SBI-4U1 Exam Review

Biochemistry

1.  Name and draw the functional groups discussed in class

2.  Name and draw the linkages discussed in class

3.  Draw structural formulas for the following:

  1. 1,4-dibromo-3-hexanol
  2. propanoic acid
  3. 2-butyl methyl ether (aka 2-methyoxybutane)
  4. butyl propanoate
  5. 3-ethyl-1-methyl-2-pentene
  6. 6-bromo-4-propyl-2-hexyne
  7. 3-chloro-butanamide
  8. 1,3-dimethylcyclohexane
  9. 1,3-dimethylbenzene

4.  Name the following molecules:

a) d)

b) e)

c) f)

5.  What is a structural isomer?

Same formula, different arrangement of atoms.

6.  Give an example of a pair of structural isomers. Write their chemical formulas, and draw their structural formulas.

Glucose and fructose, C6H12O6

7.  Name and describe the biological macromolecules discussed in class. Include the following: constituent monomers, linkages that join the monomers, and sketch an example of each.

Lipids (triglycerides) – fatty acid + glycerol, ester linkage

Nucleic acids – nucleotides, phosphodiester bond

Protein – amino acids, peptide linkage

Carbohydrates – monosaccharide, glycosidic linkage

Metabolic processes

1.  What is the difference between passive transport, and active transport? Give an example of a substance that is moved across the cell membrane by each of these methods.

Passive – moves substances along their concentration gradients; no energy required. Example: oxygen into cells

Active – moves substances against their concentration gradients; energy is required. Example: sodium potassium pump.

2.  What is ATP, and how does it provide energy for cellular processes?

Adenosine triphosphate. Primary energy-providing molecule in a cell. Energy is released by hydrolyzing the bond between the 2nd and 3rd phosphate groups.

3.  What are oxidation and reduction? Give (general) examples of each.

Oxidation – Loss of electrons. Ex. Can also be loss of H, loss of energy, gain of O

Reduction – Gain of electrons Ex. Gain of H, gain of energy, loss of O

4.  What type of macromolecule is an enzyme? What function does an enzyme have? How is it important for metabolism?

Protein. Biological catalyst, specific to a certain substrate. Lowers the activation energy for reactions to occur. Important because all metabolic reactions are catalyzed; would not occur without the presence of an enzyme.

5.  Name and describe the four stages of cellular respiration, in order.

What goes into each stage? What comes out of each stage? What coenzymes are involved? Where does each stage occur? How is this stage important for the overall goal of cellular respiration?

In / Out / Coenzymes / Where / Importance
Glycolysis / glucose / pyruvate,
ATP,
NADH / NAD+ / Cytoplasm / Breaks C-C bonds of glucose and stores the free energy in NADH and FADH2
Minimal ATP production
Pyruvate ox. / pyruvate / Acetyl coA
CO2
NADH / NAD+ / Mitochondrial matrix
Krebs / Acetyl coA / CO2,
ATP
NADH
FADH2 / NAD+
FAD / Mitochondrial matrix
ETC / Electrons
(from FADH2, NADH) / ATP
NAD+
FAD / Inner membrane / Bulk of ATP is produced via chemiosmosis

6.  In what stage is most of the ATP synthesized in cellular respiration, and by what enzyme?

Electron transport/chemiosmosis. ATP synthase.

7.  What force drives the bulk synthesis of ATP as described above?

Electrochemical gradient (proton-motive force)

8.  What is the overall equation for cellular respiration?

C6H12O6 + O2 à 6CO2 + 6H2O + energy

  1. Where is each of the reactants utilized?

Glucose – Glycolysis

Oxygen – Electron transport chain – final electron acceptor

  1. Where is each of the products produced?

Carbon dioxide – Pyruvate oxidation (2) and Krebs (4)

9.  List the components of the electron transport chain, in order

NADH dehydrogenase, ubiquinone, cytochrome b-c1 complex, cytochrome C, cytochrome oxidase complex

.

10.  What is anaerobic respiration, and why does it occur?

Anaerobic “respiration” refers to alternative metabolic pathways that occur when oxygen is not available.

11.  Describe the two types of anaerobic respiration.

  1. Ethanol fermentation – yeast, bacteria. Pyruvate is decarboxylated, then reduced by NADH. End product: ethanol, and NAD+ is regenerated so glycolysis can continue.
  2. Lactic acid fermentation – humans. Pyruvate is reduced by NADH. Product: lactic acid, and NAD+ is regenerated.

12.  Label the structures of a chloroplast:

13.  Name and describe the two stages of photosynthesis.

14.  What goes into each stage? What comes out of each stage? What coenzymes are involved? Where does each stage occur? How is this stage important for the overall goal of photosynthesis?

In / Out / Coenzymes / Where / Importance
Light reactions / Light energy
H2O / NADPH
ATP
O2 / NADP+ / Thylakoid membrane / Stores solar energy as chemical energy.
Produces the NADPH and ATP required for carb. Production
Light-independent reactions (Calvin cycle) / CO2
ATP
NADPH / G3P
NADP+ / Stroma / G3P is used to build glucose monomers

15.  Where does each of the two stages occur? Same as above

16.  What is the overall equation for photosynthesis?

6CO2 + H2O + light energy à 6O2 + C6H12O6

  1. Where is each of the reactants utilized?

Carbon dioxide – Calvin cycle. Carbon is fixed by rubisco.

Water – Electron transport chain (light rxns) – Water is split by Z protein to replenish electron deficit in photosystem I. Also Calvin.

Light energy – Photoexcitation in the ETC – photosystems I and II

  1. Where is each of the products produced?

Oxygen – Electron transport chain. Produced when water is split.

Glucose – G3P from Calvin is used to synthesize glucose.

17.  What is the pigment at the reaction centre of a photosystem, and what role does it play?

Chlorophyll a – absorbs energy, electrons get excited and pass along the ETC

18.  What is the function of the pigments in the antenna complex of a photosystem?

Absorb other wavelengths of light and transfer their energy to chlorophyll a.

19.  What is rubisco, and what reactions does it catalyze?

Must abundant enzyme in the world; catalyzes the fixation of carbon dioxide to RuBP in the Calvin cycle. It also catalyzes the fixation of oxygen to RuBP (photorespiration).

20.  What is a C3 plant?

A “typical” plant – one that produces a 3-C intermediate first in the Calvin cycle. Particularly susceptible to photorespiration.

21.  Describe the relationship between carbon dioxide concentration and photosynthetic rate in a C3 plant.

As the concentration of CO2 rises, the photosynthetic rate increases. This will occur until the enzymes of the Calvin cycle are saturated, at which point a plateau will then occur. Generally, the higher the concentration of ambient CO2, the higher the plateau

22.  Describe the relationship between light intensity and photosynthetic rate in a C3 plant. (Include a definition of the light-saturation point).

At low light intensities, light intensity limits the photosynthetic rate. The amount of NADPH and ATP produced depends on availability of light. As light intensity increases, the light-saturation point is reached: this is the point where light is no longer the limiting factor – it will be either CO2 or temperature. The Calvin Cycle enzymes are saturated so increasing NADPH and ATP will not increase the overall rate of photosynthesis.

23.  List the components of the photosynthetic electron transport chain, in order.

Photosystem I, plastoquinone (Q cycle), b6-f complex, plastocyanin, photosystem II, ferredoxin, NADP reductase

24.  Mitochondria and chloroplasts have a structural feature in common: what is this feature?

Double membrane structure (inner and outer). Ideal for building up H+ reservoir for chemiosmosis

25.  What is the endosymbiotic theory? Describe how each partner in the symbiotic relationship would benefit from this type of relationship.

The theory that mitochondria and chloroplasts were once free-living organisms that were engulfed by a primitive cell. Supported by independent genomes and replication machinery.

Host cell benefits from the energy produced by mitochondria, and the glucose generated by chloroplasts. Engulfed organelle has the benefit of shelter and safety.

Molecular genetics

1.  What is the difference between mitosis and cytokinesis?

Mitosis = The division of the nucleus.
Cytokinesis = the division of the cytoplasm, organelles, and membrane.

2.  Describe the structure of DNA.

Two strands of deoxyribonucleotides, hydrogen bonded together, and running anti-parallel to one another. Nucleotides are connected by phosphodiester bonds between the sugars and phosphates. Molecule twists into a helical shape.

3.  What is complementary base-pairing?

Bases of opposite strands pair predictably. Each pair contains one purine and one pyrimidine.

A-T

G-C

In RNA, A pairs with Uracil instead of with T

4.  What is the central dogma of molecular biology?

DNA à RNA à protein

5.  Complete the following table by describing the events of each process:

Initiation / Elongation / Termination
DNA replication / Helicase unzips the double strands. Polymerase III binds / DNA Pol III adds free nucleotides in the 5’ to 3’ direction / DNA Pol falls off
Transcription / RNA Polymerase recognizes a promoter sequence and binds / RNA Pol adds free RNA nucleotides in the 5’ to 3’ direction / RNA Pol recognizes a specific termination sequence
Translation / Ribosome recognizes 5’ cap in eukaryotic mRNA and binds / Amino acids are brought to the ribosome by tRNAs / Stop codon is recognizes. Ribosome disassembles.

6.  Name the enzymes involved in DNA replication, and list their functions.

  DNA helicase - Breaks H-bonds between DNA strands /   DNA polymerase III – Adds on deoxyribonucleotides to form a new DNA strand.
  DNA gyrase – Relieves tension caused by DNA strands unwinding around each other. Does this by cutting and re-ligating the DNA strands. /   DNA polymerase I – Removes RNA primers and replaces them with deoxyribonucleotides. Also proofreads the newly-formed strand. Excises any erronenously-incorporated nucleotides and replaces them with correct ones.
  single-stranded binding proteins – Binds to the unpaired bases once helicase unwinds the strands. Prevents re-annealing of strands /   DNA ligase – Forms phosphodiester bonds to join the sugar phosphate backbones of DNA strand fragments.
  RNA primase - Produces small RNA primers to provide a free 3’ end for elongation to occur /   DNA telomerase – In prokaryotes, and in eukaryotic germ line cells, prevents the shortening of telomeres during successive rounds of replication.

7.  Name the enzymes involved in transcription, and list their functions.

RNA polymerase – Unwinds the DNA. Adds ribonucleotides to the growing strand

8.  How does the information in mRNA direct the production of a polypeptide? What organelles/molecules are involved in this process? What is the name of this process?

·  mRNA is read in triplets called codons

·  codons dictate the amino acids that are to be incorporated

·  ribosome reads the codons, tRNA brings appropriate amino acid

·  process is translation

9.  What is the genetic code? What does it mean to say that the genetic code is “redundant”?

The genetic code is the “translation” dictionary from RNA to amino acid.

10.  How is protein synthesis different in a eukaryotic cell, as compared with a prokaryotic one?

Eukaryotes – Possess membrane-bound organelles. Transcription and translation occur in separate parts of the cell. Post-transcriptional modifications are required, and the ribosome recognizes the 5’ cap on the transcript.

Prokaryotes – Transcription and translation are coupled. Prokaryotic genes lack introns and are not processed after transcription. The ribosome recognizes a sequence called the Shine Dalgarno sequence.

11.  Name and describe the types of point mutations.

Insertion – A base is inserted

Deletion – A base is deleted

Substitution – A base is switched out for another

12.  What is a frameshift mutation? Which type(s) of point mutations can result in a frameshift?

A mutation that results in a shift of the reading frame. Insertions and deletions can result in a frameshift.

13.  What are silent, nonsense, and missense mutations?

Silent – No effect on protein structure

Nonsense – One amino acid is substituted for another.

Missense – A codon is converted into a stop codon. Protein synthesis is prematurely truncated.

14.  Gel electrophoresis is a method that separates DNA fragments according to their sizes, measured in base pairs (or kb – 1000 bp), within a gel matrix:

  1. What causes the migration of fragments?

A current is applied.

  1. In which direction will fragments migrate?

DNA is negatively charged. It will migrate away from the negative electrode, towards the positive.

  1. Which fragments will migrate the farthest?

The smallest will migrate farthest.

15. 

  1. What is recombinant DNA?

A fragment of DNA composed of DNA from two or more different sources.

  1. Describe the following, and how they are used in producing recombinant DNA:
  2. Restriction endonucleases

“Molecular scissors” – Cut desired DNA fragments

  1. DNA ligase

“Molecular glue” – Ligate fragments together by forming phosphodiester bonds between the backbone fragments

  1. Plasmids

Serve as vectors – vehicles for carrying the recombinant DNA into a biological system where it can then be transcribed and translated.

  1. Describe two applications of recombinant DNA.

Producing synthetic proteins, such as insulin.

Conferring pesticide resistance to plants.

16.  What is Hardy-Weinberg equilibrium, and what is the equation that describes it? Make sure to define all of the variables and terms in the equation.

States that allele frequencies do not change from generation to generation, within a population.

p2 + 2pq + q2 = 1

p2 = genotype frequency of homozygous dominant (AA)

2pq = genotype frequency of heterozygous Aa

q2 = genotype frequency of homozygous recessive (aa),

where p = allele frequency of A and q = allele frequency of a

17.  Two alleles for a locus A exist in a population: A and a. Homozygous dominant individuals make up 49% of the population.

  1. What are the allele frequencies for A and a?

AA = p2 = 0.49 à p = 0.7

Therefore allele frequency of A is 0.7, or 70%

Allele frequency of a is 1-0.7 = 0.3 = 30%

  1. How much of the population is Aa, and how much is aa?

Aa = 2pq = 2(0.7)(0.3) = 0.42 or 42%

aa = q2 = (0.3)2 = 0.09 or 9%

18.  What conditions must be met in order to maintain Hardy-Weinberg equilibrium?

·  large population

·  equal mating opportunities

·  no mutations occur

·  no migration occurs

·  no natural selection