Bacterial Metabolism

1
Chapter 6

• Bacterial Metabolism

2
Do You Remember??

• Laws of Thermodynamics
• Dissecting a Chemical Reaction
• Endergonic /Exergonic reactions
• What Is Metabolism?
• Anabolic/Catabolic Reactions
• Coupling these reactions

3
Enzymes and Energy in Metabolism

• What Are Enzymes?
• Enzymes Catalyze All Cellular Reactions
• (What is a catalyst?)
• Are made of?
• Are used up?
• Can they interact with many different kinds of
  molecules?
• Enzymes catalyze chemical reactions by?

4
More About How Enzymes Work

• Old Model Lock and Key Model
• Newer Model Induced Fit

5

• Enzymes lower the activation energy so a reaction
  is more likely to occur
• Enzymes weaken chemical bonds in the substrate

Figure 6.3, page 165
6
Naming Enzymes

• Enzymes can be named in one of two ways
• By their function
• By the substrate on which they act
• Examples
• Sucrase
• Lipase
• Oxidase
• Hydrolase

7
Some Enzymes Require Cofactors

• Some enzymes are made entirely of protein
• Other enzymes require the addition of a
  complementing substance a cofactor

8
Cofactors An Example

• Carbonic Anhydrase
• The gray sphere is zinc (a metal) acting as a
  cofactor

9
Coenzymes

• Coenzymes
• a subclass of cofactors that are organic
  molecules (but not proteins)

10

• Enzymes Often Team Up in Biochemical Pathways
• A metabolic pathway is a sequence of chemical
  reactions working in step-wise fashion to produce
  a final product
• each reaction is catalyzed by a different enzyme
• the product of one reaction serves as the
  substrate for the next

Figure 6.4, page 166
11
How Enzymes Work In a Cell

• All enzymes working at the same time would cause
  chaos in a cell
• Therefore, enzymes must be turned on off in the
  cell
• Enzyme Inhibition
• Competitive Inhibition
• Non-Competitive Inhibition
• Enzyme Activation

12
An Entire Biochemical Pathway Can Also Be
Inhibited

• Feedback Inhibition

13
ATP

• Energy in the Form of ATP is Required for
  Metabolism
• ATP (adenosine triphosphate) is the cellular
  energy currency, providing energy for
• Movement
• Cell division
• Protein synthesis
• Etc.

14

• Energy is released from ATP when the bond holding
  the last phosphate group on the molecule is
  broken, producing
• adenosine diphosphate (ADP)
• a free phosphate group high-energy electrons
• Energy will be acquired by molecule that bonds
  the phophate group

15

• Adding a phosphate group to a molecule is called
  phosphorylation
• Enzymes that transfer a phosphate from one
  molecule to another are called kinases
• ATP cannot be stored because it is relatively
  unstable
• energy must be stored in more stable forms like
  glycogen, starch or lipids (in prokaryotes),
  which can then be used to form ATP

16
CATABOLIC PATHWAYS

• Major catabolic pathways break organic molecules
  down Use harvested potential energy to form ATP
• Formation of ATP in a cell Respiration
• 2 major pathways Fermentation and Aerobic
  Respiration
• Both start with Glycolysis

17
Catabolic Pathways An Overview

• Glycolysis
• A 10 step pathway
• Aerobic resp. and ferm. both start here
• All steps are catalyzed by enzymes
• Does not require O2 or specialized membranes
• Occurs in the cytoplasm
• All cells do this
• Because of last 3 items, is viewed as an ancient
  pathway

18
Catabolic Pathways Overview, cont.

• Aerobic Respiration
• Is comprised of 2 pathways
• Krebs Citric Acid Cycle
• An Electron Transport System
• It follows glycolysis
• Requires O2, Special Membranes, Special Electron
  Transporting Proteins
• Because of last 2 items, is viewed as a more
  recent pathway

19
Step 1 in Aerobic Respiration or Fermentation
Glycolysis

• Glycolysis splits 1 glucose molecule into 2
  pyruvate molecules
• Steps 1-3 Energy Requiring Reactions
• Step 4 Molecule Breaks in Half
• Steps 5-10Energy Harvesting Reactions
• Net yield for glycolysis is 2 ATP 2 NADH

20
(No Transcript)
21
Glycolysis Can Run Backward Gluconeogenesis

• Working backward and up through glycolysis is
  called gluconeogenesis
• Steps 1, 3 and 10 in glycolysis are irreversible
• (Would this be an anabolic or a catabolic
  pathway?)

22
Aerobic Respiration, ContKREBS CITRIC ACID
CYCLE

• The Krebs Cycle extracts additional energy from
  pyruvate following glycolysis
• Synthesizes building block molecules
• Before entering Krebs Cycle, pyruvate molecules
  coming from glycolysis must pass through an
  intermediate step

23
The Intermediate Step

• Before entering the Krebs cycle, enzymes
• remove a carbon from each pyruvate molecule to
  form acetate
• combine the carbon with coenzyme A (CoA) to form
  acetyl-CoA
• This releases 1 NADH and 1 CO2/pyruvate
• Is also called the Grand Central Station Step
  because many building block molecules are
  synthesized at this step

24
The Intermediate Step
25
Krebs Citric Acid Cycle

• For each two pyruvate molecules that enter the
  cycle, the following molecules are formed
• 4 CO2
• 2 ATP
• 6 NADH
• 2 FADH2

26
NADH and FADH2 Are Electron Carriers!These
molecules will carry electrons to an electron
transport system (if one is present)

• The Krebs cycle functions like a constantly
  turning wheel
• picking up pyruvate molecules from glycolysis
• spitting out CO2, and transferring electrons to
  ATP, NADH, and FADH2
• Note the ATP made at the bottom of the cycle

27

• OXIDATIVE PHOSPHORYLATION
• The Big Gun
• Pairs of electrons are passed from one chemical
  substance to another (electron transport),
  releasing energy
• The energy released is used to pump H ions
  across a membrane
• NADH and FADH2 provide the source electrons for
  oxidative phosphorylation
• Oxygen bonds with the electron pair at the end of
  the chain, acquires 2 protons, which forms water

28
Oxidative Phosphorylation
29
Oxidative Phosphorylation Occurs on an Electron
Transport Chain

• Electrons moving through the protein electron
  carriers provide the energy to pump protons
  across a membrane (chemiosmosis)
• Forms a concentration gradient of protons on one
  side of the membrane
• As the protons flow through ATP synthase, the
  energy (proton motive force) is used to
  phosphorylate ADP and form ATP

30

• Fermentation
• Produces ATP Using an Organic Final Electron
  Receptor
• Fermentation is used
• when oxygen and other alternative electron
  acceptors are unavailable
• When electron transport carrier proteins are not
  available (the organism doesn't have the genetic
  code for these carriers)
• No functional specialized H membrane is present

31
Fermentation Reforms NAD

• NADH ? NAD Electron pair H
• Electron pair and H will be donated to an
  organic molecule
• NAD must be reformed so that glycolysis step 5
  can occur (NAD oxidizes glyceraldehyde-3-phospha
  te)

32
Two Common Fermentation Pathways

• Pyruvate ? lactate
• In our muscle cells
• Pyruvate? CO2 ethanol
• In yeast cells
• Used commercially to produce risen bread and
  alcoholic beverages

33
Prokaryotes Have Many Different Fermentation
Pathways A Way We Identify Species
34
Bioremediation
35
Other Aspects of Catabolism

• Other Nutrients Represent Potential Energy
  Sources
• Many mono-, di-, and polysaccharides can be
  energy sources for prokaryotes
• They must all be prepared before being processed
  by
• Glycolysis
• the Krebs cycle
• oxidative phosphorylation

Figure 6.12, page 179
36

• Catabolism of Fats
• Pathway is known as b-oxidation
• C-H bonds in fats store large amounts of energy,
  making fats good energy sources
• See board for chemical reactions
• Catabolism of Proteins
• Cells use proteins for energy when fats and
  carbohydrates are lacking
• Deamination is the replacement of the amino group
  in a protein with a carbonyl group in protein
  breakdown
• See board for chemical reactions

37

• Anaerobic Respiration Produces ATP Using Final
  Electron Acceptors Other Than Oxygen
• In anaerobic respiration, anaerobes use molecules
  other than O2 as the final e- receptor on the ETC
• For example NO2, NO3, H2So2, etc.
• Anaerobic respiration produces less ATP than
  aerobic respiration
• We will talk more about this in lab

38
ANABOLIC PATHWAYS

• Carbohydrate Synthesis Lipid Synthesis
• Protein Synthesis
• DNA Synthesis

39
6.4 The Anabolism of Carbohydrates

• Photosynthesis Is a Process to Acquire Chemical
  Energy
• In photosynthesis, light energy is converted to
  chemical energy, which is stored as an organic
  compound
• In prokaryotes, it is carried out in the cell
  membrane or thylakoid lamella, in eukaryotes in
  organelles called chloroplasts
• The green pigment chlorophyll a absorbs light
  energy
• Some bacteria use other pigments, such as
  bacteriochlorophylls
• some archaea use bacteriorhodopsin

Figure 6.15, page 183
40
Some Prokaryotes Harvest Electrons and Protons
from H2S Some from H2O
41
Photosynthesis

• Photosynthesis is divided into two sets of
  reactions
• energy-fixing reactions
• carbon-fixing reactions

42
The Carbon-Fixing Reaction The Calvin Cycle
43
Stromatolites Examples of Early Oxygenic
Photosynthesis
44
Oxygenic Photosynthesis and the Great Oxidation
Event
45
Patterns of Metabolism

• Autotrophs and Heterotrophs Acquire Their Carbon
  in Different Ways
• Autotrophs synthesize their own foods from simple
  carbon sources like CO or CO2 Self Eaters
• Photoautotrophs use light as their energy source
• Chemoautotrophs use inorganic compounds as their
  energy source

46

• Heterotrophs acquire carbon from large organic
  molecules Other Eaters
• Photoheterotrophs use light as their energy
  source and organic compounds as their source of
  carbon
• Chemoheterotrophs use organic compounds both for
  energy and carbon sources
• Saprobes feed exclusively on dead organic matter
• Parasites feed on living organic matter