Week 3 Review

Question 1

What is energy and matter?

Answer 1

Energy is the ability to work, while matter is a substance made up of various types of particles that occupy physical space.

Question 2

What are the 4 most abundant elements of life? Which is the most to least abundant?

Answer 2

Most to least 4 most abundant elements of life: (CHNO)

Carbon
Hydrogen
Nitrogen
Oxygen

Question 3

How do atoms combine to form molecules? What is the role of electron shells?

Answer 3

• The number of elections in an electron shell determines the stability of an atom
• An electron shell is the space in which electrons orbit around an atom
• Atoms with incomplete outer shells/electrons interact with other atoms, forming bonds (molecules)

Question 4

What are the major types of bonds? How are they formed?

Answer 4

Ionic bonds:
Attractions between opposite charges. Ions are formed by giving/accepting electrons

Covalent bonds:
Atoms share one or more electrons

Hydrogen bonds:
Between molar molecules

Question 5

What is the difference between organic vs. inorganic molecules? Classify H2O, CO2, and C6H12O2 as organic or inorganic.

Answer 5

Organic: always contains carbon and hydrogen
Inorganic: typically lack carbon

H2O = inorganic b/clack of carbon
CO2 = inorganic b/c lack of hydrogen
C6H12O2 = organic

Question 6

What are the 4 major types of biomolecules? Explain each in terms of their monomer and
polymer, function, and typical structure.

Answer 6

Carbohydrates
Function: cell structures and energy source
Monosaccharides (monomers): simple sugars made up of 3-7 carbons
Polysaccharides (polymers): consist of tens or hundreds of monosaccharides

Lipids
Function: energy storage, insulation, waterproofing, hormones, hardening of membranes
Monomer: glycerol
Polymer: fatty acids

Proteins
Function: makeup structure of cells, synthesis of enzymes
Monomer: amindo acid (AA)
polymer= protein
Primary protein structure is a chain of amino acids
Secondary protein structure occurs when hydrogen bonds hold the sequence of amino acids
Tertiary protein structure occurs when certain attractions are present between alpha helices and pleated sheets
A quaternary protein structure is a protein consisting of more than one amino acid chain

Nucleic Acids
Function: genetic material, energy
Monomer: nucleotides
Polymer: DNA, RNA, and ATP

Question 7

How is ATP generated?

Answer 7

Substrate level phosphorylation: Synthesis of ATP by direct transfer of a phosphate group from a substrate to an ADP

Oxidative phosphorylation: The energy released from the transfer of electrons from one compound (oxidation) to another (reduction)
Electron transport chain

Photophosphorylation: energy released from the transfer of electrons of chlorophyll through carrier molecules to generate ATP
Light causes chlorophyll to give up electrons

Question 8

What are redox reactions and what is the role of electron carriers?

Answer 8

Oxidation: removal of electrons
Reduction: addition of elections

Redox reaction: an oxidation reaction coupled with a reduction reaction

Electron carriers carry electrons and deliver them to another molecule

Question 9

What is chemiosmosis? How is ATP generated via this method?

Answer 9

Electron carriers transport electrons to an electron transport chain and protons are pumped through channels of the cell membrane, forming an area of high concentration on one side of the membrane and an area of low concentration on the other side of the membrane

After the proton (H+) gradient is created, protons diffuse down the gradient through a transport protein called ATP synthase.

As protons move down the ATP synthase, energy is generated to couple ADP and P to make ATP

Question 10

Where does chemiosmosis take place in mitochondrion, chloroplasts, and prokaryotes?

Answer 10

Prokaryotes: cell membrane
Mitochondrion: inner membrane
Chloroplasts: thylakoids membrane

Question 11

What are synthesis vs decomposition reactions?

Answer 11

Synthesis: atoms, ions, or molecules combining to form new, larger molecules

Decomposition: Molecules splitting into smaller molecules, ions, or atoms

Question 12

How do collision theory and activation energy affect the rate of a chemical reaction?

Answer 12

Collision theory: all atoms, ions, and molecules are continuously moving and colliding with one another
- The rate of the chemical reaction depends on the frequency of collisions between atoms, ions, and molecules

Activation energy: the amount of energy needed to disrupt the electron configuration so electrons can be rearranged
- The higher the activation energy, the slower the chemical reaction will be

Question 13

Do enzymes lower or increase activation energy? How is this depicted in a graph (reaction coordinate vs energy)

Answer 13

Enzymes lower activation energy. In a graph, the one with an enzyme will have a lower energy of activation. The one without an enzyme will have a higher hill for activation energy.

Question 14

What are the characteristics of enzymes and how are they named?

Answer 14

• Biological catalysts that change the rate of a reaction without being consumed
• Lowers the activation energy
• Specific and efficient

Nomenclature:
Usually: substrate + suffix (-ase) Ex: lactase digests lactose
Named by type of class: reactions that they undergo

Question 15

What is the composition of enzymes?

Answer 15

• Mainly composed of protein
• The protein part is called the Apoenzyme
• Some proteins contain cofactors that are non-proteins (coenzymes that activate the apoenzymes)
• Holozyme is the name for the whole active enzyme

Question 16

Explain the catalytic activity, including its cyclic nature.

Answer 16

An active site available on an enzyme is where the substrate will bind

The substrate binds to an available active site on an enzyme

The product will be made

Product is released

The enzyme is recycled after the product is released

Question 17

Compare and contrast the lock and key vs induced fit model. Which model is most likely true?

Answer 17

Lock and key:
- The key is the substrate and the lock is the enzyme: they fit like a lock and key
- As soon as the substrate (key) binds to the enzyme (lock), it will catalyze a reaction
- The substrate is specific to the enzyme and the enzyme does not change shape

Induced fit:
- The substrate is specific to the enzyme and the enzyme changes its shape, engulfing the substrate and holding it in place

The inducted fir model is most likely true

Question 18

What factors influence activity? Explain the role of each:
* cofactors, temperature, pH, substrate concentration, inhibitors (competitive,
noncompetitive/ allosteric)

Answer 18

Cofactors: help substrate bind to the enzyme

Temperature: molecules move faster at higher temperatures. Enzyme denatures (loss of tertiary structure) when not at optimal temperature.

pH: above or below optimal pH changes the shape, extreme change denatures the enzyme

Substrate concentration: as substrate concentration increases, enzyme activity increases until the maximum rate

Inhibitors:
Competitive inhibitors: bind active site and prevent substrate binding
Noncompetitive inhibitors: (reversible)

Bind to another part of enzyme = allosteric site (changes the Enzyme’s shape in the process)

Question 19

Compare and contrast catabolism and anabolism. What is the role of ATP in both of these processes? Which uses hydrolysis and dehydration synthesis?

Answer 19

Catabolism: decomposition reactions in a cell
- Releases energy (ATP)
- Hydrolysis

Anabolism: synthesis of molecules in a cell
- Uses energy (ATP)
- Dehydration synthesis

Question 20

What are the phases of cellular respiration?

Answer 20

Glycolysis
Krebs Cycle
ETC and chemiosmosis

Question 21

What molecules are involved in each phase of cellular respiration? What major products are made?

Answer 21

Glycolysis: glucose is made into 2 pyruvate molecules

Krebs Cycle: pyruvic acid (pyruvate) is oxidized into 3 CO2

ETC and chemiosmosis: NADH and FADH2 into NAD+, FAD, water, and ATP

Question 22

Where does each phase of cellular respiration take place in prokaryotes and eukaryotes?

Answer 22

Prokaryotes:
Glycolysis = cytoplasm
Krebs Cycle = cytoplasm
ETC and chemiosmosis = plasma membrane

Eukaryotes:
Glycolysis = cytoplasm
Krebs Cycle = mitochondrial matrix
ETC and chemiosmosis = mitochondrial inner membrane

Question 23

Which phases of cellular respiration produce ATP by substrate-level phosphorylation/oxidative phosphorylation?

Answer 23

Glycolysis: substrate-level phosphorylation

Krebs Cycle: substrate-level phosphorylation

ETC and chemiosmosis: oxidative phosphorylation

Question 24

How much ATP is made by substrate-level phosphorylation and oxidative phosphorylation?

Answer 24

Substrate level phosphorylation: 4 ATP
- 2 ATP from glycolysis, 2 from Krebs cycle

Oxidative phosphorylation 34 ATP

Question 25

What is the overall yield after each phase? At the end of aerobic respiration?

Answer 25

Glycolysis: 2 ATP, 2NADH, 2 Pyruvate

Krebs Cycle:
Per pyruvate: 4 NADH, 1 FADH2, 1 ATP, 3 CO2
Per glucose: 8 NADH, 2 FADH2, 2 ATP, 6 CO2

ETC and chemiosmosis: 34 ATP

Question 26

How does the yield differ between eukaryotes and prokaryotes and why?

Answer 26

Eukaryotes = 36 ATP
Prokaryotes = 38ATP

In prokaryotes, they don’t have organelles so they don’t have to spend extra energy for transportation.

Question 27

What are other types of glycolysis and how do they relate to metabolism?

Answer 27

Pentose-phosphate pathway:
- Operates simultaneously to glycolysis
- Yields 5-carbon sugars
- Used for nucleotide synthesis
- D3P enters glycolysis

Enter-Deuderoff pathway:
- Alternate to glycolysis yields less ATP but more NADH
Found in some aerobes

Question 28

Compare and contrast aerobic and anaerobic respiration. What are the last electron acceptors for each type of respiration?

Answer 28

Aerobic:
- Uses oxygen
- The last electron acceptor is oxygen

Anaerobic:
- Doesn’t use oxygen
- The last electron acceptor is an inorganic molecule (other than O2) and sometimes an organic molecule

Question 29

What would be the result if certain molecules interfered with each phase of cellular respiration?

Answer 29

They can disrupt the process of ATP production and even kill the cell

If molecules are interfering with each phase of cellular respiration, then the process would slow down or halt. For instance, the Kreb Cycle requires Oxaloacetate to combine with acetyl-CoA to form Citrate. If there is not enough Oxaloacetate in the process, then the Kreb Cycle can not proceed. The electron transport chain requires O2 as the terminal electron acceptor. If O2 is not available, then the ETC also can not proceed further and will halt.

Question 30

Why do some cells undergo fermentation? What phase does fermentation share with cellular respiration?

Answer 30

Some cells undergo fermentation when there is an absence of oxygen and no ETC or terminal electron acceptor. This is an alternate way to oxidize NADH. Glycolysis is the cellular respiration phase sharing fermentation.

Question 31

Name examples of bacteria and their fermentation products.

Answer 31

Candida and Saccharomyces - ethanol and CO2 (beer, bread)

klebsiella candida- formic acid, lactic acid, ethanol, acetoin (chardonnay wine)

Streptococcus and Lactobacillus - Lactic Acid (sauerkraut, yogurt, cheese)

Escherichia shigella- acetic, formic, lactic, and succinic acid (vinegar, cosmetics, pharmaceuticals)

Question 32

How are lipids, proteins, and carbohydrates catabolized? Where do these biomolecules enter the phases of cellular respiration?

Answer 32

Carbohydrates: Broken down by exoenzyme into glucose. They enter in glycolysis
- Starch (polysaccharide) uses amylase to break into glucose
- Lactose (disaccharide) uses lactase to break into galactose and glucose
- Sucrose (dissarchide) uses sucrase to break into fructose and glucose

Lipids: They are broken down into fatty acids and glycerol. Fatty acids are converted into acetyl CoA by beta-oxidation and enter directly into the Krebs cycle. Glycerol is converted into G3P (the intermediate molecule in glycolysis) and is made into pyruvic acid

Protein: Broken down by exoenzyme into amino acids. Amino acids can be further broken down using specific enzymes. The enzyme deaminase removes the amino group in the amino acid, making ammonium (NH4+), which enters the Krebs Cycle. An enzyme called decarboxylase removes the carboxyl group from the amino acid