1) addition of oxygen

2) removal of hydrogen/dehydrogenation (includes removal of 1 proton and 1 electron)

3) removal of electrons

obtain energy by oxidizing some reduced inorganic compound (e.g NH₃ -> NO₂^-; "negativize") and their C from CO2

(only a few bacteria here)

obtain energy by photosynthesis and C from CO2

(eg. higher plants, eukaryotic algae, blue-green bacteria, etc.)

obtain energy from photosynthesis and C from organic compounds

(eg. photosynthetic bacteria, eukaryotic algae)

obtain energy by oxidizing reduced organic compunds and C from the same compounds 

(eg. higher animals, protozoans, fungi, common bacteria)

Sulfur

1) needed in what structures?

2) obtained from?

1) 2 AA's and coenzymes

2) sulfates or S-containing AA's

Phosphorus

1) needed to

2) obtained from 

1) make phosphate for nucleic acids, phospholipids, ATP, vitamins

2) as phosphate

Optimum temp = 10C

Min = -10C

Max = 20C

Optimum = 20 - 40C

Min = 10C

Max = 50C

Optimum = 55-75C

Min = 45C

Max = 80C

some archaebacteria which require high NaCl concentrations for growth

optimal = 25%

min  = 10%

max = 30-35% saturation

break down, energy released

(energy released is trapped for storage in ATP by merging ADP with another Pi)

synthesis, input of energy

(energy comes from hydrolysis of ATP by removing an Pi to form ADP)

chemically modify a molecule to a higher energy state (by oxidation or dehydration) and transfer the energy to ADP to form ATP

occurs during glycolysis and TCA

Electron Transport phosphorylation

oxidative phosphorylation

OxPhos where?
1) proks 

2) euks

1) cell membrane

2) inner mitochondrial matrix

anaerobes usually continue metabolism after glycolysis with this pathway that passes off electrons (and protons) to organic compounds to reduce them

Photo Phosph where?

1) prok

2) euk

1) cell membrane

2) inner chloroplast membrane

enzymes require them in their active site to carry electrons and protons

nicotinamide adenine dinucleotide (phosphate)

1) is used in oxidation rxns

2) is used as a source of reducing power in biosynthetic reactions

1) flavin adenine dinucleotide

2) flavin mononucleotide

both can accept 2 e-s and 2 protons

a few bacteria are capable of using their ETS even in the absence of oxygen by replacing O2 with some other inorganic compound as their final electron acceptor 

This only happens in the absence of oxygen

Other inorganic final electron acceptors;

allows organisms to use ETS in environments where others cannot (because O2 is not readily available as a final e- acceptor);

more efficient than no ETS, less efficient than with O2 as final e- acceptor -> because these compounds are not as far down the energy hill

NAD+

 NADPH + H+

NADH + H+

NADP+

glycolysis, found in most proks and euks

can be used both aerobically and anaerobically

glycolytic enzymes are 

1) located

2) questionable because

3) function in

1) on cell surfaces of bacteria and some euks (eg. protozoa and pathogenic fungi)

2) they lack sequences that typically are associated with transport across membranes or anchoring to cell walls or membranes, but are still transported/held there; maybe by charge or hydrophobic interactions 

3) production of ATP on the cell surfaces to support extracellular energy dependent activities

* also improve metabolic efficiency of RBC's

Glucose + 2Pi + 2ADP + 2NAD⁺ -->

2Pyruvate + 2ATP + 2NADH + 2H⁺ + 2H₂O

coenzymes

NAD+= oxidizing agent

NADH = reducing agent

NAD+ is limited in living cells

NADH is reoxidized to NAD+ to continue generating ATP

ATPs generated per

1) NADH

2) FADH2

1) 3 ATPs / NADH

2) 2 ATPs / FADH2

pyruvate ----> lactate

|

v

2NADH +2H⁺ --->       2NAD+

Lactobacillus, Lactococcus, and Streptococcus

ferment foods and beverages

pyruvate  -->  acetaldehyde --> ethanol

|                        | 

v                        v

decarboxylation             NADH --> NAD+

Genera that use alcoholic fermentation

uses

members of genus Propionibacterium = facultative anaerobes that produce acid (prop, acetic, and CO2) as end products

used in Swiss cheese

genus Clostridium produce mixture of acetone, butanol, isopropanol, butyric acid, CO2, etc. as fermentation products

produces acetone for gunpowder

butanol for rubber/tires

genera (Escherichia, Salmonella, Shigella) produce organic acids (-ates) plus ethanol, CO2, and H2

not commercially useful but analysis of this identifies enteric organisms in fecally contaminated foods

reoxidize reduced coenzymes via ETS where oxygen acts as final e- acceptor

This frees the pyruvate made in glycolysis to be further catabolized in the TCA cycle

TCA enzymes located in ___ in

1) proks

2) euks

1) cytoplasm

2) interior mitochondrial matrix

1) pyruvate --> 3 CO2

2) fatty acid portion of fats

3) all 20 protein AA's

2 pyruvate + 2 ADP + 2Pi + 8NAD⁺ + 2FAD

---> 6CO2 + 2ATP + 8NADH + 8H+ + 2FADH₂

functions as a carrier of short chain organic acids in metabolism

attaches to acetic acid via nucleophilic attack

fatty acids/many AA's enter pathway by way of acetyl-CoA

2 from substrate level phosphorylation

24 from ETS reox of 8 NADH

4 from ETS reox of 2 FADH2

30 TOTAL

(note recently NADH = 2.5 & FADH2 = 1.5)

Glycolysis:  net 2 from SLP, 6 from ETS reox of 2 NADH

TCA Cycle:  30 (separate notecard)

38 TOTAL / glucose

protein enzymes with niacin or riboflavin derivatives in their active sites to carry electrons and protons

either with NAD coenzymes or FAD/FMN coenzymes

non heme iron proteins

proteins with 1,2,or4 iron atoms in active sites

also can accept only e-s, not protons

iron atom not complexed with a heme group but rather is held in place by interaction with sulfur residues

(Coenzyme Q or ubiquinone)

small, lipid-soluble organic compounds found in the membranes of organisms with ETS

can be reduced or oxidized by accepting/donating 2 protons and 2 e-s

as e-s are passed to ETS components (coenzymes/e- carriers) and sent into the cytoplasm, the corresponding protons are dumped outside the membrane which establishes an H+ gradient that can be used to do work

H+/proton gradient established in the ETS that can be coupled to do work.  

ATPases also can use this gradient to produce ATP from ADP and Pi 

OR

to hydrolyze ATP to ADP and Pi and pump protons back across the membrane and reestablish the gradient for further use

Storage polymers

homo/hetero?

examples (3) with monomers

homopolymers

glycogen starch (polyglucoses)

volutin (polyphosphates)

poly-B-hydroxybutyrate

1) UDP-sugar

2) ADP-sugar

which is used where?

1) eukaryotic glycogen synthesis

2) bacteria glycogen synthesis

a carrier and an activator

it carries the 1 side of the merge

and phosphorylates the other side of the merge/makes it available for nucleophilic attack

structural polymers

homo/hetero?

examples (3) with monomers

USUALLY homopolymers

cellulose (polyglucose)

chitin (poly-N-acetylglucosamine)

peptidoglycan (heteropolymer of amino acids and amino sugars)

Informational molecules

homo/hetero?

usage

examples with monomers

heteropolymers

storage/expression of genetic information

DNA (polymer of dNTPs=deoxyribonucleotide triphosphates)

RNA (polymer of NTPs)

Proteins (polypeptides; polymers of AA's)

DNA

DNA replication

Transcription

RNA

Translation

Protein

reverse transcription

enzyme?

originally found in?

RNA serves as a template for DNA synthesis

reverse transcriptase (RT)

retroviruses (eg. HIV)

telomeres

enzyme?

protective repetitive DNA caps at the end of the 3' end of linear chromosomes in eukaryotes that protect the DNA molecule from shortening after replication

telomerase = a reverse transcriptase plus an RNA molecule to serve as a template for DNA synthesis)

rapidly dividing cells

(eg. skin, embryos, cancer cells)

Is DNA synthesis semi conservative

why?

YES

each strand of replicated DNA consists of one new strand and one old

1) dNTPs/activated subunits

2) DNA polymerases

3) DNA template

4) A primer (DNA or RNA); if RNA primer is used repair enzymes are required to replace RNA with DNA

5) Various replication proteins (helicase, single stranded DNA-binding proteins, RNA polymerase)

6) DNA ligase

catalyze rxn

(dNTPs)n -----> DNA + nPPi

i.e. they add nitrogenous bases to the old strand of DNA removing 2 phosphates from the dNTP and forming a new strand of DNA corresponding to the template

5' ---> 3'  (on the new strand)

that it is it adds nucleotides to the OH present on the 3' end of the template strand

DNA polymerase III:

1) one on the front of the protein which forms the phosphodiester bonds between nucleotides of the old strand and the free standing ones to form a new strand; moves 5' to 3'

2) one beyond that site that breaks said bonds if mistakes present

works as a proof reader; moves 3' to 5' along new strand 

DNA polyerase I also has:

3) some have a 3rd active site ahead of site 1 (addition) that removes old DNA/RNA strnads to prepare for addition (removal of primers or mistakes); moves 5' to 3' behind poly #1

removes RNA primer and replaces it with DNA at the start of leading strand and on each Ogazaki fragment of the lagging strand;

repair enzyme that excises damaged DNA segments and replaces them with correct segments

repair enzyme

only produced during stationary phase of growth and mutants lacking this enzyme show no defects

do not proofread (no 3' to 5' exonuclease activity)

provide adaptive mutations thorugh SOS repair

produced in conditions of stress and fill gaps in the same regions of both strands of DNA

multi protein complex at the replication fork that contains several proteins including 2 helicases, 2 primases, 2 DNA pol III molecules

hence why the lagging strand is looped through the complex

1) ribosomal

2) messenger

3) transfer

used to activate amino acids for protein synthesis and to translate the information in mRNA molecules into a sequence of amino acids in a polypeptide chain 

73-95 nucleotides in loops/cloverleaf with one loop as anticodon loop 

1) NTPs as activated subunits/monomers

2) RNA polymerase ie. DNA-dependent RNA polymerase

3) DNA template (only one strand of dsDNA)

*different strands are used as templates on different genes

1) Initiation

2) Elongation

3) Termination

RNA polymerase finds promoter sequence on a DNA molecule that 1) identifies gene and 2) tells RNA pol which strand to copy

RNA pol binds tighter to DNA and unwinds (about 17 bp = a transcription bubble) 

Initiates RNA synthesis at start of the gene

RNA pol matches free living NTPs with those on the ssDNA template and attaches/polymerizes them via H-bonds

termination sequences (last base in coding region in transcribed before term seq) on DNA molecule signal RNA pol to stop RNA synthesis

nascent RNA molecule disjoins, DNA strands region bases of transcription bubble and RNA pol dissociates from DNA

time takes to build mRNA molecule?

and # of AA's on it to build an average protein?

15 seconds

200-300 AA's

1) base pair error occurs every ___ nucleotides in DNA replication of E coli

1) " " every ____ in RNA synthesis 

1) 10⁸ - 10⁹ nucleotides

2) 10⁴ nucleotides

Prok vs. Euk Transcription

(5 comparisons/contrasts)

1) Prok = 1 RNA pol

Euk = 4-5 RNA pol

2) Prok = most have polycistronic mRNAs

Euk = VERY few have polycistronic

3) Prok = usually do not process mRNA

Euk = post transcriptional modifications

4) Both usually process tRNA and rRNA

5) Prok = transcription/translation closely coupled; proteins associate with mRNA before it is completely synthesized

Euk = this does not usually happen

Types of Euk RNA pol

location and type of RNA it synthesizes?

1) nucleolus - rRNAs

2) nucleus - all mRNAs

3) nucleus (also) - all tRNAs and 1 type of rRNA

4) mitochondria - all mitochondrial RNAs

5) chloroplasts (plants and algae) - all chloroplast RNAs

ie. polygenic

encode several proteins via several open reading frames each of which can be translated into a polypeptide 

N terminal

methionine (Eukarya and Archaebacteria)

N-formyl methionine (Bacteria, Mitochondria, Chloroplasts

direction of translation

protein is built from which end to which end

1) free activated subunits that consists of an AA attached to carrier tRNA

2) mRNA as template 

(H-bonds form between nbs on mRNA and tRNA to transmit information)

3) ribosome - site of protein synthesis

4) ATP & GTP to provide required energy

5) various protein factors

site for protein synthesis

E coli/poor growth medium has as few as 2000

Rich growth medium 20,000-30,000

40% tRNA and 60% protein by weight

1) Bacterial ribosomal subunits

2) how are they dissociated?

3) composed of how many proteins?

4) 3 types of rRNA?

1) 50S and 30S subunits

2) by reducing Mg2+ concentration

3) 55

4) 50S subunit has 5S and 23S

30S subunit has 16S

1) Activation of AA's

2) Formation of 70S initiation complex

3) Elongation (synthesis)

4) Termination

Activation of AA's in Protein Synthesis

enzyme used

- carbonyl group on AA is activated by attachment to OH group of ribose at 3' end of specific tRNA molecule to form aminoacyl-tRNA

- catalyzed by aminoacyl-tRNA synthetases

- ATP hydrolyzed to AMP here

Formation of 70S initiation complex

Elongation

Termination

1) abortive/premature termination of polypeptide synthesis and release of the polypeptide if an incorrect AA appears

2) slowing of the synthetic process to check codon-anticodon match at the A site of the ribosome

error rate = 1 in every 10-20k

how long does it take to synthesize an average protein

molecular weight

ATPs used

15-30 seconds

30,000-40,000 MW

1000 ATPs

in euks, transcription takes place in the nucleus where there are no functional ribosomes

mRNAs must migrate out of the nucleus through pores in nuc membrane to get to ribosomes

large complexes of many ribosomes associated with mRNAs

serve to increase the efficiency of protein synthesis

these complexes also prevent an mRNA molecule and its ribosomes from being degraded by intracellular RNases that turn over RNA molecules

H2O2

O2-

OH+

nonsense codons

stop codons

UAA

UAG

UGA