Exam Five Flashcards
What is the ultimate electron acceptor in oxidative phosphorylation?
O2
In oxidative phosphorylation, the proton is moved from the ____________ to the _________________
mitochondrial matrix; intermembrane spaces
A proton gradient is formed in between the mitochondrial matrix and the intermembrane spaces. Which has a higher proton concentration?
intermembrance space
What is the proton motive force?
the proton gradient that powers the ATP synthase and produces ATP
What is the tendency of a substrate to accept electrons?
reduction potential
How does the reduction potential change as the ETC progresses?
becomes more positive/favorable as the chain goes on
What does the protonmotive force power?
ATP synthase
How many multiprotein clusters are there?
4
Which complexes pump protons into the intermembrane space?
I, III, and IV
What is the electron donor in complex I?
NADH
What is the electron acceptor in complex I?
Q
What are the main electron transport components in complex I?
FMN and Iron-Sulfur Clusters
What is the enzymatic name for complex I?
NADH-CoQ Reductase
What is the electron donor in complex II?
Succinate
What is the electron acceptor in complex II?
Q
What are the main electron transport components in complex II?
FAD
What is the enzymatic name for complex II?
Succinate CoQ reductase or succinate dehydrogenase
What is the electron donor in complex III?
QH2
What is the electron acceptor in complex III?
cytochrome c
What are the main electron transport components in complex III?
Rieske ISP, cyt c, cyt bL, and cyt bH
What is the enzymatic name for complex III?
cyt. c oxidoreductase
What is the electron donor in complex IV?
cyt c
What is the electron acceptor in complex IV?
O2
What are the main electron transport components in complex IV?
cyt a, Cu
What is the enzymatic name for complex IV?
cyt c oxidase
How can you skip complex I in the ETC?
start from succinate DH
what are the flavin containing electron carriers?
FMN or FAD
What is a nonpolar mobile electron carrier?
ubiquinone
How many electrons do FMN and FAD accept at a time?
Up to two
How many electrons do FMN and FAD donate at a time?
one
What are the proteins called that contain porphyrin?
cytochromes
How many electrons do iron-sulfur clusters carry?
one
How many sulfur atoms are present in a cluster if there are 2 iron atoms?
2
What occurs during complex I?
FMN accepts two electrons from NADH, several iron-sulfur clusters pass one electron at a time toward the Q binding site, and 4 protons are moved to the intermembrane space
What occurs during complex II?
FAD accepts two electrons from succinate, electrons are passed one at a time via iron-sulfer centers to ubiquinone
What occurs during complex III?
it accepts two electrons from QH2 to reduce cyt c, translocate 4 protons to the intermembrane space
What occurs during the Q cycle?
2 electrons from QH2 split and require another molecule of QH2 to complete the cycle
What is the main reaction of the Q cycle?
QH2 + 2 cyt c (Fe3+) —> Q + 2 cytc (Fe2+)
What is cytochrome c?
a soluble heme-containing protein in the intermembrane space
What is cytochrome c’s job?
carry a single electron from the complex III to cytochrome c oxidase (complex IV)
Cytochrome c is ________
a. integral membrane protein
b. a part of complex III
c. a part of complex IV
d. peripheral membrane protein
d. peripheral membrane protein
is heme hydrophilic or hydrophobic?
hydrophobic
What is the hydrophilic part of cytochrome c?
Lys
Cytochrome c has a large amount of Lysine residues. Therefore it is a/an (acidic/basic) protein because its pI is (high/low)
basic; high
cytochrome c oxidase (complex IV) contains __ heme groups
2
What ions are present in cytochrome c oxidase?
copper
What does CuA do?
accepts electrons from cytochrome c
What does CuB do?
transfers electrons to oxygen
Where does O2 get reduced to water?
matrix
Which inhibitor of the ETC stops the chain after NADH and before Q?
rotenone
Which inhibitor of the ETC stops the chain after Cyt b and before Cyt c1?
antimycin A
Which inhibitor of the ETC stops the chain after Cyt (a + a3) and before O2?
cyanide or carbon monoxide
electron carriers before the block (inhibited spot) become _________ and those after the block become __________
reduced;oxidized
How does the F0 subunit of ATP Synthase rotate?
by H+ flow
Which parts of ATP synthase rotate?
F0 and gamma
Which parts of ATP synthase do not rotate?
catalytic parts
O form of ATP synthase means
open: binding site for ADP and Pi is open
L form of ATP synthase means
loose: ADP and Pi bind to site L
T form of ATP synthase means
tight: catalytically active
From which conformation is ATP released from ATP synthase?
O
How many ATP are released per one revolution of ATP synthase?
3
How many protons does it take to drive one revolution of the camshaft to produce 3 ATP molecules?
9-12
In which direction to ATP synthase operate?
either direction, depending on concentrations
electron transport translocated protons and formed a concentration gradient and a charge gradient across the membrane
chemiosmosis
energy created by the proton gradient
proton motive force
How many protons move to the intermembrane space if you start with 1 NADH molecule?
10
How many protons move to the intermembrane space if you start with 1 Succinate molecule?
6
What is the P:O ratio?
phosphorylation of ADP per oxygen atom
What is the approximate P:O ratio for NADH oxidation?
2.5 ATP/O
What is the approximate P:O ratio for QH2 oxidation?
1.5 ATP/O
How many protons are needed for one complete rotation of ATP synthase?
number of c subunits in ATP synthase
what is a chemical that can diffuse through the nonpolar membrane?
uncoupler
Why is an uncoupler important in biochemistry?
it can move H+ across the membrane without ATP synthase
Dichyclohexylcarbodiimide (DCCD) reacts with Asp and Glu residues in the c-s.u. of F0 and blocks ATP synthase activity. What happens to the rate of electron transport if DCCD is added to the respiring molecule?
the rate will decrease, although NADH will continue to oxidize at first, but the protons will get backed up and not be converted to ATP, reducing the rate
ATP synthesis can be uncoupled from ETC to generate _______
heat
Why does uncoupling ATP synthesis generate heat?
the protons pass through and nothing happens, so the energy is transferred to heat
What is the only irreversible step in the ETC?
complex IV (cyt c oxidase)
What regulates the ETS?
cyt c oxidase
What regulates cyt c oxidase?
level of oxidation/reduction of cyt c
What regulates the level of redox of cyt c?
NADH and ATP
When is the ETS rate the highest?
when [NADH]»_space;» [NAD] and [ADP]»_space;» [ATP]
What facilitates the movement of specific molecules within an organism?
transport proteins
one thing moves one direction
uniport
2 things move one direction
symport
2 things move opposite directions
antiport
What kind of transport protein is GLUT 1?
uniport
What is the goal of the malate/aspartate shuttle?
move NADH from the cytosol into the mitochondria
How does the malate/aspartate shuttle work?
moves the electrons as malate and then uses it to reduce NAD+ to produce NADH in the mitochondria
Why is the glycerophosphate shuttle considered as a part of complex II?
it adds to the pool of QH2
How does the glycerophosphate shuttle work?
takes an NADH molecule to the mitochondria as FADH2, but makes less ATP
How does ATP get moved from the mitochondria to the cytosol?
ADP-ATP translocator
What symport helps facilitate the move of ATP from the mitochondria to the cytosol?
Pi-H+ symport
light energy is converted to ATP in a plant’s __________
chloroplasts
What is the main idea of respiration?
NADH —-> H2O
What is the main idea of photosynthesis?
H2O —-> NADPH
Where does the proton gradient accumulate in photosynthesis?
thylakoid lumen
Where does the proton gradient accumulate in respiration?
intermembrane space
Photosynthesis happens at the interface of _________
stroma and thylakoid
Respiration happens at the interface of _________
matrix and intermembrane
what is the membrane electron transport in photosynthesis?
plastoquinone (Q)
what is the membrane electron transport in respiration?
CoQ
What is the source of electrons in photosynthesis?
water
What is the source of electrons in respiration?
NADH
What is the final electron acceptor in photosynthesis?
NADP+
What is the final electron acceptor in respiration?
O2
Why do lipids yield more energy per carbon than carbohydrates?
fatty acids are much more reduced compared to carbohydrates
What is the enzyme in the small intestine that releases fatty acids?
lipase
What activates lipases?
glucagon and epinephrine
What happens to the fatty acids after being cleaved off from TG?
beta oxidation
How is the fatty acid “activated” for beta oxidation?
it is attached to CoA
What is used to form one thioester bond to activate a fatty acid?
2 ATP equivalent of free energy
What is the transporter to take a fatty acid from the cytosol to the mitochondria for beta oxidation?
acyl-carnitine/carnitine transporter
How does beta oxidation work?
2 carbons at a time are oxidized/degraded as acetyl-coa
Describe the spiral pathway of beta oxidation
each round takes two carbons off the chain from the carboxyl end, which produces 1 acetyl-coa, 1 QH2, and 1 NADH, consisting of 4 enzymatic steps
Why is it called beta oxidation?
the attack occurs on the beta carbon (second carbon from the carbonyl carbon)
The 4 reactions/2 carbons per round of beta oxidation produces _______
1 QH2, 1 NADH, and 1 acetyl-coA
What are the 4 enzymes of beta oxidation?
- acyl-coa dehydrogenase (AD)
- enoyl-coa hydratase (EH)
- 3-L-hydroxyacyl dehydrogenase (HAD)
- beta-ketoacyl-coa thiolase (KT)
What is the energy yield of beta oxidation?
14 ATP
Would unsaturated fatty acids yield more or less energy than the saturated fatty acid?
less
Odd number carbon double bonds lose how much ATP overall?
1.5
Even number carbon double bonds lose how much ATP overall?
2.5
What mechanisms are controlled so only one goes on at a time?
beta oxidation and fatty acid synthesis
Where does fatty acid biosynthesis occur?
cytosol
How does acetyl-coa get to the cytosol from the mitochondria to produce fatty acids?
tricarboxylate transport system
How and where is acetyl-coa produced?
in matrix from fatty acid oxidation or pyruvate dehydrogenase
What is the 2 carbon donor for fatty acid biosynthesis?
malonyl CoA
Why is the conversion of acetyl-coa to malonyl-coa so important?
it is the first committed step and one of the rate controlling steps
What affects the conversion of acetyl-coa to malonyl-coa?
citrate stimulates it, long chain fatty acids inhibit it, and insulin activates the enzyme
What is the acyl carrier for synthesis?
ACP
What is the overall goal of fatty acid synthesis?
attach acetate unit from malonyl-coa to a growing chain and then reduce it
What are the four enzyme-catalyzed steps of fatty acid synthesis?
condensation of the chain with activated acetate, reduction of carbonyl to hydroxyl, dehydration of alcohol to trans-alkene, and reduction of alkene to alkane
How is the growing fatty acid chain initially attached to the enzyme?
thioester linkage
What is required if you a have a fatty acid beyond a saturated 16C?
elongases in ER or mitochondria OR desaturases for unsaturated fatty acids
Where is there a futile cycle control in fatty acid biosynthesis?
Acetyl-CoA carboxylase: inhibited by AMP- and cAMP-dependent phosphorylation and activated by insulin-dependent phosphorylation
What is the controlling point of F.A. oxidation?
lipase
What is the controlling point of F.A. synthesis?
ACCase
How does insulin affect lipids?
it activates phosphatases that dephosphorylate enzymes, which activate ACCase and increase fatty acid synthesis
How does glucagon affect lipids?
it triggers cAMP production, which activates proteinase kinase A, which phosphorylates enzymes that activate TG lipases and inhibit ACCase, increasing oxidation of F.A., decreasing synthesis of F.A., and decreasing cholesterol synthesis
What is another alternative fate for acetyl-coa when large amount from fats inhibits the citric acid cycle?
ketone bodies
What is the purpose of ketone bodies?
provide fuel during starvation for the brain, heart, and skeletal muscles
What are the three ketone bodies?
acetoacetate, acetone, and D-beta-hydroxybutyrate
What organ is the source of ketone bodies?
liver
What is the name of the enzyme that is a major controlling point of cholesterol biosynthesis, inhibited by phosphorylation, and is what statin inhibits?
HMG CoA reductase
How does statin work?
lowers serum cholesterol by inhibiting HMG CoA reductase
Where does digestion and absorption of dietary lipids occur?
small intestine
Why do we need to package the dietary lipids before sending them to other tissues?
they are nonpolar and cannot be transported otherwise
What transfers lipids from the intestine to the liver?
chylomicrons
What transfers lipids from the liver to other tissues?
VLDLs and LDLs
What transfers lipids from other tissues to the liver?
HDL
Which is denser, fat or protein?
protein
Low density = (high/low) fat?
high
High density = (high/low) fat?
low
What is bad cholesterol?
LDL
What is the purpose of LDLs?
deliver cholesterol and cholesterol esters to cells
What is missing in people with familial hypercholesterolemia?
LDL receptor
What is good cholesterol?
HDL
What is the purpose of HDLs?
remove excess cholesterol from cells
What is required for HDLs?
membrane transporter/flippase
How many genes does the X chromosome carry?
about 1500
How many genes does the Y chromosome carry?
about 100
What comprises a nucleotide?
a five-carbon sugar, a nitrogen containing ring, and one or more phosphate group
What are the purines?
adenine and guanine
What are the pyrimidines?
cytosine, thymine, and uracil
Do purines or pyrimidines have two rings?
purines
Do purines or pyrimidines have one ring?
pyrimidines
What is the difference between ribose and deoxyribose?
ribose has one extra OH group compared to deoxyribose
Why does DNA twist?
once you make a double stranded structure, it twists to accommodate its size
In which direction does DNA run?
antiparallel
Is DNA right or left handed?
right
How many base pairs are there per turn of DNA?
10
Exposed ____ binds to ______ to reduce repulsion in DNA
P; Mg2+
Are the base pairs interior or exterior to the helix axis?
interior
Edges of base pairs exposed at grooves can be recognized by what?
DNA binding proteins
DNA strands make double stranded helix by _______ bonds between the bases
hydrogen
The ________ of the bases in DNA are the information.
sequence
The _________ of the bases in DNA is the key in transmitting the information.
complementarity
When can double-stranded nucleic acids be denatured?
at high temperatures
What occurs to DNA at lower temperatures?
complementary polynucleotides anneal
What kind of bonds always remain intact throughout DNA denaturation and renaturation and why?
covalent bonds so that the genetic code itself remains intact
What occurs if you rapidly cool denatured/separated DNA?
improper base pairing
What is the Tm?
melting temperature of DNA
The higher the ___ content, the higher the Tm
GC
Why does GC content raise the Tm?
stacking energy
What does stacking energy mean?
the energy required to untwist the DNA
The Tm is also equal to….
the temperature at which 50% of the DNA has been denatured
What does the hybridization technique do?
identify where partner is
What does southern blot identify?
DNA to DNA hybridization
What does northern blot identify?
RNA-DNA hybridization
What does western blot identify?
protein to antibody reaction
What do restriction enzymes do?
digests the phosphodiester bonds that connect nucleotides
How do restriction enzymes know where to cut?
they recognize very specific patterns of 4-6 bases in DNA, normally in palindrome format
What is the purpose of dideoxy sequencing?
figure out base order/sequence
What is the purpose of polymerase chain reaction (PCR)?
amplify sections of DNA
DNA polymerase adds deoxynucleotides at the ___ end of the growing chain of nucleic acid
3’
Where does DNA polymerase add the complementary nucleotides?
the 3’ - OH of the primer
What are the ingredients for a DNA sequencing reaction?
DNA, primer, dNTPs, ddNTPs, DNA polymerase, buffer
Why does DNA polymerase stop elongation when ddNTP is added instead of dNTP?
ddNTPs lack a 3’-OH group, so no more NTPs can attach
What is PCR?
enzymatic amplification of a segment of DNA
What are the ingredients for a PCR reaction?
DNA, primers (a pair), dNTPs, DNA polymerase (normally Taq polymerase), buffer
What are the 3 steps of PCR?
- strand separation
- primer annealing
- primer extension
At what temperature does strand separation occur?
90-95 degrees C
At what temperature does primer annealing occur?
45-55 degrees C
At what temperature does primer extension occur?
70 degrees C
What are the four things PCR is used for?
- identify mutations
- site-directed mutagensis
- detection of signature sequences
- forensic use
How many strands of DNA are used in sequencing reactions?
one
How many strands of DNA are used in PCR reactions?
two
Is the inner membrane of the mitochondria directly permeable to small molecules and hydrogen ions?
no
The electron transport chain operates (independently/dependently) of other metabolic processes.
dependently
Where is H+ ion concentration higher?
intermembrane space
Where is the pH higher?
matrix
What are the two electron transport inhibitors?
cyanide and rotenone
What is the uncoupling agent that increases membrane proton permeability?
FCCP
What is the ATP synthase inhibitor that binds to F0 and blocks the proton channel?
oligomycin
What is the transport inhibitor that binds to inward-facing site of ATP-ADP translocase?
bongkrekic acid
What provides the energy that excites the electrons in the chlorophyll molecules?
light
What is the source of the electrons that replace the excited electrons lost from chlorophyll?
water
What is the first step of ATP synthase?
protons from the intermembrane space bind to proton binding sites on c subunits
What is the second step of ATP synthase?
as the c ring rotates past the a subunit c, subunits release their protons into the matrix
What is the third step of ATP synthase?
the gamma subunit rotates past the a subunit, c subunits release their protons into the matrix
What is the fourth step of ATP synthase?
the gamma subunit rotates and interacts with the three alpha-beta subunit pairs, causing conformational changes in the beta subunits
What is the last step of ATP synthase?
each beta subunit binds ADP and Pi, converts ADP + Pi to ATP, and releases ATP once during one turn of the gamma subunit
How is oxaloacetate modified to a form that can be transported out of the matrix?
transamination
Which compound transfers reducing equivalents (electrons) into the mitochondrial matrix?
malate
What kind of reaction is the first reaction of beta oxidation?
oxidation
What kind of reaction is the second reaction of beta oxidation?
hydration
What kind of reaction is the third reaction of beta oxidation?
oxidation
What kind of reaction is the fourth reaction of beta oxidation?
cleavage
What does CAT1 do?
converts carnitine into acyl-carnitine
What does CAT2 do?
converts acyl-carnitine into carnitine
Which of the three ketone bodies is the only one reduced to alcohol form?
beta-hydroxybutyrate
Which of the three ketone bodies is only made up of three carbons?
acetone
Increased levels of which cholesterol is associated with atherosclerosis?
LDL
Do nucleosides contain a phosphate group?
no
What is the product when a base bonds at C1 of ribose or deoxyribose?
nucleoside
Are nucleosides found in both RNA and DNA?
yes
What is true for both DNA and RNA?
sugars are connected with a 3’-5’ phosphodiester link
What is true for RNA only?
it commonly exists in a variety of secondary structures
Which purine has a ketone?
guanine
Which purine doesn’t have any oxygens?
adenine
Which pyrimidine only has one ketone group?
cytosine
Which pyrimidine has two ketone groups, but no methyl group?
uracil
Which pyrimidine has two ketone groups AND a methyl group?
thymine
