Test 3 Flashcards
metabolism
all the chemical reactions that take place within an organism
metabolic pathway (catabolic)
involves the breakdown of a molecule into smaller subunits, releasing energy stored in the chemical bonds of reactants
metabolic pathways (anabolic)
involves the synthesis (construction) of cellular molecules and macromolecules from smaller subunits, consuming energy
work
accomplishing a changes in the position or state of matter
kinetic energy
energy associated with movement
potential energy
stared energy due to structure or location
First Law of Thermodynamics
energy cannot be created or destroyed, but can be transferred/transformed from one type to another
Second Law of Thermodynamics
everything in the universe is subject to spontaneous disorder
entropy
measure of disorder/chaos
free energy
portions of systems energy that is usable for work when temperature and pressure are uniform
exergonic
releases energy
endergonic
requires energy
ATP
adenosine triphosphate - the universal energy currency of a cell
catalyst
chemical agent that speeds up the rate of a chemical reaction without being consumed by the reaction
enzymes
specialized catalytic proteins found in living cells
ribozymes
RNA molecules with catalytic properties
activation energy
initial input of energy needed to start a reaction (push reactants over an energy barrier)
substrate
reactant that binds to enzymes activate site
active site
the shape-specific building site on an enzyme into which its substrate fits
induced fit
the temporary gripping of substrate by an enzyme, due to shape change confirmation of the enzyme on order to have tight interactions with the substrates
cofactor
non-protein helpers that bind to enzymes to maximize their function and are the reason why you should take daily multivitamin supplements
coenzyme
organic molecules that help to optimize enzyme function, but are left uncharges by a reaction
free
free
competitive inhibition
the inhibitor binds to an active site of an enzyme, directly blocking any substrate from binding
noncompetitive inhibition
the inhibitor binds to an allotteric site not the active site changing the enzymes shape
allosteric regulation
a situation in which a proteins function at one site is affected by the binding of a regulatory molecule at a separate site
allosteric site
specific receptor region on an enzyme that is not the active site
activator
a molecule capable of stabilizing enzyme shape and function
inhibitor
will cause that enzyme to lose its functional shape
feedback inhibition
high levels of an “end product: of a metabolic pathway can inhibit the reaction that produces more of the product
cooperativity
the binding of one substrate to a multi-unit enzyme stabilizes favorable shape conformation for all of the other enzyme subunits
Is a cell a closed system
no
Why is some energy lost as heat during energy transfer
When energy is lost as heat it is the energy of random molecular motion and the universe tends towards entropy which is the measure of disorder
When would the coupling of endergonic reactions occur spontaneously
if the net ∆G is negative.
What are ATP molecules often used for
to store the energy harvested from exergonic reactions for later use in endergonic reactions
What type of molecule will have more potential energy
larger molecules have more than smaller ones
how do enzymes and ribosomes effect biological reactions
by lowering the activation energy needed for a reaction to begin
Are ribosomes and enzymes consumed during a reaction
no
What is an example of a catabolic reaction
cellular respiration
what is an example of an anabolic reaction
photosynthesis
Why do cells use enzymes, rather increase their temperature, to overcome the activation energy needed for a reaction to begin?
temperature increase can only push reactants to the transition site, enzymes can (1) position reactants together to facilitate bonding (2) strain bonds in reactants to make it easier to achieve transition state (3) change the local environment
Does an enzyme alter the ∆G value of a chemical reaction?
enzymes do not have an impact on ∆G
Can one type of enzyme bind to a large number of different substrate types?
No, an enzyme is made to bond to one specific substrate.
What happens when an enzyme is saturated in a solution with substrate
the speed of the reaction will plateau
Is the inhibition of an enzyme always a reversible event?
It is not ALWAYS reversible but it is pretty common
Can increasing substrate levels “overcome” both competitive and noncompetitive inhibition? Why or why not?
Increasing substrate levels can over come competitive inhibitor because it becomes more likely for the enzyme to react with the substrate. It will NOT be able to over come noncompetitive inhibition because this type of inhibitor changes shape and fits into the enzyme not allowing for anything to bind
What gave rise to the large diversity of enzymes that we observe today?
evolutionary processes acting upon random mutations
What is an example of kinetic energy
the energy of running water
what is an example of potential energy
water behind a dam because of its altitude above sea level
If a reaction is able to proceed spontaneously (after inertia is overcome), will it result in a higher or lower amount of entropy being present?
lower
In order for a reaction to be spontaneous (after inertia is overcome), does the value of ∆G need to be positive or negative?
negative
How might an enzyme strain substrates in order to make them more likely to undergo a chemical reaction
temporarily gripping of substrates due to change in shape
Why do temperature and pH affect the function of enzymes?
at high temperatures, enzymes can function at a faster rate, but if it gets too high then it can cause the enzyme to denature
Would all allosteric regulation be classified as noncompetitive inhibition?
Practically all of them, there are a few unique cases in which this would be untrue
What are some of the ways in which metabolic pathways are regulated in living systems
feedback inhibition
When are enzymes needed in a metabolic pathway
every step of the way due to enzyme-substrate structural specificity
cellular respiration
catabolic process by which living cells obtains energy from organic molecules. Primarily ATP and NADH
fermentation
process used by organisms to break down organic fuels on the absence of oxygen
aerobic respiration
uses oxygen in a step wise process
redox reactions
involve the transfer of one or more electrons from one reactant to another
oxidation
loss of electrons
reduction
addition of electrons
electron transport chain
the final stage of respiration that involves a group of proteins complexes and small organic molecules embedded in the inner mitochondrial membrane, many of which are cytochromes
chemiosmosis
coupling of redox reactions to ATP synthesis
ATP synthase
a transmembrane enzyme located on the crustal of the inner mitochondrial membrane, that is capable of synthesizing ATP from ADP and Pi
facultative anaerobes
yeast and many bacteria can survive by switching between fermentation or aerobic respiration
glucose
the main type of sugar in the blood and is the major source of energy for the body’s cells
NAD+
the oxidized form of nictotinamide adenine dinucleotide, a coenzyme that can except enzymes becoming NADH
NADH
the reduced form of nicotinamide adenine dinucleotide, which temporarily stores electron during cellular respiration
glycolysis
a series of reactions that ultimately splits glucose in pyruvate
citric acid cycle
a chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules begun in glycolysis by oxidizing acetyl CoA to carbon dioxide; the second major stage inn cellular respiration
pyruvate
an important metabolic product for energy-producing biochemical pathways
Acetyl coa
the entry compound for the citric acid cycle in cellular respiration
oxaloacetate
an intermediate of the citric acid cycle where it reacts with acetyl cow to form citrate
How does the general transfer of energy occur
it occurs when matter (food) passes from producers to primary consumers to secondary consumers
what happens to energy during every energy transfer
some usable energy is lost due to heat loss as part of the universal tendency towards entropy
What molecules will be used to store energy harvested from the exergonic reactions of cellular respiration
ATP, NADH, FADH2
What is the energy depleted form of ATP
ADP
What is the energy depleted form of NADH
NAD+
What is the energy depleted form of FADH2
FADH+
what is the overall equation for cellular respiration
C6 H12 O6 + 6O2 –> 6CO2 + 6H2O + ATP
Has an oxidized molecule gained or lost potential energy?
lost potential energy
Has a reduced molecule gained or lost potential energy?
gained potential energy
What are the oxidized and reduced forms of the electron acceptor NAD+?
NAD+ is the oxidize from and the reduced form is NADH
Where does glycolysis take place
cytoplasm
What is the difference in glycolysis in other living things
there is none, glycolysis is similar ion all living things
can glycolysis occur without oxygen
it can when fermentation is used
What is the large-scale purpose of glycolysis
the breakdown of glucose with minor energy yield
What is incoming 6-carbon glucose molecule turned into during glycolysis
2 3-carbon molecules of pyruvate
Where does the breakdown of pyruvate take place
mitochondrial matrix
What happens to both of the 3 carbon pyruvate molecules formed during glycolysis
they both lose a carbon becoming 2 carbon acetyl cow molecules
What happened to the lost carbon molecule from the 3 carbon private that was formed during glycolysis during the breakdown of pyruvate
Co2 is produced from the carbon and one NADH is produced from this
Where does the citric acid cycle take place
the motochondrial matrix
What is the purpose of the citric acid cycle
small-scale breakdown of glucose with further energy yield
What molecule os created during each turn of the cycle
a 2 carbon acetyl-coA molecule joins a 4-carbon ocaloacetate molecules to create a 6-carbon intermediate molecule
What happens to the 6-carbon intermediate molecule (this is occurring during the citric acid cycle)
it slowly breakdown further to a 4 carbon intermediate molecule and a co2 molecule is released and a NADH molecule is produced
what is the last step of the citric acid cycle
the cycle reforms a 4 carbon oxaloacetate molecule that will continue to crank the cycle for the next round
For every 2 pyruvate molecules the overall products of the citric acid cycle would be…
4 CO2, 2 ATP, 6NADH, AND 2 FADH2
How is ATP, NADH,and FADH2 created
this is made possible due to structural alterations of intermediate molecules
where is the electron transport chain
this set if reactions is occurring in the inner membrane of the mitochondria
free
free
What happened to the electrons donated by oxidized NADH and FDAH2 molecules
they will be passed down an electron carrier chain of proteins, resulting in the pumping of hydrogen protons into the mitochondrial intermembrane space, and that these protons will be allowed to flow back into the mitochondrial matrix only through an ATP synthase channel, thereby creating ATP
What is the final electron acceptor of an aerobic electron transport chain
oxygen
When are most ATP molecules created
the electron transport chain
How much ATP is created in total during cellular respiration
ideally 38
Does the ideal 38 ATP often yield from cellular respiration
no because the conversion of glucose to usable energy oil not 100% efficient
What will happen to the citric acid cycle if there is a lack of oxygen
it will derail because there will be a lack of NAD+ and FAD+ produced from he electron transport chain
what will happen to the electron transport train if the there is a lack of oxygen
it will derail because oxygen is a vital reactant in the final electron acceptor
When oxygen is not present, what two survival strategies can be used by different types of organisms?
“breathing” substances other than oxygen (anaerobic respiration involving all three stages of cellular respiration, but using alternate final electron acceptors in their electron transport chains) and fermentation (involving only the glycolysis stage of cellular respiration with its substrate-level phosphorylation)
Is fermentation more or less effective than aerobic and anaerobic respiration
its equally as effective
If oxygen is present, what happens to facultative anaerobes
they will switch back to aerobic cellular respiration in order to maximize ATP production
What is the main goal of both alcoholic fermentation and lactic acid fermentation
to regenerate a supply of NAD+ in order to allow glycolysis to continue in the absence of oxygen
Which of the three stages of aerobic respiration of hypothesize to be the oldest
glycolysis
How can carbohydrates produce energy in cellular respiration
they can be fed into various chemical reaction steps
How can intermediate molecules serve as raw material building block inputs for anabolic reactions
they may be diverted from the purpose of providing energy
How can a cell control the rate of aerobic cellular respiration via feedback inhibition?
An important enzyme in glycolysis (phosphofructokinase) can be inhibited by high levels of either ATP or citrate/citric acid; when levels of both of ATP and citrate/citric acid are low, this enzyme will operate much more quickly, increasing a cell’s rate of aerobic cellular respiration.
TRANSFORMATION
a cellular changing in genotype and phenotype due to acquire foreign substance
semiconservative replication
when each new daughter DNA molecule will contain one old strand and one new strand
Which team of scientists was responsible for first creating (and explaining) a model of the double helix structure of DNA molecules?
Watson and crick
Prior to any understanding that DNA forms the genetic material of cells, what type of molecule was originally hypothesized to make up a cell’s genetic material?
proteins
Which team of scientists used studied bacteriophage activity to be able to infer that the DNA of a virus (and not the protein coat of a virus) is what enters a bacterial cell in order to cause infection?
Avery, McCarthy, and MacLeod
Why is it true that equal amounts of A vs. T, and also C vs. G, will be present in a DNA molecule?
Because they are pairs on the DNA Double helix
Who was the first to understand that equal amounts of A vs. T, and also C vs. G, will be present in a DNA molecule?
Chargaff
How was X-ray crystallography used to understand the spiral (helical) structure of DNA molecules?
it allowed the determination of the helical 3D shape of DNA molecules based on the diffraction of X-Rays present
What are the subunits that make up DNA and RNA
nucleotides
What are the sequences of events for DNA replication
the unwinding of the DNA molecule by DNA helicase, the addition of primer “start signs”(made of RNA) by DNA primase, the addition of new nucleotides (to form the new DNA strand) by DNA polymerase, the editing out of the RNA primers by a different form of DNA polymerase, and the joining together of Okazaki fragments by DNA ligase.
Why are Okazaki fragment created during DNA replications?
to allow DNA polymerase to synthesize the lagging strand in segments
How is DNA replication made more rapid
Understand that the process of DNA replication is made more rapid by the fact that DNA polymerase has binding sites (active sites) for all four types of nucleotides (A, C, T, and G), so it is ready to add any of these into a growing new DNA strand at any time.
DNA polymerase
An enzyme that catalyzes the elongation of new DNA by the addition of nucleotides to the 3’ end of the existing chain
DNA helicase
an enzyme that untwists the double helix of DNA at replication forks, separating the two strands and making them available as template strands
primer
a short polynucleotide with free 3’ end, bound by complementary base pairing to the template strand and elongated with DNA nucleotides
DNA primase
an enzyme that joins RNA nucleotides to make a primer during DNA replication, using the parental DNA strand as a template
leading strand
the complimentary DNA strand synthesized continuously along the template strand towards replication fork int he mandatory 5’ to 3’ direction
lagging strand
a discountinuosly synthesized DNA strand that elongates by means of Osaka. fragments, each synthesized in a 5’ to 3’ direction away from the replication fork
Okazaki fragments
a short segment of DNA synthesized away from the replication fork on a template during DNA replication. Many such segments are joined together to make up the lagging strand of newly synthesized DNA
DNA ligase
a linking enzyme essential for DNA replication; catalyzes the covalent bonding of 3’ end of one DNA fragment to the 5’ end of another DNA fragment
What does semiconservative DNA replication do
helps ensure the copying of an original DNA molecule is rapid and accurate
how semiconservative DNA replication helps to ensure that the copying of an original DNA molecule, while very rapid, is also very accurate
(with a significantly lower error rate than might be expected due to chance, alone, since extensive post-replication “editing/proofreading” of the new strand (against the older strand) is subsequently carried out by DNA polymerase enzymes
