Ch 5: Metabolism

Question 1

What is metabolism?

What is its ultimate function?

Answer 1

sum total of all biochemical reactions within a cell; their ultimate function is to reproduce the organism

Question 2

What is catabolism and anabolism?

How are they made possible?

Answer 2

Catabolism: breakdown of complex organic molecules into simpler ones - energy is released (exergonic)

Anabolism: building complex organic molecules from simpler ones; energy is used (endergonic)

Coupling of these reactions is made possible through ATP - energy retrieved from catabolism is stored in ATP and later released to drive anabolic reactions

Question 3

Describe redox

Answer 3

Oxidation and Reduction Reactions
Electron transfer from an electron donor to an electron acceptor
Reactions always occur simultaneously
Cells use electron carriers to carry electrons
Three important electron carriers:
Nicotinamide adenine dinucleotide (NAD+)
Nicotinamide adenine dinucleotide phosphate (NADP+)
Flavine adenine dinucleotide (FAD) → FADH2

Question 4

Redox includes the transfer of what two things? What is this reaction called?

Answer 4

In biological systems, redox often includes the transfer of both the electron and the accompanying proton (electron + proton = hydrogen), so they’re often called dehydrogenation reactions

Question 5

What is an enzymes role in metabolism?

Answer 5

Enzymes are organic catalysts

Increase likelihood of a reaction

Question 6

What are the six categories of enzymes based on mode of action?

Answer 6

• Hydrolases break bonds
• Isomerases rearrange molecules
• Ligases or polymerases make bonds
• Lyases break bonds
• Oxidoreductases transfer electrons thru redox
• Transferases transfer organic functional groups

Question 7

What is an enzyme and what are two characteristics?

Answer 7

Proteins which catalyze reactions in cells by lowering the activation energy (make reactions more efficient)

Enzymes are not altered or destroyed during the reaction (can be used over and over)

Enzymes exhibit specificity (they can drive one reaction but can’t drive a different reaction)

Question 8

What are substances acted upon by the enzymes called?

Answer 8

Substrates

Question 9

Maximum number of substrate molecules an enzyme molecule can convert to product each second is called what?

Answer 9

turnover number

Question 10

What is the typical enzyme turnover rate?

Answer 10

Typically turnover time = 1 – 10,000 reactions per second for each enzyme

Some turnover numbers are as high as 400,000 - 500,000 per second for each enzyme!

Question 11

Describe the structure of an enzyme

Answer 11

All contain protein - can be entirely protein, some have other components

Protein portion is called the apoenzyme

Non-protein component is the co-factor
Co-factors can be either organic or inorganic (he says inorganic)

If a co-factor is a complex organic molecule, it is called a coenzyme (he says organic)

When fully assembled they form the holoenzyme

Some enzymes are RNA molecules called ribozymes

Question 12

Describe 5 steps of enzymatic action

Answer 12

1. Substrate binds to active site on the surface of enzyme
2. Temporary intermediate complex forms - enzyme-substrate complex
3. Substrate transformed (other molecule added, molecule rearranged, bond broken, etc.)
4. Transformed substrate (product or products) no longer conforms to the active site, is released from enzyme
5. Unchanged enzyme is ready to react with more substrate molecules

Question 13

What are four factors influencing enzyme rates?

Answer 13

Temperature

pH

Substrate Concentration

Inhibition

Question 14

Describe the effect of temperature on enzymes.

What happens if temperature increases, gets above optimum, or below minimum?

Answer 14

Temperature – as temperature begins to increase, enzymatic activity increases due to an increase in molecular collisions

At some point (unique for each enzyme) optimum temperature will be reached. Enzyme operates at peak efficiency.

Higher temperatures (above optimum) will cause protein portion of enzyme to denature (unravel) destroying the function.

Each enzyme will have a minimum, optimum and maximum operating temperature.

Question 15

Describe the effect of pH on enzyme activity. What is the effect of extreme pH changes?

Answer 15

As with temperature, enzymes will have a minimum, optimum and a maximum pH.

Alterations away from the optimum may affect protein’s shape & effectiveness

Extreme pH changes can cause the protein portion to denature, destroying the enzyme function

Question 16

Where does a noncompetitive enzyme inhibitor (allosteric inhibitor) bind?

Answer 16

Allosteric site, located on the bottom of enzyme, changes shape of the active site.

Question 17

Where does a competitive enzyme inhibitor bind?

Answer 17

Directly on active site so that the active site is altered

Question 18

In end product inhibition, what switched off the pathway?

Answer 18

Making excess product

Question 19

Energy is stored through formation of ATP (ADP + P = ATP), what is this process called?

Answer 19

Phosphorylation

Question 20

What are three types of phosphorylation?

Answer 20

Substrate-Level Phosphorylation: direct transfer of phosphate to ADP from phosphorylated substrate

Oxidative Phosphorylation: electrons transferred from organic compounds to electron carriers (NADH and FADH2); energy is transferred down an electron transport chain, which is then used to generate ATP

Photophosphorylation: light energy is trapped and an electron transport chain is used to generate ATP

Question 21

What is it called when the enzyme and the substrate are connected?

Answer 21

Enzyme-substrate complex (E-S)

Sometimes called intermediate form

Question 22

What are the three major phases of carbohydrate catabolism? What is the intermediate phase?
How many ATP are made for each glucose molecule?

Answer 22

Three phases – making a total of 38 ATP for each glucose molecule

1) Glycolysis – splits glucose (6-Carbons) in half making two (3-carbon) pyruvic acid molecules — process releases a small amount of energy and small amount of NADH

“Bridge Step” takes us into mitochondria

2) Krebs Cycle – extracts energy from pyruvic acids (small amount) power is in the reduction of organic molecules like NADH and FADH2
3) Electron Transport Chain – extracts lots of energy by oxidizing those carriers and using it to make ATP

Question 23

Describe glycolysis

Answer 23

The splitting (oxidizing) of a 6-carbon glucose molecule into two 3-carbon acids (pyruvates) which will be further broken down across the bridge and through Krebs’ Cycle
Preparatory phase – costs cell energy (2 ATP)
Energy conserving phase – produces energy (4 ATP)

Cost = 2 ATP

Gain = 4 ATP through substrate level phosphoylation & 2NAD+ reduced to 2NADH

Produces two pyruvic acids (pyruvates) to send over bridge to Krebs’ Cycle

Glycolysis occurs in the cytoplasm of both prokaryotes and eukaryotes

Question 24

Describe the bridge

Answer 24

Occurs in cytoplasm

2 pyruvates are oxidized into 2 Acetyl CoA

2NAD+ are reduced to 2NADH

CO2 released (decarboxylate group)

2 Acetyl CoA goes to mitochondria matrix

Question 25

Describe the Krebb cycle

Answer 25

In the matrix of the mitochondria

Acetyl CoA is oxidized

CO2 is decarboxylated

2 ADP turned to 2 ATP through substrate level phosphorylation

6NAD+ reduced to 6NADH

2FAD+ reduced to 2FADH2

Question 26

Describe the electron transport chain

Answer 26

10 NADH and 2 FADH2 unload electrons and protons (H+) into ETC. Chain is oxidized and reduced until it reaches O, the final electron acceptor.

NADH enters at first protein – ejects a pair of H+ from matrix across the inner membrane of the mitochondrion

Ejects two more pairs of H+ at the next two steps in the chain

A total of 3 pairs of H+ have been ejected when an NADH completes it’s passage along the chain

FADH2 also uses the electron transport chain but can’t enter at the first step

Each pair of H+ ions passes through an ATP-Synthase molecule making one ATP as they pass through

10 total NADH producing 3 pairs of protons each will make 30 ATP

2FADH2 producing 2 pairs of protons each will produce 4 ATP

2 ATP from gyclolysis

2 ATP from Krebb

2 hydrogen meet up with O to make H2O, which we breath out

Question 27

How is the anaerobic respiration in prokaryotes different?

Answer 27

Final Electron acceptor is an inorganic molecule other than O2 (nitrous oxide, nitrate, methane)

2 ATP gained from glycolysis, pyruvate leads to fermentation yielding 2 ATP, Acetyl CoA (untapped energy) leads to lactic acid, ethanol, or other.

This style of respiration is much less efficient than aerobic respiration, so, organisms that do it produce less total ATP. Because of this, anaerobic bacteria tend to grow slower than aerobes

Question 28

What is fermentation (mostly cares about the last two)?

Answer 28

After glycolysis, the pyruvates can be further metabolized by taking alternate pathways; fermentation is one. Fermentation:

Releases energy from sugars or other organic molecules
Does not require O2 (but can often occur in presence of O2)
Does not use Krebs or Electron Transport Chains
*Uses an organic molecule for electron acceptor
*Produces few ATP (one or two per start molecule)
End products contain much of original energy
ethanol
lactic acid

Question 29

Describe fermentation test for bacterial identification

Answer 29

PR test
Fermentation Test Medium contains:
Protein (casein for us)
one specific carbohydrate (maltose, fructose, glucose, etc)
pH indicator (color change if uses carbohydrate)
Durham tube (little glass tube) to collect gas if it is produced

Purple Carbohydrate Broth
Turns yellow if organism can use
The particular carbohydrate for
energy source (lactose, sucrose, glucose, or mannitol)– bubble indicates gas produced

Phenol Red Carbohydrate Broth
Turns yellow if organism can use
The particular carbohydrate for 
energy source.  Bubble indicates
Gas produced

Question 30

What is the generalized equations? 10 pt on test. Say what are the products/reactants and where they are produced.

Answer 30

Glucose (glycolysis/cytoplasm) +O2 (ETC final e- acceptor/cristae of mitochondria) —–> Co2 (bridge and krebs/cytoplasm and matrix of mitochondria) + ATP (everywhere but bridge) + H2O (ETC in cristae)