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BIO FINAL EXAM 2nd Half
Mcanelly
212
Biology
Undergraduate 3
12/10/2012

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Term
Cells use chemical energy stored in organic molecules to regenerate _____, which powers work
Definition
ATP
Term
includes both aerobic* and anaerobic* respiration but is often used to refer to aerobic respiration
Definition
cellular respiration
Term
Energy is captured in the form of____ and lost as ___
Definition
ATP...heat
Term
in ____ a substance loses electrons
Definition
oxidation
Term
in ______ a substance gains electrons (amount of positive charge is reduced)
Definition
reduction
Term
Chemical reactions that transfer electrons between reactants are called
Definition
redox reactions
Term
An electron loses ________ energy when it moves from a less electronegative atom toward a more electronegative atom.
Definition
potential
Term
The electron donor is called the _____ agent
Definition
reducing
Term
The electron receptor is called the _____ agent
Definition
oxidizing
Term
Coenzyme _____ is a key electron carrier in redox reactions.
Definition
NAD+
Term
NADH passes the electrons to the
Definition
electron transport chain
Term
3 stages of cellular respiration
Definition
glycolysis, citric acid cycle and oxidative phosphorylation
Term
breaks down glucose to pyruvate
Definition
glycolysis
Term
finishes breaking down glucose
Definition
citric acid cycle
Term
oxidative phosphorylation
Definition
accounts for hte ATP synthesis because its powered by redox reactions
Term
breaks down pyruvate to alcohol or lactic acid
Definition
fermentation
Term
substrate level phosphorylation involves transfer of a
Definition
phosphate from a substrate molecule to ADP
Term
glycolysis takes place in the ___
Definition
cytosol
Term
glycolysis generates NO
Definition
CO2
Term
ATP is a substrate for _____. But_____ is also allosterically
inhibited by ATP and activated by AMP
Definition
PFK
Term
the electron transport chain _____ generate ATP as it passes electrons from one recipient molecule to hte next
Definition
DOES NOT
Term
the # of ATP molecules produced per molecule of NADH is
Definition
2.5
Term
the # of ATP molecules produced per molecule of FADH2 is
Definition
1.5
Term
difference between lactic acid and alcohol is that in alcohol ___ is produced
Definition
CO2
Term
_____ pathways don't have to rely on glucose
Definition
catabolic
Term
oxidative phosphorylation is the synthesis of ATP dependent on
Definition
electrons flow
Term
The _____ takes place within the mitochondrial matrix
Definition
citric acid cycle
Term
The ________ and _______ produced by the cycle of glucose metabolism relay electrons extracted from food to the electron transport chain
Definition
NADH and FADH2
Term
The electron carriers that are reduced during the citric acid cycle must be ____ to take part in the cycle again.
Definition
reoxidized
Term
ATP is synthesized by reoxidation of electron carriers in the presence of O2.

this is the process of
Definition
oxidative phosphorylation
Term
2 stages of oxidative phosphorylation:
Definition
electron transport and chemiosmosis
Term
The respiratory chain is located in the inner _____
Definition
mitochondrial membrane
Term
During electron transport _______ are also actively transported.
Definition
protons
Term
_____ accumulate in the intermembrane space and create a concentration gradient and charge difference—potential energy!
Definition
protons
Term
Protons diffuse back into the mitochondria through ATP synthase, a channel protein.
Diffusion is coupled to ATP synthesis.

this describes
Definition
chemiosmosis
Term
glucose -> NADH -> electron transport chain -> proton-motive force -> ATP

this is the energy flow of
Definition
cellular respiration
Term
how much ATP is made from cellular respiration?
Definition
about 32
Term
carry out fermentation or anaerobic respiration and cannot survive in the presence of O2
Definition
obligate anaerobes
Term
In a _____ anaerobe, pyruvate is a fork in the metabolic road that leads to two alternative catabolic routes
Definition
facultative
Term
pathways funnel electrons from many kinds of organic molecules into cellular respiration
Definition
catabolic
Term
Fatty acids are broken down by _______ and yield acetyl CoA
Definition
beta oxidation
Term
fatty acids yield ____
Definition
acetyl CoA
Term
An oxidized gram of ____ produces more than twice as much ATP as an oxidized gram of carbohydrate
Definition
fat
Term
in anabolic pathways the body uses ______ to build other substances
Definition
small molecules
Term
DNP uncouples
Definition
oxidative phosphorylation
Term
_____ inhibits one of the proteins in the electron transport chain.
Definition
cyanide
Term
_______ and ATP are coupled, you can't have one without the other
Definition
electron transport
Term
_____ (Complex V) is a molecular motor also in the lipid bilayer, driven by proton passage through a channel that lets them back in again.
( all occurs in inner membrane of the mitochondria )
Definition
ATP synthase
Term
In concert with this electron transport, ______ are pumped out of the mitochondria into the inter-membrane space by Complexes I, III and IV, creating a higher pH (less acidic) within the innner mitochondrial matrix.
Definition
protons
Term
DNP uncouples
Definition
electron transport & ATP
Term
- specialized fat cells, much richer than normal in mitochondria
Definition
brown fat
Term
It provides a proton channel from outside to inside, dissipating the proton gradient without making ATP, thus causing the ETC to run faster, creating...heat!
Definition
thermogenin...found in brown fat
Term
in photosynthesis... Plants take in CO2, produce ______, and release water and O2
Definition
carbohydrates
Term
what is the reverse of cellular respiration?
Definition
photosynthesis
Term
-As in the mitochondria, separate membranes inside the organelle contain the proteins involved in electron transport and ATP synthesis.
-Accumulation of H+ within a membrane bound space creates a concentration gradient which drives ATP synthesis.

these are characteristics of
Definition
both photosynthesis and cellular respiration
Term
water is the source of ____ released during photosynthesis
Definition
O2
Term
Photosynthesis is an ______ process; the energy boost is provided by light
Definition
endergonic
Term
in photosynthesis ____ is oxidized and ____ is reduced
Definition
water is oxidized.... carbon dioxide is reduced
Term
the type of rays that are most electromagnetic are
Definition
gamma/cosmic
Term
When a photon meets a molecule it can be:
Scattered—
Definition
photon bounces off the molecule
Term
When a photon meets a molecule it can be
transmitted=
Definition
photon is passed through the molecule
Term
When a photon meets a molecule it can be
absorbed=
Definition
—molecule acquires the energy of the photon. The molecule goes from ground state to excited state
Term
____ Absorb in red and blue regions, transfer the energy to chlorophylls—carotenoids and phycobilins
Definition
accessory pigments in photosynthesis
Term
Energy can pass to another molecule if:
Target molecule is very near
Orientation is correct
Has appropriate structure

the molecules that meet this criteria are called
Definition
photosystems
Term
the ________ (pigment molecules bound to proteins) funnel the energy of photons to the reaction center
Definition
light harvesting complexes
Term
photosystem _____ functions first
Definition
2
Term
when combined _______ & ______ engage in linear electron flow which produces ATP and NADPH using light energy
Definition
photosystem 1 and 2
Term
Light energy oxidizes water → O2, H+, and electrons.

this happens in photosystem __
Definition
2
Term
____________ Uses only photosystem I and produces ATP, but not NADPH
Definition
cyclic electron flow
Term
in cyclic electron flow _____ ____ is released
Definition
NO OXYGEN
Term
_____________ generates extra ATP which funds the Calvin cycle
Definition
cyclic electron flow
Term
Chloroplasts and mitochondria generate ATP by ________, but use different sources of energy
Definition
chemiosmosis
Term
Mitochondria transfer ______ energy from food to ATP
Definition
chemical
Term
chloroplasts transform _______ energy into the chemical energy of ATP
Definition
light
Term
light reactions generate ATP and increase the potential energy of electrons by moving them from ____ to ____
Definition
H20 to NADPH
Term
stroma has a _____ H+ concentration
Definition
low
Term
Cyclic electron flow may protect cells from _______ damage
Definition
light-induced
Term
The Calvin cycle uses ATP and NADPH to convert ______ to _________
Definition
CO2 to sugar
Term
For net synthesis of 1 G3P, the calvin cycle must take place _____ times, fixing ___ molecules of CO2
Definition
3
Term
Carbon fixation (catalyzed by rubisco)
Reduction
Regeneration of the CO2 acceptor
(RuBP = ribulose bisphosphate)

THESE ARE THE 3 PHASES OF THE
Definition
calvin cycle
Term
to generate one _________ , More energy goes into making a molecule of glucose than is taken out in cellular respiration
Definition
3 carbon sugar
Term
On hot, dry days, plants close ____, which conserves H2O but also limits photosynthesis
Definition
stomata
Term
hot, arid conditions for carbon fixation are favorable for a process called ____
Definition
photorespiration
Term
_____ is a response to decreased carbon dioxide and increased oxygen levels when the stomata are closed
Definition
photorespiration
Term
Photorespiration limits damaging products of light reactions that build up in the absence of the _____
Definition
calvin cycle
Term
In many plants, _______ is a problem because on a hot, dry day it can drain as much as 50% of the carbon fixed by the Calvin cycle
Definition
photorespiration
Term
____ & _____ Attach the CO2 to something else using a different enzyme
Then peel off the CO2 and send it to the Calvin cycle.
as an alternative to photorespiration
Definition
C4 & CAM plants
Term
____ plants minimize the cost of photorespiration by incorporating CO2 into four-carbon compounds in mesophyll cells
This step requires the enzyme PEP carboxylase
Definition
C4
Term
the enzyme ______ has a higher affinity for CO2 than rubisco does; it can fix CO2 even when CO2 concentrations are low
Definition
PEP carboxylase
Term
These four-carbon compounds are exported to _____ cells, where they release CO2 that is then used in the Calvin cycle
Definition
bundle sheath cells
Term
____ plants open their stomata at night, incorporating CO2 into organic acids...which are then released in the day and used in the calvin cycle
Definition
CAM
Term
______ is the basis of inheritance
Definition
DNA
Term
When Griffith mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic
this proves that
Definition
DNA can transform bacteria
Term
a change in genotype and phenotype due to assimilation of foreign DNA.
Definition
transformation
Term
viruses that infect bacteria are called
Definition
bacteriophages
Term
viruses are basically DNA (or in some cases RNA) wrapped in a ___ coat
Definition
protein
Term
DNA is a polymer of
Definition
nucleotides:
nitrogenous base,
phosphate group
deoxyribose
Term
DNA is a polymer of
Definition
nucleotides:
nitrogenous base,
phosphate group
deoxyribose
Term
Erwin Chargaff reported that DNA composition _____
Definition
varies from one species to the next
Term
Chargaff’s rule states that in any species there is an equal number of
Definition
A and T bases, and an equal number of G and C bases
Term
a crucial piece of DNA structure came through ____
Definition
x-ray crystallography
Term
Rosalind Franklin had also concluded that there were two _____ sugar-phosphate backbones, with the nitrogenous bases paired in the molecule’s interior
Definition
anti-parallel
Term
the two guys that used franklin's work in combo with their own to do hte DNA structure are
Definition
crick and watson
Term
It is a double-stranded helix of uniform diameter
It is right-handed
It is antiparallel


these are the characteristics of
Definition
DNA structure
Term
DNA structure predicts the _____
Definition
method of replication
Term
Watson and Crick’s ________ model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand
Definition
semiconservative
Term
the ____ model which was rejected, said that each strand is a mix of old and new
Definition
dispersive
Term
the ____ model which was also rejected said that the two parent strands rejoin
Definition
conservative
Term
THESE ARE THE TWO STEPS OF

1. The double helix is unwound, making two template strands

2. New nucleotides are added to the new strand at the 3′ end and joined by phosphodiester linkages. Sequence is determined by complementary base pairing.
Definition
DNA REPLICATION
Term
where the two DNA strands are separated, opening up a replication “bubble” is called the
Definition
origins of replication, where replication begins (ori)
Term
on the lagging strand, the enzyme DNA ligase forms a ______ bond between 3' OH of the growing strand and the 5'phosphate in front of it
Definition
phosphodiester bond
Term
a Y-shaped region where new DNA strands are elongating at the end of each replication bubble... this is called the
Definition
replication fork
Term
A eukaryotic chromosome may have _____ of origins of replication
Definition
hundreds or thousands
Term
in DNA replication, Synthesis of the daughter strands proceeds in the ___ to __ direction.
Definition
5' to 3'
Term
in DNA replication New nucleotide can only be attached to an available 3’ __ on the ____
Definition
carbon on the deoxyribose
Term
____ are enzymes that untwist the double helix at the replication forks
Definition
helicases
Term
____ binds to and stabilizes single-stranded DNA until it can be used as a template
Definition
single stranded binding protein
Term
corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands
Definition
topoisomerase
Term
DNA replication begins with a short ____—a starter strand.
The____ is complementary to the DNA template.
Definition
RNA primer
Term
____ -an enzyme—synthesizes the primer one nucleotide at a time.
Definition
primase
Term
new DNA strand begins at the _____ end
Definition
3'
Term
in DNA replication.._________ attaches nucleotides to the 3′ end of the deoxyribose sugar component
-Uses the RNA primer as the starting point
Definition
DNA polymerase
Term
DNA GROWS from the ___ end to the ____ end.
Definition
5' to the 3'
Term
Nucleotide precursers for DNA =
Definition
dNTP
Term
What is the difference between ATP, the energy carrier and dATP the adenosine nucleotide building block for DNA?
Definition
Deoxyribose sugar in dATP
Term
Each nucleotide that is added to a growing DNA strand is a ______ because fo the 3 phosphate groups that were added
Definition
nuceloside triphosphate
Term
dNTP supplies adenine to ____ and is similar to the ATP of energy metabolism
Definition
DNA
Term
As each monomer of dNTP joins the DNA strand, it loses two phosphate groups as a molecule of ___
Definition
pyrophosphate
Term
the mechanics of DNA elongation _____ between the two strands
Definition
differ
Term
Leading strand: DNA synthesized continuously. Away from __, towards ______
Definition
away from origin towards replication fork
Term
The lagging strand is synthesized as a series of segments called _______, which are joined together by ______
Definition
okazaki fragments which are joined together by DNA ligase
Term
Cells have three repair mechanisms:
_____
___ repair
____ repair
Definition
proofreading, excision repair and mismatch repair
Term
During replication:
DNA polymerases _____ newly made DNA, replacing any incorrect nucleotides
Definition
proofread
Term
DNA can be damaged by environmental agents such as UV light, x rays, cigarette smoke, etc. When this happens the damage can often (but not always) be repaired by nucleotide ____ repair.
Definition
excision
Term
in ____ repair, A nuclease cuts out and replaces damaged stretches of DNA
Definition
excision
Term
Limitations of ________ create problems for the linear DNA of eukaryotic chromosomes
The usual replication machinery provides no way to complete the 5' ends, so repeated rounds of replication produce shorter DNA molecules
Definition
DNA polymerase
Term
Eukaryote chromosomes have repetitive sequences at the ends called
Definition
telomeres
Term
_____ are protective and prolong cell division, especially in rapidly-dividing cells, like bone marrow.
Definition
telomeres
Term
the enzyme _____ contains an RNA sequence—acts as template for telomeric DNA sequences
Definition
telomerase
Term
the flow of genetic information:

DNA nucleotide sequence --> _____ to the mRNA sequence ---> ____ to amino acid sequence (polypeptide)
Definition
transcribed to mRNA sequence ---> translated to the amino acid sequence of polypeptides
Term
the genotype is the ____ sequence
the phenotype is the ___ sequence
Definition
DNA nucelotide= genotype

amino acid=phenotype
Term
Archibald Garrod saw a disease phenotype— alkaptonuria—occurring in children who shared more alleles as first cousins.

this investigation gave evidence that genes code for ___
Definition
proteins
Term
____ organisms are Easy to grow or observe; show the phenomenon to be studied.
Definition
MODEL
Term
Beadle and Edward concluded that Based on their results they developed a ______, which states that each gene dictates production of a specific enzyme.

later revised to
Definition
one gene one enzyme hypothesis

one gene one polypeptide
Term
Beadle and Edward concluded that Based on their results they developed a ______, which states that each gene dictates production of a specific enzyme.
Definition
one gene one enzyme hypothesis
Term
what is the central dogma of molecular biology?
Definition
DNA transcribes to RNA which translates to a protein
Term
In a eukaryotic cell, the _______ separates transcription from translation
Definition
nuclear envelope
Term
A ____ transcript is the initial RNA transcript from any gene
Definition
primary
Term
The mature mRNA exits the nucleus through the nuclear pores and attaches to ______ and translation of the message into polypeptide begins.
Definition
ribosomes
Term
Single-strand _____ can fold into complex shapes by internal base pairing.
Definition
RNA
Term
So ___ nucleotides per amino acid is the smallest possible code that will provide enough information for at least 20 amino acids.
Definition
3
Term
Any single set of three nucleotides is called a ___ , and the set of all possible three-nucleotide combinations is called ___ or ___
Definition
codon... combos are called the genetic code or the triplet code
Term
what part of transcription is for eukaryotes only?
Definition
Post-transcription modification
Term
Initiation
Elongation
Termination
Post-transcription modification (eukaryotes only)


these are the 4 steps in
Definition
transcription
Term
during initiation of transcription ______ catalyzes the synthesis of mRNA, separates the two DNA strands & polymerizes the ribose nucleotides
Definition
RNA polymerase
Term
DNA sequence that tells RNA polymerase “attach here”.
Definition
promoter region
Term
RNA polymerase unwinds the DNA and begins ribose nucleotide polymerization

what part of transcription is this describing?
Definition
initiation
Term
Nucleotides added in 5’ to 3’ direction (just like DNA synthesis)

what part of transcription is this describing?
Definition
elongation
Term
Transcription stops when RNA pol reaches a specific nucleotide sequence on the template: ____
Definition
the termination sequence
Term
only eukaryotes need _____ which mediate the binding of RNA polymerase and the initiation of transcription
Definition
transcription factors
Term
The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a ____ ____ complex
Definition
transcription initiation complex
Term
A promoter called a _____ is crucial in forming the initiation complex in eukaryotes
Definition
TATA box
Term
Transcription progresses at a rate of ___ nucleotides per second in eukaryotes
Definition
40
Term
A sequence RNA polymerase adds a polyadenylation sequence: AAUAAA

The transcript is released another 10-35 nucleotides past the polyA sequence.

The transcript is a ____ that undergoes additional processing before it leaves the nucleus
Definition
pre-mRNA
Term
____ consist of a variety of proteins and several small nuclear ribo-nucleoproteins (snRNPs) that recognize the splice sites
Definition
spliceosomes
Term
It can form a three-dimensional structure because of its ability to base-pair with itself
Some bases in RNA contain functional groups that may participate in catalysis
RNA may hydrogen-bond with other nucleic acid molecules


these three reasons are why RNA can function as an ____
Definition
enzyme
Term
introns may contain sequences that regulate ___
Definition
gene expression
Term
Proteins often have a modular architecture consisting of discrete regions called _____. In many cases, different exons code for the different _____ in a protein
Definition
domains
Term
Exon ______ may result in the evolution of new proteins
Definition
shuffling
Term
1. Collect the right amino acids
tRNA
first tRNA carries start codon (Met)
2. Join together mRNA, ribosome and tRNA
3. Bring in tRNAs in order as mRNA is “read”
4. Connect the amino acids
5. Continue until stop codon reached

these are the steps of ___
Definition
translation
Term
Each carries a specific amino acid on one end and Has an anticodon on the other end
Definition
tRNA
Term
Flexible pairing at the third base of a codon is called _____ and allows some tRNAs to bind to more than one codon
Definition
wobble
Term
this enzyme ___ has to make a correct match between a tRNA and an amino acid in order to have accurate translation
Definition
the enzyme aminoacyl-tRNA synthetase
Term
_____ bring together tRNA anticodons with mRNA codons in protein synthesis, and has more rRNA than a protein
Definition
ribosomes
Term
1. A = aminoacyl tRNA binding site
Incoming tRNA bringing the next aa in the polypeptide sequence
2. P = peptidyl-tRNA binding site
Holds growing polypeptide chain
3. E = exit site
tRNA exits the ribosome

these are the 3 ______ sites that ____ attaches to in each sequence
Definition
binding sites that tRNA
Term
Termination of translation occurs when a stop codon in the mRNA reaches the ____ site of the ribosome
Definition
A
Term
The A site accepts a protein called the _____ factor which causes the addition of a water molecule instead of an amino acid.
This reaction releases the polypeptide, and the translation assembly then comes apart
Definition
release
Term
A number of ribosomes can translate a single mRNA simultaneously, forming a ____ which enable a cell to make many copies of a polypeptide very quickly
Definition
polyribosome
Term
Often, translation isn't enough. Polypeptide chains are modified after translation or targeted to specific sites in the cell in order to make a ______ protein
Definition
functional
Term
During and ____ synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape
Definition
after
Term
besides folding How else can proteins be modified?
____ated or ____lated
Definition
methylated or phosphorylated
Term
Polypeptide synthesis always begins in the ____. Synthesis finishes there unless the polypeptide signals the ribosome to attach to the ER
Definition
cytosol
Term
Polypeptides destined for the ER or for secretion are marked by a _____
Definition
signal peptide
Term
_____ ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell
Definition
bounds
Term
can ribosomes switch from free to bound?
Definition
YES.
Term
How does cell “know” whether the protein stays in cytoplasm or goes to ER?
A ____ binds to the signal peptide
Definition
signal-recognition particle (SRP)
Term
what is the only exception to the central dogma?
Definition
Viruses: Non-cellular particles that reproduce inside cells; many have RNA instead of DNA.
Viruses can replicate by transcribing from RNA to RNA, and then making multiple copies by transcription.
Term
After infecting a host cell a copy of the viral genome is incorporated into the host’s genome to make more RNA.
this type of virus is called a _____
Definition
retrovirus
Term
are changes in the genetic material of a cell or virus
Definition
mutations
Term
are chemical changes in just ONE base pair of a gene
Definition
point mutations
Term
The change of a single nucleotide in a DNA template strand can lead to the production of an ____
Definition
abnormal protein
Term
_____ mutation: No change in protein.
Definition
silent/neutral
Term
____ mutation: Amino acid substitution.
Definition
missense
Term
____ mutation= Stop codon introduced in the middle.
Definition
nonsense
Term
_____ mutations in proteins are due to insertion or deletions in the DNA.
Definition
frameshift
Term
The molecular basis of sickle-cell disease: a ___ mutation
Definition
point
Term
It might be a little counter-intuitive, but ___ frameshift changes can actually cause the sequence to revert back to normal.
Definition
3
Term
This process produces some ATP and carbon dioxide in the mitochondrion.
Definition
citric acid cycle
Term
The immediate energy source that drives ATP synthesis by ATP synthase during oxidative phosphorylation is the
Definition
H+ concentration across the membrane holding ATP synthase
Term
Which metabolic pathway is common to both fermentation and cellular respiration of a glucose molecule?
Definition
glycolysis
Term
In mitochondria, exergonic redox reactions
Definition
provide the energy that establishes the proton gradient.
Term
The final electron acceptor of the electron transport chain that functions in aerobic oxidative phosphorylation is
Definition
oxygen
Term
What is the oxidizing agent in the following reaction?
Pyruvate + NADH + H+ S Lactate + NAD+
Definition
pyruvate
Term
When electrons flow along the electron transport chains of mitochondria, which of the following changes occurs?
Definition
The pH of the matrix increases.
Term
What provides electrons for the light reactions?
Definition
h20
Term
What provides the carbon atoms that are incorporated into sugar molecules in the Calvin cycle?
Definition
CO2
Term
The light reactions of photosynthesis supply the Calvin cycle with
Definition
ATP & NADPH
Term
Which of the following does not occur during the Calvin cycle?
Definition
RELEASE OF OXYGEN
Term
In mechanism, photophosphorylation is most similar to
Definition
oxidative phosphorylation in cellular respiration
Term
Which process is most directly driven by light energy?
Definition
removal of electrons from chlorophyll molecules
Term
The site of translation is
Definition
ribosomes in the CYTOPLASM
Term
Which of the following does not occur during RNA processing?
Definition
mRNA attaches to the small subunit of a ribosome
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