midterm 2 Flashcards
bioenergetics
the study of how energy flows through living
what state is a cell constantly in
constant activity preforming all sorts of work requiring energy
what are the types of work a cell needs to preform?
chemical, mechanical and transport
energy used by living things demonstrates ….
the first law of thermodynamics
what is the first law of thermodynamics
energy can be transferred and transformed but not created or destroyed
where does the energy come from to preform cellular work
chemical reactions
what is metabolism
the totality of an organism’s chemical reactions
what are the two options when it comes to chemical reactions
releases energy
needs energy
describe exergonic reactions
energy is releases and it is spontaneous
what does spontaneous mean
energetically favorable
what delta g is exergonic reactions
negative delta g
decribe what the exergonic graph looks like
the reactants free energy is much higher than that of the products
describe endergonic reactions
energy is required and it is nonspontaneous
what does non spontaneous mean
not energetically favorable
what is the delta g sign for an endergonic reaction
positive delta G
two words that describe exer - and ender reactions
exer- release
ender- consumption
describe the graph of an endergonic reaction
the reactants free energy is much lower than the products free energy
energy coupling? what mediates it most of the time?
ATP mediates most energy coupling in cells and provides an immediate source of energy to power cellular work
the cell does what in regards to endergonic and exergonic reactions
the cell couples endergonic and exergonic reactions
free energy is the
release or consumption of energy
Free energy defines whether
the reaction is exergonic or endergonic
hydrolysis of ATP
releases energy –> exergonic
what is ATP made of
an inorganic phosphate + ADP + energy
energy released by ATP hydrolysis can be
used to directly drive chemical/ mechanical reactions
enzyme function…
lower energy barrier to drive chemical reaction
LOOK AT ENERGY PROFILE of an exergonic reaction and try to draw with all labels
…
enzymes lower what?
THE ACTIVATION ENERGY
WHAT is the fancy name for enzymes
biological catalysts
what does the activation energy control
allows cells to control when chemical reactions occur
how many times can an enzyme be used?
UNLIMited- can be saturated but always reusable
describe the events of the enzyme substrate complex
1) substrates enter the active site
2) substrates are held in active site by weak interactions
3) the active site lowers Ea
4) substrates are converted to products
5) products are released
6) active site is available for new substrates
REPEAT
what is special abt enzymes
they have structural specificity for their substrates
how does temp affect enzymes
temperature- each enzyme has a different optimal temperature
how does ph affect enzymes
each enzyme has optimal ph
what environmental factors can effect enzyme function
temp and ph
competitive inhibition is
when a competitive inhibitor binds at the active site which blocks the substrate from binding
noncompetitive inhibition is
when a noncompetitive inhibitor binds to the enzymes allosteric site which changes the shape of the active site not allowing the substrate to fit anymore
what is induced fit
when the enzyme snuggles the substate when it binds
cellular respiration refers to
catabolic reaction used to generate ATP
what does catabolic mean
exergonic energy releasing process
how do organic molecules yield energy
through oxidation
what is chemiosmosis
energy coupling mechanism used to generate ATP
describe the energy cycle
the products of photosysnthesisi become the reactanst in cellular repiration while the reactants of cellular respiration become the reactants for photosynthesis
energy from catabolism helps what process
turn adp + P into ATP
aTP can be used for
cellular work
what does the mitochondria host
the site of cellular respiration in all eukaryotic cells
defects in mitochondrial function
are associated with degenerative disease, cancer, and aaging
what are symptoms of inherited genetic mitochondrial disease
muscle weakness, neurodegeneration, metabolic dysfunction
two components of redox reactions
oxidation and reduction
what happens in cellular respiration (think electrons)
relocation of electrons from food to oxygen –> relesed energy used to synthesize ATP
in celluar respiration, glucose is
oxidized
in cellular respiration, oxygen is
reduced
oxidized means
e- + H+ are removed
reduction means
e- and H+ are added
organic compounds like glucose posess
potential energy
why do organic compounds like glucose possess potential energy
as a result of the arrangement of electrons in the bond between their atoms
cellular respiration is a ________ explosion
controled
in cellular respiration what is the initial donor molecule
glucose
in cellular respiration what is the final acceptor molecule and through what
oxygen by an electron transport chain
how is cellular respiration a controlled explosion
controlled release of energy for synthesis of ATP through the transport of electrons from the initial donor molecule to the final acceptor molecule by ETC
what is NADH
an electron carrier
what is mediated by NADH
transfer of electrons from fuek to transport chain
dehydrogenase enzymes do what?
strip 2 H atoms (2H+ and 2 e-) from glucose
where do the 2H atoms that dehydrogenase strip go to
one H+ is release
pass one H+ and 2e- to NAD+ to form NADH
describe oxidation or reduction of NADH/NAD+
reduction of NAD+=> NADH
oxidation of NADH=> NAD+
NAD+ is oxidizing agent version of NADH
once NADH has electrons it
transfers the electrons from food to the electron transport chain where the energy os harnessed to generate ATP
NADH move ___ to ____
e- to ETC
1H=?
(`H+) + e-
what can be used as fuel for cellular respiration
proteins, carbohydrates, and fats
most basic description of cellular respiration
relocation of electrons from food to oxygen in which released energy is used to synthesize ATP
3 stages of cellular respiration
glycolysis, (pyruvate oxidation) + citric acid cycle, oxidative phosphorylation (aka electron transport chain and chemiosmosis)
what type of ATP is produced in glycolcysis
substrate level
what type of ATP is produces in citric acid cycle
substrate level
what type of ATP is produced in Electron transport chain & chemiosmosis
oxidative
glycolysis takes place in the
cytosol
what happens in glycolsysis
converts glucose to pyruvate
gylycolysis generates what?
substrates for citric acid cycle (pyruvate) and oxidative phosphorylation(NADH)
what are the products of glycolysis
2 pyruvate + 2 water + 2ATP + 2NADH + (2H+)
what is the investment phase
in glycolysis when 4 atps ate formed but 2 are used SO there is a total of 2 ATP genrated
what is substrate level phosphorylation
the phosphate is coming from a substrate rather than inorganic phosphate as in oxidative phosphorylation
what is the intermediate stage
pyruvate oxidation
where does pyruvate oxidation occur
Mitochondrial matrix
what happens in the intermediate stage
pyruvate is converted to acetyl CoA
what are the products of the intermediate stage
Co2, NADH, Acetyl CoA
what is added to pyrvate to create acetyl CoA
coenzyme A
how does pyruvate move into mitochondrial matrix
USING ACTIVE TRANSPORT MECHANISM
1 glucose=?
TWO pyruvates
the citric acid cycle takes place in
the mitochondrial matrix
the citric acid cycle is also known as the
krebs cycle or Tricarboxylic acid cycle
what enters the citric acid cycle
acetyl CoA
for each acetyl CoA that enters the citric cycle
2Co2
3NADH
1FADH2
1ATP or GTP
what could be different in some cells about the citric acid cycle
some cells generate GTP instead of ATP
oxidative phosphorylation creates what percentage of ATP in cellular respiration
90%
what is the third stage of cellular respiration
oxidative phosphorylation
where does oxidative phosphorylation occur
inner mitochondrial membrane
what are the two parts of oxidative phosphorylation
electron transport chain and chemiosmosis
what starts the ETC
the NADH and FADH2 donating electrons
all of the protein complex electron carries of the ETC
cellular respiration
power proton pumps that send protons to the intermembrane space generating high H+ concentration in the intermembrane space
the ETC uses energy from the donated electrons to
PUMP PROTONS TO THE INTERMEMBRANE SPACE
the chain of the ETC…
alternate between oxidized and reduced states as they pass the electrons form less to more electronegative compounds being oxygen the final acceptor producing water
the electrons in the ETC go from
less to more electronegative compounds
where does chemiosmosis occur
the inner mitochondrial membrane
ATP synthase allows…
passive transport of H+ back to the matrix
the proton motive force of atp synthase has the ability to…
produce work
the flow of H+ through synthase results in
joining of ADP + Pi to form ATP
what mechanism is used to make ATP
energy coupling mechnaism –> proton motive force
the flow of protons is like water…
in a stream moving waterwheel
the force of the stream of protons moves…
THE ROTAR OF ATP synthase that catalyses the addition of Pi to ADP forming ATP
how many atps does oxidative phosphorylation make
about 26 or 28
for 1 glucose the citirc acid cycle produces how many atp
2 atp
what is the maximum atp per glucose for cellular respiration
about 30 0r 32 atp
what is special about pyruvate
is is a key juncture in cellular respirtation
the continuation of cellular respiration after the intermediate stage requires
O2 present
if O2 is not present after the intermediate stage
then fermentation will occur
WHAT ARE THE TWO TYPES OF FERMENTATION
ethanol or lactate
alcohol fermentation or lactic acid fermentation
high level overview of photosynthesis
converts solar energy into chemical energy
photosynthesis is the source of
oxygen and reduced carbon for all other life forms
what is reduced carbon
sugars, fats, proteins
photosynthesis is the basis …
of life for all higher trophic levels on the planet
the byproduct of photosyntheSIS AND its affect on planet
O2 is byproduct
has transformed the chemistry of the planet
when the earth formed what was the atmosphere like?
reducing atmosphere, no O2
what were the first cells like
anaerobic, simple enzymes and reaction
what did the first photosynthetic cell look like
o2 production, c fix, chemiosmotic ATP synthesis
what is the great oxidation event
O2 accumulation
what happened 4.6 billion years ago
the earth formed
what happened 3.7 billion years ago
the first cell appeared
what happened 3.4 billion years ago
first photosynthetic cell appeared
what happened 3.0 billion years ago
great oxidation event
what happened 1.7 billion years ago
cellular respiration
photosynthesis is what process
the process bywhich light is convereted to chemical energy stored in sugar and other molecules
atp syntheis is driven
by an electrochemical gradient across a membrane
NADPH and ATP produced by light reaction are used in..
the calvin cycle to produce sugar
plants are….
PRIMARY species
everything excluding plants are
secondary species
Autotrophs
produce reduced carbon(sugar) using light or chemical energy
examples of photoautotrophs
higher plants, protists, algae. cyanobacteria
heterotrophs examples
animals, fungi, many bacteria
what are heterotrophs
they obtain organic materical (energy) from other organisms
who do heterotrophs rely on
they rely on photoautotrophs for food and O2
Jan Baptist Van Helmont believed that
the biomass of plants came from water only
in photosynthesis what is reduced and what is oxidized
co2 is reduced
water is oxidized
in photosynthesis, co2…
gains e- to form sugar
in photosynthesis water…
loses e- to form O2
describe the electrons in photosynthesis
they increase in energy potential as they move from water to sugar
photosynthesis takes place in
chloroplast
most of the leafs chloroplasts are found in
MESOPHYLL cells
why are plants green??
CHLOROPHYLL
why is chlorophyll important
they absorb light used for photosynthesis
on the absorption spectra..
chlorophyll and other leaf pigments absorb light
action spectrum shows that
photosynthetic rate corresponds to light absorption
what color light is best for photosynthesis
red and blue light
how does chlorophyll absorb light
ELECTRONS IN THE PORPHYRIN RING ACCEOT ENERGY FROM PHOTONS
how is light energy conserved
when electrons go to an excited state
the porphyrin ring has a
magnesium at the center
when chlorphyll absorbs a photon of light …
the energy is conserved by an electron going to a higher energy state
how is energy from excited state lost as
heat or flueorescence with emission of a photon of red light
chlorophyll under UV light shows up as
red light
what are the 2 processes involved in photosynthesis
light reactions and the calvin cycle/ dark reactions
where do light reactions take place
in the thylakoid membranes
where do dark reactions take place
in the stroma
IN the calvin cycle, atp provides
chemical energy
in the calvin cycle , NADPH provides
reducing power
the large trans-membrane complexes…
process energy in redox reactions
what are tghe large trans-membrane complexes
photosystem 2, cytochrom complex, photosystem one
what are the mobile electron carriers in the ETC of light reactions
Pq, Pc, Fd
what are Pq. Pc, Fd and what are they capable off
they are small molecules or proteins that act as wires that move between the complexes
they are capable of redox rxn (accept or donate e-)
what does the ETC of light reactions create
proton gradient
the proton gradient created by the light reaction ETC …
drives ATP synthesis
what are the inputs of the light reaction
h2o and light energy
what are the outputs of the light reaction & chemiosmosis
NADPH, ATP and o2
the thylakoid space has a …
high H+ concentration
the stroma of the thylakoid has a
low H+ concentration
what are the three steps of the calvin cycle
fixation, reduction, regeration
what does the calvin cycel need as a reactant
co2 + ATP & NADPH ( from light reaction)
what does the calvin cycle produce simplest
CH2O (sugar)
whate does the calvin cycle create after multiple cycles
sucrose
how many sugars from the calvin cycle to produce sucrose
3C sugars
where is the sucrose then taken
export to roots, shoots, fruits
what is the structure of DNA
double helix
what is the base pairing rule
purine with a pyrimidine
what words describe DNA replication
semi-conservative
what is the key difference betwen fermentation and cellular resp.
oxygen isnt final electron acceptor but lactate is
leber’s disease is caused by
a rare mitochondrial disorder
leber’s diseases main effectt is
loss of vision
the porohyrin ring of the chlorophyll has what type of bonds
double bonds
in 1850s who discovered something and what was it
mendel- hereditary factors
IN 1869 who discovered something and what was it
Friedrich Miescher discovers nucleins from pus
In 1881 who discovered something and what was it
Albrecht Kossel discovers nucleins made of 5 distinct nucleotides and renames to DNA
in 1875-1890s who discovered something and what was it
unknown- but meiosis and mitosis worked out via microscopy and cytology
In 1902 who discovered something and what was it
Walter Sutton- chromosome theory of inheritance
1930s who discovered something and what was it
Thomas Morgan- shows genes are located on chromosomes
Why did so many people think that proteins were the genetic material
20 amino acids is greater than 4 nucleotides - aka longer alphabet
Dr. Frederick Griffith did what experiment and what did the experiment find
he mixed heat killed pathogenic cells with living nonpathogenic r cells and found that the mouse died with living S cells (pathogenic)
this showed TRANSFORMATIOn, that bacteria can take up external instruction to change themselves
Dr. Oswald Avery …
identified DNA as the transforming susbtance
a virus is …
DNA sometimes RNA enclosed by a protective coat, often simply protein
Hershey and Chase experiment + conclusion …
made radioactive sulfer and injected it in phage DNA and protein (two seperate experiments) –> only the radioactive DNA was found in the pellet
proof that DNA is the hereditary material
Chargaff’s rules …
4 same nucleotides in every organism
A is always equal to amount of T
C is always equal to amount of G
who made an incorrect structure of DNA
Pheobus Levene -1931
who discovered the double helix
Rosalind Franklin
how did ROsalind Fraklin and Maurice Wilkins picture the double helix
using x-ray crystallographic images
the x-ray image of the double helix allowed…
Watson to deduce the width of the helix and the spacing of the nitrogenous bases
what is the diameter of DNA
2nm
how far are the bases apart
0.34 nm apart
one full turn in dna happens
every 10 base pairs
what is on the outside of DNA
the phosphate backbone
the 5’ end has …
phosphate attached to the 5th carbon of the sugar
the 3’ end has a …
hydroxyl attached to the 3rd carbon of the sugar
purine + purine=
too wide
pyrimidine + pyrimidine =
too narrow
purine + pyrimidine=
width consistent with x-ray data
A-T bond …
is a double bond
c-g bond…
is a triple bond
since the two strands or DNA are complementary…
each strand acts as a template for building a new strand in replication
semiconservative means that
each copy contains one original strand and one newly synthesized strand
how does the DNA unwind to start replication
the hydrogen bonds between the bases are broken
DNA replication occurs in the …
5’ to 3’ direction
what are telomeres…
sequences of DNA at the end of chromosomes
where does replication happen
origins of replications
what are origins of replication
site where the two DNA strands are seperated openig a replication bubble
what is special abt eukaryotic chromosomes
they may have hundreds of even thousands of origins or replication
in what direction does replication take place
replication proceeds in both directions from each origin, until the entire molecule is copies
at the end of each replication bubble there is a
replication fork
what is a replication fork
a y-shaped region where new DNA strands are elongating
helicases…
are enzymes that untwist the double helix at the replication forks
single-strand binding proteins…
binds to and stabilizes single stranded DNA until it can be used as a template also removes proteins from DNA
topoisomerase…
corrects overwinding AHEAD of replication fork by breaking, swiviling and rejoining DNA strands
why is topoisomerase important to doctors
it is a target of chemotherapy drugs + cipro bc inhibiting this will cause DNA to break down and cause apoptosis
DNA polymerases 3 …
are enzymes that catalyze the elongation of new DNA at replication fork
what do most DNA polymerase 3 require
a primer and a DNA template strand
rate of elongation in bacteria
500 nucleotide per second
rate of elongation in humans
50 per second in human cells
the nucleus is full of…
nucleoside triposphates
what are nucleoside triphosphates
dATP, dCTP, dGTP, dTTP
where does the energy for the new phosphodiester bond come from (DNA replication)
comes from the 2 phosphates of the nucleoside tripphosphate ( 1 of the phosphate stays attached to the base)
the initial nucleotide strand in DNA replication is
a short RNA primer
primase…
is an enzyme that can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as templae
what can DNA polymerase 3 not do
initiate synthesis of polynucleotide ; only adds nucleotides to 3’ end
how long is the rna primer
5-10 nucleotides long
the 3’ end of the RNA primer …
serves as the starting point for the new DNA strand
leading strand=
continuous strand of newly snthesized DNA
lagging strand=
short sequence of newly synthesized DNA
okazaki fragments=
series of lagging strand
how are the lagging strands joined
by DNA ligase t
how are the lagging and leading strand different
the leading stand has one RNA primer per active origin of replication while the lagging strand receives several
what does DNA polymerase 1 do
replaces RNA primer with DNA nucleotides
what does DNA ligase do
join the two okazaki fragments replacing RNA primer with DNA
works after DNA polymerase 1 removes RNA
DNA polymerase extra job is to
proofread newly made DNA, replacing any incorrect nucleotides
what is a mismatch repair
repair enzymes correct errors in base pairing
how can DNA be damaged
by exposure to harmful chemicals or physical agents such as cigarrets smoke and z-rays, can also undergo spontaneous change
what happens in nucleotide excision repair
a nuclease cuts out and replaces a damaged stretches of DNA
the polymerase gomes and adds new bases
DNA ligase comes and joins them
Xeroderma Pigmentosim
lacks the ability to repair DNA damages like thymine dimers and hence is extremely sensitive to sunlight
