Chapter 4 - Cellular Metabolism

Question 1

Metabolism and types of reactions

Answer 1

all chemical reactions in the body

Types of reactions: 
- Anabolism
- Catabolism

- About 60% of energy released from catabolic reactions is released as heat, with the rest being used as energy(ATP) for cellular processes or to build smaller molecules into larger ones

Question 2

Type of Anabolic Reaction

Answer 2

dehydration synthesis; joins molecules by removing water molecules

- Joining monosaccharides together forms 1 water molecule
- Joining a glycerol head(takes 3 -H) and 3 fatty acid molecules(-OH from each) creates a triglyceride with 3 water molecules
    - When joining amino acids, the -OH is removed from the Carboxyl group and a -H is removed from the Amino group to create the a dipeptide and a water molecule

Question 3

Type of Catabolic reaction

Answer 3

Hydrolysis: break down of macromolecules by splitting a water molecule
○ Responsible for digestion

Question 4

Intermediary Metabolism, Primary metabolites and secondary metabolites

Answer 4

• Intermediary metabolism: the process that obtains, releases and uses energy
• Primary Metabolites: products of metabolism essential to survival
• Secondary Metabolites: products not essential to survival but may provide an advantage or enhancement

Question 5

Enzymes

Answer 5

speed up metabolic reactions by lowering the activation threshold

- Most enzymes are globular proteins: spherical in shape and water soluble
- Can be recycled, extremely specific, and particular to a substrate

Question 6

Regulatory enzymes

Answer 6

catalyzes one step of metabolic pathways which sets the rate for the rest of the sequence of reactions

Question 7

Rate Limiting Enzymes

Answer 7

• As enzymes in metabolic pathways can become saturated, meaning increasing the substrate concentration doesn’t affect rate of reaction this enzyme is known as a Rate limiting enzyme:
  
  • This normally occurs at the start of the pathway and prevents intermediate products unnecessarily accumulating if this rate limiting enzyme was in a difference position in the sequence
  • If a product inhibits the rate limiting reg enzyme this is negative feedback

Question 8

Factors altering enzymes

Answer 8

Cofactors: a small organic, or ion component which activates enzymes

coenzyme: When it is an organic non protein molecule that activates enzymes

Denaturation: changes in the molecular structure of a protein due to excessive heat, radiation, electricity or fluids with extreme pH values

Question 9

Energy

Answer 9

the capacity to change something or to do work
- Heat
- Light
- Sound
- Mechanical
- Chemical
- Electrical

• cannot be created or destoryed, only transformed

Question 10

Release of Chemical Energy

Answer 10

• Chemical energy is held in the bonds between atoms of molecules and is released when bonds are broken
  • Inside our body we use processes of oxidation to break down macromolecules, releasing energy which is then used to power anabolic reactions
  • Enzymes assist in lowering activation energy required for oxidation
  • Cells capture about 40% of energy released during cellular respiration which is transferred as high energy electrons to form ATP

Question 11

ATP structure

Answer 11

• Composed of adenine, ribose sugar which form to make adenosine
  
  • and 3 phosphates
  • Bond between Second and third phosphate is attached by high energy bonds and can be broken to release stored energy

Question 12

Steps, locations and products of Cellular Respirations

Answer 12

1. glycolysois
   - cytosol
   - 2 ATP, 2 pyruvic molecules, 2 NADH
2. Citric acid
   - mitochondrion matrix
   - 2 ATP, 6x CO2, NAHD, FADH2 per glucose molecule
3. ETC
   - Cristae(inner membrane)
   - 32 ATP, 6x water,

Question 13

Steps in Glycolysis

Answer 13

Energy Investing:
1. 2 phosphate groups from 2 ATP are added to a glucose molecule at each end during phosphorylation forming fructose 1,6 diphosphate

Energy Harvesting: 
2. The 6-carbon glucose(F16D) is cleaved into 2x 3-carbon molecules DHAP and GAP(both isomers)
3. As body cannot break down DHAP it is rearranged(isomerized) into a second GAP molecule which both are broken down to release energy
4. 2x NADH, 2x 3-carbon molecules(pyruvic molecules) and 4x ATP(2x profit ATP) is synthesized

Question 14

What happens after Glycolysis if there is no oxygen present

Answer 14

Anaerobic Pathway:
- If there is no oxygen present, it can’t act as the final electron acceptor at the end of the ETC,
- therefore NADH needs to give its hydrogen atoms back to pyruvic acid, forming Lactic acid and 2x ATP

Downside of this pathway is that while it regenerates NAD to pick up more high energy electrons, the buildup of lactic acid eventually inhibits glycolysis due to the acidic nature of lactic acid

Question 15

What happens after Glycolysis if there is oxygen

Answer 15

Aerobic Pathway:
- If enough oxygen is present, then the pyruvic acid is synthesized into an acetyl coenzyme A molecule which can enter the mitochondria and complete CR

Link Reaction:
1. Mitochondrial enzymes remove two hydrogen atoms, a carbon atom and two oxygen atoms from pyruvic acid
- This generates NADH and CO2 and leaves a 2-carbon acetic acid
2. CoA then joins with the 2-carbon molecule to form Acetyl CoA

Question 16

Citric Acid Cycle Process

Answer 16

• Occurs twice for each glucose molecule(inputs is a single acetyl coA molecule which 2 is made from 2 GAP molecules)
  • Begins with the 2-carbon acetyl CoA molecule(acetyl CoA) which combines with a 4 carbon oxaloacetic molecule to form a 6-carbon molecule(citric acid)
  • This undergoes a series of reactions until it gets back to the 4 carbon oxaloacetic acid which is ready to go again with a new set of 2 carbon acetyl CoA molecules

Question 16

Electron Transport Chain Steps

Answer 16

Oxidative Phosphorylation:

- NADH and FADH release high energy electrons at different enzymes along the chain which give up their energy a little bit at a time, allowing it to be captured(too much at a time and its like an explosion where energy cannot all be captured)
- Energy is captured by enzymes and used by ATP synthase to create ATP
- The final enzyme in the ETC gives up a pair of now low energy electrons which combined with 2 hydrogen molecules and the final receptor oxygen molecule form water

Question 17

Gene, Genome and Exome

Answer 17

Gene: sequence of nucleotide bases along one DNA strand containing information for a protein

Genome: whole set of DNA

Exome: small portion of the genome that codes for proteins

Question 18

Purines v Pyrimidines

Answer 18

○ Purines: 2 organic ring structures(A, G)
○ Pyrimidines: single organic ring structure(U, T, C)

Question 19

DNA replication

Answer 19

• Happens during S phase of interphase
  • Hydrogen bonds break between complementary base pairs, allowing strands to separate
  • DNA polymerase catalyzes the formation of a new complementary strand based off of a template strand by attaching free nucleotides
  • DNA ligase binds them to create a new phosphate backbone, forming a new DNA strand containing 1 strand of new DNA and 1 strand of old DNA; semiconservative replication

Question 20

Protein Synthesis

Answer 20

Central Dogma of biology is that proteins are synthesised through transcription of DNA into RNA and translation of RNA into amino acids

Question 21

Transcription steps

Answer 21

a. RNA polymerase binds to promoter region on a region of DNA and unwinds it, creating a transcription bubble, exposing the base sequence

• It moves along, pairing complementary nitrogenous RNA bases to the DNA sequence until it reaches the terminal sequence at which it releases the newly formed mRNA and releases from DNA

Question 22

Post transcription modifications

Answer 22

• Introns are spliced our of mRNA
  
  • Exons, regions of coding DNA are joined together in the absence of introns
    This difference in exon/intron regions allow for creation of different proteins

Question 23

Steps in Translation

Answer 23

• The mRNA is transported to a ribosome where it binds and begins to read the codons
  
  • A tRNA molecule, with a complementary anticodon to the first codon read on the mRNA sequence, binds to the mRNA strand bringing the corresponding amino acid
  • A second tRNA molecule brings the corresponding amino acid for the second mRNA codon and both tRNA molecules release their amino acids releasing energy for them to form a peptide bond and begin a polypeptide chain
  • Process repeats until all corresponding amino acids have been added to the chain and the polypeptide chain forms its 3d shape
    
    • Once the stop codon has been read by the ribosome, it releases mRNA and the synthesized polypeptide chain, and the ribosome disassembles

Question 24

Structure and function of ribosomes

Answer 24

• The smaller subunit binds to a molecule of mRNA near the first codon
  - Larger subunit provides ribozyme and ribosomal proteins which create energy to form peptide bonds

Question 25

ways mutations can occur: Spontaneous

Answer 25

free nitrogenous bases can be in unstable forms and if inserted into new DNA sequences, they can generate errors in sequence

Question 26

Ways mutations can occur: induced

Answer 26

response of exposure to mutagens like UV radiation
○ E.g. prolonged exposure to UV rays can cause double bonds to form between adjacent thymine bases, causing kinks in the double helix, creating space for incorrect bases to be inserted during replication

Question 27

Nature of Genetic Code which enables it to protect against mutations

Answer 27

some amino acids correspond to more than one codon
○ Usually 2,3 codons specifying the same amino acid only differ in the third base of the codon
○ Mutations in the third base often don’t change the amino acid, but just its genetic code
○ Mutations in the second base, the substituted amino acid is often similar to the shape of the correct one and its not changed enough to affect function

Question 28

Types of mutations

Answer 28

Missense mutation: replacement of 1 amino acid

Nonsense mutation: changes codon into a stop codon prematurely