polar molecules (like sugars) and some proteins

Question 15

What is a buffer and how do they work?

Answer 15

Substances that minimize changes in pH (made up of a weak base and weak acid)

If an acid is added and hydrogen ions are in excess, the weak base component accepts them from solution. If a base is added and hydrogen ions are depleted, the weak acid component donates them to the solution

EX: H2CO3 is an important buffer in living systems that moderates pH changes in blood plasma and the ocean

Question 16

What is evaporative cooling and how does it work?

Answer 16

As liquid water evaporates, the surface that remains cools down.

In evaporation, the water molecules with the greatest kinetic energy and thus highest temperature leave as vapor which leaves the molecules with the least kinetic kinetic and thus lowest temperature behind.

Question 17

What properties of carbon make it so important to life?

Answer 17

It has 4 valence electrons meaning it can form up to 4 covalent bonds (including single, double, or triple bonds)

This means carbon can form large molecules that can be chains, ring shaped, or branched

Question 18

What are functional groups?

Answer 18

Groups attached to the carbon skeleton of an organic molecule that determine its chemical properties and behavior

Question 19

Carbohydrates

Answer 19

Structure: C, H, O

Function: serve as fuel (short term energy storage) and building material

Monomers: Monosaccharides (EX: glucose, fructose, ribose)

Polymers: Disaccharides (EX: lactose, maltose, sucrose) and polysaccharides (starch, glycogen, cellulose, chitin)

Bond: Glycosidic linkages between monomers

Question 20

What are the types of polysaccharides and their function?

Answer 20

Storage polysaccharides include starch and glycogen. They are hydrolyzed when needed to provide sugar (energy) for cells. Starch is found in plants and glycogen is found in animals in muscle and liver cells

Structural polysaccharides include cellulose and chitin. They are used as building material for structures that protect the cell/organism. Cellulose is a major component of plant cell walls. Chitin is found in the exoskeleton of arthropods and cell walls of fungi

Question 21

Lipids

Answer 21

Structure: C, H, O. Lipids are hydrophobic compounds consisting of hydrocarbon/ nonpolar regions

Function: long term energy storage (fats), insulation/protection of vital organs, structural components of cell membranes (phospholipids), and signaling molecules (hormones)

Monomers: Glycerol and three fatty acid tails. Altogether it’s called triglyceride or triglycerol

Polymers: Lipids (EX: fats, oils)

Bond: Ester linkage between glycerol and the fatty acids

Question 22

Saturated vs Unsaturated vs Trans fats?

Answer 22

Saturated: maximum # of hydrogens, packed close together, all single bonds between carbons, solid at room temperature, EX: butter

Unsaturated: has some double bonds between carbons, not packed closely enough together to solidify, liquid at room temperature, kinks/bends in the fatty acid chains, EX: oil

Trans: when hydrogens are synthetically added to unsaturated fats to form saturated fats

Question 23

What are steroids?

Answer 23

Carbon skeleton made up of four rings that are fused together

EX: Cholesterol (common component of animal cell membranes). Cholesterol produces hormones like estrogen and testosterone

Question 24

What is the structure of phospholipids?

Answer 24

Hydrophilic head (includes a phosphate group) and hydrophobic tail (two fatty acid tails with one bent). They are arranged in a phospholipid bilayer with tails facing the interior and heads facing the cytosol/extracellular environment.

Question 25

Proteins (elements, function, monomer, polymer, bond, examples)

Answer 25

Structure: C, H, O, N

Function: perform most of the work in your cells (enzymes, movement, membrane receptors)

Monomers: Amino acids
20 different amino acids that vary in their R groups or side chains
All of them consist of a carbon atom bonded to a hydrogen atom (top), an amino group NH2 (left), a carboxyl group COOH (right) and an R group (bottom)
Amino acids differ in composition of elements, charge (positive, negative, neutral), polarity (polar, nonpolar), and shape (long chain, short chain, ring shape)

Polymers: Polypeptides that fold into proteins (EX: hemoglobin)

Bond: peptide bonds between NH2 and COOH of different amino acids

Question 26

Primary structure of proteins

Answer 26

Linear sequence of amino acids; determines final 3D structure of the protein because different amino acids will be differently attracted to each other and thus form different bonds which leads to a different structure

Question 27

Secondary structure of proteins

Answer 27

Interactions between components of the polypeptide backbone that fold and coil the polypeptide chain; stabilized by hydrogen bonds

alpha helix has a coiled shape like a slinky
beta pleated sheet has an accordion shape

Question 28

Tertiary structure of proteins

Answer 28

Interactions between side chains that coil and fold the polypeptide chain; hydrophobic interactions (cluster away from water), hydrogen bonds (hold polar side chains together), van der Waals forces (hold nonpolar side chains together), ionic bonds (hold positively and negatively charged side chains together), and disulfide bridges

Globular proteins like enzymes are held in position by these R group interactions

Question 29

Quaternary structure of proteins

Answer 29

Multiple polypeptide chains fold into one large protein (only applies to some proteins)

Subunits come together

Question 30

How does protein structure affect function?

Answer 30

Most proteins function by recognizing and binding with other molecules based on shape. For example, substrates fit into the active site of enzymes. If the structure of proteins change (via a mutation that affects the primary structure aka sequence of amino acids) the protein will become nonfunctional

Question 31

How does the environment affect protein structure and function? (Hint: denaturation)

Answer 31

Extreme changes in pH, temperature, or salt concentration can lead to denaturation which is when proteins lose their shape and ability to function because their weak chemical bonds are destroyed and the protein unravels

Enzymes often have a specific temperature or pH level that is ideal for activity. In humans, this is 35 C and pH = 7

Question 32

Nucleic Acids

Answer 32

Structure: C, H, O, N, P

Function: store genetic material in the form of DNA that can be inherited by offspring; also codes for proteins that determine phenotype

Monomers: Nucleotides (5 carbon sugar, negatively charged phosphate group, nitrogenous base)

Polymers: Nucleic acids (EX: DNA and RNA)

Bonds: hydrogen bonds between bases and covalent bonds(called phosphodiester linkages) between sugars + phosphate groups in the sugar phosphate backbone

Directionality - the two sugar phosphate backbones of DNA run anti parallel in opposite 5’ —> 3’ directions

Question 33

How does a nucleotide differ from a nucleoside?

Answer 33

A nucleotide consists of a nitrogenous base, a phosphate group, and a sugar. A nucleotide does not have a phosphate group

Question 34

Name differences between DNA and RNA

Answer 34

DNA contains deoxyribose and RNA contains ribose.

DNA is double stranded while RNA is single stranded. The two DNA strands are anti parallel in directionality.

DNA consists of the bases A, T, C, G while RNA consists of A, U, C, G

DNA stores hereditary information and programs all the cell’s activities; carries genes which are segments on DNA. RNA carries genetic instructions for building proteins from DNA to ribosomes

Question 35

Pyrimidine vs Purine?

Answer 35

Pyrimidines have one ring (C, T, U) and purines have two rings (A, G). One purine must bind with one pyrimidine to keep a uniform width of DNA

Question 36

How many hydrogen bonds do adenine and thymine form?

Answer 36

Two

Question 37

How many hydrogen bonds do cytosine and guanine form?

Answer 37

Three

Question 38

Name similarities between DNA and RNA

Answer 38

Both DNA and RNA have three components – a sugar, a phosphate group, and a nitrogenous base — that form nucleotide units.

Both are linear molecules with 5’ and 3’ ends.

Question 39

Amphipathic

Answer 39

Phospholipids are amphipathic meaning they have both a hydrophobic and hydrophilic region

Question 40

What happens to the protein in denaturation?

Answer 40

The hydrogen bonds in the protein’s secondary, tertiary, and quaternary levels break, leaving only the primary structure. The protein unravels, losing its characteristic 3D structure, and thus becomes nonfunctional.

Question 41

What level of protein structure are peptide bonds?

Answer 41

Primary

peptide bonds are between amino acids

Question 42

What allows insects to walk on water?

Answer 42

Hydrogen bonds between molecules at the surface of the water provide surface tension, which allows the water surface to deform but not break under the insect.