Lec Exam 2

metabolism

the sum of all catabolic and anabolic reactions

anabolism

synthesis of complex molecules in living organisms from simpler ones together with the storage of energy

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constructive metabolism

catabolism

breakdown of complex molecules in living organisms to form simpler ones, together with the release of energy

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destructive metabolism

redox reactions

transfer of electrons (H) from donors to acceptors 

always occur simultaneously 

cells use electron carriers (H atoms) to shuttle them around 

most anabolic reactions 

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Important ones 

* Nicotinamide adenine dinucleotide (NAD+) 


* Nicotinamide adenine dinucleotide phosphate (NADP+) 
* Primarily used in photosynthesis 


* Flavin adenine dinucleotide (FAD) 

conditions that affect enzymatic activity

* temperature


* pH
* competitive and noncompetitive inhibition
* feedback inhibition

temperature

insufficient temperature for enzymes, typically increased temperatures, leads to denaturation 

psychrophile – organisms that prefers to or can grow at lower temperatures 

* Listeria can grow at refrigerator temperatures (outbreaks in prepackaged food – lettuce, deli meats, cheese) 
* Cool temperatures can inhibit growth and reproduction of bacteria 
* Do not become denatured when frozen 

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Mesophiles – organisms that prefer to grow best at or around body temperature 

* Not limited to growing at this temperature 


* E coli., Serratia, pseudomonas 

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Thermophiles and hyperthermophiles – organisms that prefer to grow at high temps 

* Majority are archaea 

pH

* Most enzymes work best at a pH close to 7.35 (human pH)
* Organisms that can grow at more acidic pH acidophiles 
* Lots of fungi 


* Those that grow at more alkaline pH are alkaliphiles 


* Extreme swings in pH can affect enzyme activity and they can denature 

inhibition

competitive

* inhibitor binds to the substrate before the enzyme blocking the enzyme from binding with the substrate 
* Sulfanilamide drugs compete for the same receptors used to make folic acid (important in cell division to help make cofactors) in some bacteria 

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noncompetitive (allosteric) 

* inhibitor binds to allosteric site of the enzyme and change the composition of the active site preventing the enzyme from binding to substrate or slow it down 


* can be allosteric activators and can increase enzymatic activity for positive feedback 

feedback inhibition

enzyme's activity is inhibited by the enzyme's end product

types of enzymes

* Hydrolases


* Isomerases
* Ligases or Polymerases
* Lyases
* Oxidoreductases
* Transferases

hydrolases

commonly perform as biochemical catalysts that use water to break a chemical bond

isomerases

enzyme that catalyzes the conversion of a specified compound to an isomer

ligases/polymerases

catalyzing the reaction of joining two large molecules by establishing a new chemical bond

lyases

responsible for catalyzing addition and elimination reactions

oxidoreductases

catalyze oxidation-reduction reactions

transferases

catalyze the transfer of a group of atoms, such as amine, carboxyl, or phosphoryl from a donor substrate to an acceptor compound

enzymes

organic reactions would occur far too slowly to sustain life

* 1 mill – 10 million times slower without enzymes 

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not changed or destroyed during a reaction 

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lower the energy needed to break bonds (activation energy) 

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specific to certain sets of reactions (name often tells you) 

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made of proteins 

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activation energy is the hill that must be climbed before a catabolic reaction 

glycolysis

occurs in the cytoplasm of most cells \n

initially requires the input of 2ATP

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from this input 4 ATP are made for a net gain of 2ATP

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2 NADH are also formed which are important if oxygen is present \n

final products are 2 pyruvic acid molecules, which can enter the next cycle as long as oxygen is present

aceytl coA

\n Pyruvic acids are stripped of carbon and oxygen and converted into:

* 2 Acetyl-CoA
* 2 NADH
* 2 CO2

kreb’s cycle

2 acetyl CoA’s enter this cycle and undergo a series of reactions with acid molecules (beginning \n with citric acid, hence the name) \n

overall result is the formation of:

* 2 ATP
* 6 NADH
* 2 FADH2
* 4 CO2

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the main source of carbon dioxide that exits cells as waste to be carried by the blood stream

electron transport chain

comprised of a series of electron transport carriers in the inner mitochondrial membrane \n

electrons are transferred from FADH, NADH to the carriers and when this happens, H+ ions are \n released out of the mitochondrion. \n

last step the electrons are transferred from the carrier molecule to the Oxygen \n

H+ ions move with their concentration gradient through special membrane channels and this causes phosphates to be added to an ADP molecule to create ATP

ATP synthase

oxygen attracts hydrogens and as they move back in through ATP synthase ATP is created

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10 NADH, 2 FADH, donate hydrogens

cytochrome C – shuttle protein

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complex 4 electrons are starting to be transferred to FEA (final electron acceptor)

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creates lots of O- and creates chemiosmotic gradient to draw positive H electrons through ATP synthase

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3 turns of ATP synthase = 3 ATP

FADH only gives off enough for ATP to turn twice

fermentation

partial oxidation of sugar to release energy using an organic molecule from within the cell as the electron acceptor

NADH is oxidized to NAD+ using something within the cell. \n

Common end products are:

* C02
* Lactic Acid
* Alcohol
* Some industrial solvents – acetone, butanol

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different bacteria create different end products

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Aerobic – oxygen \n Anaerobic – hydrogen, sulfur, nitrogen containing compounds

fat metabolism

lipolysis - Triacylglycerols are broken down into glycerol and free fatty acids \n

glycerol - can easily be converted and go into one of the phases of glycolysis by forming pyruvic acids \n

free Fatty Acids - undergo beta-oxidation to become acetyl CoA molecules which can enter the citric acid cycle \n

processes are reversible \n

lipogenesis – occurs when ATP and glucose levels are high

protein metabolism

amino acids can be interconverted to allow them to enter phases of carbohydrate metabolism \n

bacteria or fungi that use protein catabolism are often related to food spoilage (i.e. the fishy smell or dead fish)

order of use of macromolecules

1. glucose
2. glycogen
3. fats = glycerol and fatty acid
4. proteins = amino acids interconverted

anaerobes

* only grow where there is no oxygen 


* Will not make SOD (superoxide dismutase)

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Obligate 

* Micrococcus luteus 


* Pseudomonas 

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Strict  

* Clostridium sporogeneses  
* Do not use oxygen and its toxic to them 
* Do not have SOD or catalase to detoxify oxygen 

aerobes

grows in the presence of air or requires oxygen for growth

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use other antioxidants to combat ROS

* Vitamins C and E 

aerotolerant anaerobes

* tolerate but do not need oxygen 


* Will not use it but if its present it does not kill them 

facultative anaerobes

* most use oxygen first 


* Can switch when oxygen runs out 
* *E coli.* 

microaerophiles

* aka capnophiles 


* Primarily grow at border between oxic and anoxic zone 
* Grow best in environments with little oxygen 
* *H pylori.* causes stomach ulcers 

photoautotrophs

* Use photosynthesis 
* Uses light and CO2 to feed itself 
* Cyanobacteria – plankton  
* Use water as electron source to reduce CO2 and produce energy and O2 as waste

chemoautotrophs

* Uses chemical compounds and organic compounds to feed itself 
* Hetero- = different 
* Can eat wide variety of things to get C from them 

singlet oxygen

(1O2)

has higher energy electrons

production of carotenoids 

superoxide radical

(O2-)

produced during incomplete reduction during aerobic respiration 

superoxide dismutase 

peroxide anion

(O22-)

hydrogen peroxide is sometimes formed during aerobic respiration and must be broken down

catalase or peroxidase enzymes

hydroxyl radicals

(OH-)

result from radiation and incomplete breakdown of peroxides

generally low because of catalase and peroxidase

quorum sensing

the regulation of gene expression in response to fluctuations in cell-population density

biofilm formation

1. free swimming microbes are vulnerable to environmental stresses
2. some microbes land on a surface and attach
3. cells begin producing and extra cellular matrix and secrete quorum-sensing molecules
4. quorum sensing triggers cells to change their biochemistry and shape
5. new cells arrive, possibly including new species, and water channels form in the biofilm
6. some microbes escape from the biofilm to resume a free-living existence and perhaps to form a new biofilm on another surface

temperature effect on growth

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psychrophiles like growing in fridge temperatures 

* Listeria can cause 
* 10 C 


* Min -> max growth temperature 
* Peak is preferred temperature

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Mesophiles – grow best at body temp 37 C 

* 98.6 F 
* Wide growth range – Serratia and pseudomonas  

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Thermophiles peak temp 65 C 

* Extra H bonds and covalent bonds 


* Help proteins maintain shape 

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Hyperthermophiles peak temp 95 C 

prokaryote and protozoa pH

preferred range 6.5-7.5 

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Acidophiles – grow better in acidic environments 

* Parts of our body naturally inhibit certain microbes 

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Alkalinophiles – grow better in alkaline environments 

* Vibrio cholera – grows best at pH 9 

osmotic pressure

Hypertonic solutions – will cause cells to shrivel 

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Hypotonic solutions – will cause cells to swell or burst 

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Halophiles – can tolerate high salt environments 

* Staph aureus is facultative halophile that can tolerate 20% salt 

selective media

* Selects for or inhibits growth of organisms 
* Use salt to select for staph 

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e.g.,

differential media

* Cause color change 
* PH change 
* Does not stop anything from growing 
* Blood  


* Homolysis – bacteria digesting RBCs 

binary fission

Asexual reproduction 

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Steps  

* Replicates chromosomes 
* Cell elongates and growth between attachments sites pushes the chromosomes apart 
* Cells form new membranes and wall across midline 
* Septum is complete and daughter cells may or may not separate 

generation time

how long it takes for a bacterial cell to grow and divide 

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average generation for E coli. Is 18 minutes 

* E coli is one of the fastest 

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staph aureus are around 20-25 minutes 

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many bacteria have generation times of 1 hour-2 hours 

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Mycobacteria  

* Cause TB 
* Between 7-10 days 
* Very slow generation time

growth phases

Lag phase can last a few days 

* Adjusting to environment 

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Log phase 

* Exponential growth 
* Target for antimicrobials 


* Work best when bacteria are very active 

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Stationary phase 

* Nutrients begin to deplete 


* Equal numbers of dead and living bacterial cells 
* Bacteria is still susceptible to antimicrobial 

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Decline phase 

* More nutrients run out 
* Begins to die off 


* Endospore formation 


* Extremely difficult to destroy 

logarithmic growth

exponential growth

persister cells

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* Different from endospores 
* Random variation 


* The ones who survive the longest in poor conditions 

direct measuring of bacterial population

* Direct microscopic count using live cells 


* More accurate than dilution 

indirect measuring of bacterial population

* serial dilution 
* estimation  

other ways of measuring bacterial population

* Turbidity of a sample can be measured with a spectrophotometer 
* Dry weights can be taken of the cell population 
* Oxygen and Carbon Dioxide consumption can be measured 


* Genetic Methods are becoming increasingly common 

DNA

* The same across all organisms 

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Principal of complementarity 

* Thymine -> Adenine 
* Guanine -> Cytosine 

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* Deoxyribose backbone 
* Highly coiled to save space 


* Protects it from being degraded 


* Essential function – to code for proteins 

prokaryote genome

bacteria

* single copies (haploid) of one or more chromosomes
* plasmids present in some
* circular or linear DNA
* DNA in nucleoid of cytoplasm and plasmids
* no histones

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archaea

* one (haploid)
* plasmids present in some
* circular DNA
* DNA in nucleoid of cytoplasm and plasmids
* histones present

eukaryote genome

* diploid chromosomes
* plasmids present in some algae, protozoa, and fungi
* linear DNA in nucleus and chloroplasts
* nonlinear DNA in plasmids and mitochondria
* histone in nuclear chromosomes not non nuclear

plasmids

* DNA that can be transferred between bacteria 

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F plasmid 

* Fertility plasmids, carry information for conjugation 

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R plasmids 

* Resistance plasmids, carry genes for resistance to other bacteria 

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Bacteriocin plasmids 

* kills bacteria of the same species or similar species to eliminate competitors 

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Virulence plasmids 

* carry genes that code for enzymes or toxins that make them pathogenic 
* Especially gram positive is through production of exotoxins 


* Can be exchanged between bacteria 

leading strand

* replicated continuously
* does not require DNA ligase
* 5’-3’
* only single RNA primer is required

lagging strand

* discontinuous growth
* formed in fragments - Okasaki fragments
* ligase is required to glue together fragments
* starting of each fragment requires RNA primer
* slower to replicate than leading

bacterial DNA replication

* replication much faster than eukaryotic bc of generation time
* bi-directionality

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methylated as created

* helps to control bacterial gene expression, initiate DNA replication, differentiate own DNA from viral DNA 

topoisomerase

winds DNA back up

helicase

unwinds DNA

polymerase

binds the strands of DNA

genotype

genetic sequence that codes for characteristics

phenotype

physical expression of gene

inducible operon

* lac operon
* Usually turned off and must be activated by inducers 


* Produces genes that make enzyme to digest lactose 

repressible operon

* trp operon
* Usually turned on and must be inhibited by repressors 
* produces tryptophan

protein synthesis

* DNA uncoils for transcription


* mRNA is produced in the nucleus
* mRNA moves to the ribosome
* Ribosome moves along the mRNA
* tRNA brings amino acids to the ribosome
* Polypeptide is produced

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bacteria

* One maybe two proteins made from translation 

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eukarya

* must cut out introns to form mRNA

triplet

3 base sequence on DNA

codon

3 base sequence on mRNA

anticodon

3 base sequence on transfer RNA

operons

* contains promoter, operator, and genes that code for end product
* has promoter and regulatory gene out front