Bio Exam 3

Kreb cycle key points 3

• pyruvic acid must be decarboxylated to acetyl CoA

• Oxidation of glucose is completed w/o O2

• NADH and FADH2 transfer e- to ETC

ETC 5

• series of redox active molecules in inner membrane

• each molecule has different E0 so e- spotaneously flow down through redox couples

• ends w/ terminal e- acceptor

• e- tower

• flows neg-pos

without O2, the ETC

gets backed up, no energy made

FADH2 is

more pos than NADH, enters ETC later

How is energy from ETC saved?

Proton Motive Force

PMF 4

• proton pumps on ETC pump protons outside membrane during redox rxn

• result is big charge and pH difference between membrane

• protons come back in through ATP synthase

• energy from: diffusive gradient, difference in pH

chemiosmosis 3

• production of ATP

• each NADH produces ~3ATP

• FADH2 makes ~2ATP cuz enters ETC later

ETC is same in human mitochondria and bacteria bc

mitochondria used to be bacteria

ATP synthase 5

• 1 revolution = 3 ATP

• one rod on side, necessary for ATP creation (coffee cup)

• hole in middle not perfectly round

• gap in proteins to release ATP/let in ADP

• has proton rings on top and protein subunits on bottom

key point of ETC and Chemiosmosis 4

• ETC last part of respiration

• proton pumps generate charge separation known as PMF

• ATP generated in ATP synthase

• per glucose molecule, 34 ATP

PMF can also be used for in prokarytes

active transport and movement of flagellum

PMF can also be used for in eukaryotes

transport of pyruvate, NADH, ATP/ADP in and out of mitochondira

Respiration in eukaryotes takes place in 2

glycolysis - cytosol

krebs and ETC - mitochondria

anaerobic respiration 2

respiration w/o O2

some bacteria ave evolved to use it

e- acceptors not as low on e- tower
anaerobic bacteria generate energy slower, grow slower

common anaerobic e- acceptors 4

carbonate (methanogensis)

sulfate

iron

nitrate

fermentation 5

• not same as anaerobic respiration

• pyruvic acid reduced by NADH, allows NAD+ to return to glycolysis

• not all organic compound are fermentable

• most well known fermentation products: lactic acid, ethanol + CO2

• only ATP produced in glycolysis

All fermentation pathways exists to

oxidize NADH back to NAD+

3 fundamental metabolic need of life

• source of energy

• source of e-

• source of carbon

6 metabolic diversity terms

• photo - light energy

• chemo - chemical energy

• Organo - organic e- source

• litho - inorganic e- source

• hetero - organic carbon source

• auto - CO2

humans are

chemoorganoheterotrophs

Many microbes can switch

their kinds of metabolism

aerobic respiration and fermentation are

chemoorganotrophy

many exergonic redox rxns dont require

organic e- donors

common inorganic e- donors

H2S, NH4+, Fe2+, H2

earliest microbes used these rxns

chemolithotrophs

get energy from rxns through PMF

chemolithotrophy example 6

• thiobacillus/sulfuromonas

• energy by oxidizing sulfur to sulfate

• made of carbon, gets carbon from CO2

• anaerobic respiration

• energy from ETC and PMF

• contributes to PMF by consuming protons inside, pumping protons outside

quinones

proton pump in ETC

Cytocromes

in ETC, contains hemes

sulfur bacteria can store sulfur

inside or outside cell

photosynthesis 2

conversion of light into ATP - light rxns

conversion of CO2 into carbs (carbon fixation) - light indepentdent rxns (NADPH)

light rxns 2

can be cyclic or non cyclic

can be oxygenic or anoxygenic

type I photosystem 8

noncyclic

oxidizes inorganics

anoxygenic

ferredoxin (pyrite) only in PS1

in Green sulfur bacteria

no proton pumps

chlorophyl in cell membrane

make H+ outside membrane, PMF, ATP synthesis

type II photosystem 7

• cyclic

• e- excited to low reduction potential by light

• e- pass through ETC

• e- return to chlorophyl, closing to cycle

• anoxygenic

• purple sulfur bacteria

• get e- for carbon fixation by displacing e- in closed cycle

oxygenic photophosphorylation 6

• Z scheme

• plants, algae, cyanobacteria

• chlorophyll oxydizes H2O to form O2 using PSII and PSI

• ETC and PMF

• instead of returning to chlorophyll, e- go to NADP+

• in membrane

where does photosynthesis happen?

prokaryotes - photosynthetic membranes, chlorosomes, or thylakoid membranes (cyanobacteria)

eukaryotes - thylakoid membranes

chlorophyll a 2

found in plants, algae, some bacteria

reflects green

bacteriochlorophyll a 2

reflects red

found in “purple” bacteria

all chlorophylls consist of 2

tetrapyrrole ring w/ Mg at center

light absorbtion affected by side group identity

carbon fixation 2

• can occur w/o light - light independent

• Calvin-Benson cycle

Calvin-benson cycle 8

• CO2 assimilated into glucose

• driven by ATP and NADPH from photosynthesis

• oxygenic photosynthesis - opposite of glucose oxidation

• in cyanobacteria, algae, purple sulfur bacteria

• Ribulose bisphosphate carboxylase (rubisco) - enzyme used in first step

• runs twice

• input 3C, release 3C, 5C stay in cycle

• carboxylation

whole cell metabolism is

walmart for anabolic rxns

desulforudis audaxviator

• lives in deep cave

• nuclear power

• chemolithoautotroph

• doubling (reproduction) time = 100-1000yrs

• no Calvin cycle

• uses free radicals

• ∆G= -149kj/mol

HOOH

exception for O oxidation state, (-I)

free radical

molecule w/ single unpaired e-

locus

location of gene on chromosome

allele 2

one of different versions of a gene on locus

results in trait variation

trait 2

• characteristic/feature that can be genetically passed down

• can be structural, metabolic, behavioral

individuals w/ advantageous traits

more likely to survive and pass on their traits

Darwin’s argument for evolution

1. individuals in a pop have genetic variation

2. Not all individuals survive to reproduce

3. individuals w/ advantageous traits reproduce more frequently

4. over time, favored traits (alleles) increase in frequency

Natural selection

process by which individuals w/ certain alleles have higher fitness

evolution 2

change in allele frequency in pops over time

individual microbes can evolve

horizontal gene transfer 3

• done by microbes

• variation from recombination

• transformation, transduction, conjugation

vertical gene transfer 3

• transfer from one generation to the next

• binary fission

• variation from mutation

Gene designation 3

• 3 lowercase italicized letters reflecting function followed by capital letter identifying gene

• Ex: lacZ

Genotype designation 2

• includes + or - to indicate functionality of allele or ∆ to indicate deletion

• Ex: lacZ-

Protein designation 2

• not italicized and usually same letters as gene w/ 1st letter capitalized

• Ex: LacZ

Phenotype designation 4

• not italicized, 1st letter capital

• may include + or - to indicate presence/absence of function

• R or S for antibiotic resistance/susceptibility

• Ex: His+, Kan^R

Wild type

naturally occurring form of gene, organism, trait which mutants are compared to

competent cell

can take DNA from environment

Becterial transformation

bacteria releases DNA into environment, competent cell picks up

Bacterial transduction

Virus takes bacterial DNA by mistake, viral transported DNA

Bacterial conjugation

by plasmids and requires sex pili in G- bacteria

Point mutation 2

• base substitution

• can result in silent, missense, nonsense

Mutation Frequency 2

• transitions: A-G, T-C 2x more common

• transversions purine to pyrimidines

Silent mutations 3

• synonymous mutations

• commonly in 3rd codon position

• degeneracy: multiple a=codons code for same AA

Missense Mutations 3

• non-synonymous mutations

• base change causes AA change

• sometimes protein can still function normally

Nonsense Mutation 2

• base change resulting in stop codon

• Higher lethallity

Frameshift mutations 2

• base insertion/deletion resulting in shift in reading frame

• only 3 possible reading frames

Reading frames 3

• normal = 0 frame

• base insertion = -1 frame

• base deletion = +1 frame

Variation in phenotype leads to

natural selection and evolution