EXAM #3 Flashcards
what is the first law of thermodynamics?
the universe contains a constant amount of energy, therefore energy is never created nor destroyed. energy simply changes from one form to another.
what is the second law of thermodynamics?
energy transformations always result in an increase in disorder in the universe. when going from one form of energy to another, the energy available to do work decreases.
why are energy transformations never 100% efficient?
because the amount of energy available to do work decreases every time energy changes forms
the degree of disorder is called ______
entropy, however, disorder is just one way to describe entropy.
another way to think about entropy is to consider the number of possible ______ and _____ a molecule can adopt.
positions and motions (collectively called microstates)
as entropy _____, the number of positions and motions available to the molecule increases
increases
in chemical reactions, what causes the entropy to increase?
most of the entropy increase occurs through the release of thermal energy, which we experience as heat.
the higher the temperature, the more rapidly molecules move, and the _____ the disorder.
higher
all cells and organisms require a constant input of energy to maintain their high degree of organization and function. what are energy inputs for cells?
energy comes either from the sun or from the energy stored in chemical compounds.
when does a chemical reaction occur?
when molecules interact. molecules called reactants are transformed into other molecules called products.
during a chemical reaction, atoms ____ their identity, but the atoms that share bonds _____.
keep
change
can chemical reactions be reversed?
yes, chemical reactions in cells are readily reversable: products can react to form their original reactants
_____ ______ is when the rate of the forward reaction equals the rate of the reverse reaction, and the concentrations of the products and reactants do not change.
chemical equilibrium
the amount of energy available to do work is called _____ ____ ______ (G).
Gibbs free energy
delta G is the free energy of the _____ minus the free energy of the ______
products
reactants
reactions with a negative delta G value that release energy and proceed spontaneously are called ______
exergonic
reactions with a positive delta G value that require an input of energy and are not spontaneous are called ______
endergonic
H = G + TS
G = H - TS
what do the variables stand for?
G = Gibbs free energy// the amount of energy available to do work
H = the total amount of energy is enthalpy
T = absolute temperature (Kelvin)
S = entropy
T*S = the total energy lost to entropy
the hydrolysis of ATP is an ______ reaction
exergonic (releases energy available to do work)
hydrolysis reactions often break down _____ into their _____, and in the process one product gains a ______ (H+) and the other gains a ______ (OH-) group.
polymers into their subunits
proton
hydroxyl
where/what does the release of energy during ATP hydrolysis come from?
breaking weaker bonds (with more chemical energy) in the reactants and forming more stable bonds (with less chemical energy) in the products
true or false: nonspontaneous reactions are infrequently coupled to spontaneous reactions
false. nonspontaneous reactions are often coupled to spontaneous reactions
catalysts are substances that ____ the rate of chemical reactions without themselves being consumed.
increase
catalysts are usually proteins called _______ which are highly ______, acting only on certain reactants and catalyzing only some reactions.
enzymes
specific
true or false: only some chemical reactions require an initial input of energy to proceed
false, all chemical reactions require an input of energy
an intermediate compound between reactants and products is formed, called the _____ _____ in which the old bonds are breaking, and the new bonds are forming simultaneously.
transition state. it is highly unstable and has a large amount of free energy
the energy input necessary to reach the transition state is called the ______ _____
activation energy (Ea)
enzymes accelerate chemical reactions by reducing the activation energy by stabilizing the _____ ____ and decreasing its free energy
transition state
enzymes form a _____ with reactants and products that allows them to emerge from the chemical reaction unchanged.
complex
describe a chemical reaction catalyzed by an enzyme (reactant is called a substrate)
1) substrate (S) combines with an enzyme (E) to form first complex (E-S)
2) the substrate (while with the enzyme E-S) is converted to a product (E-P)
3) finally the complex disassociates, releasing the enzyme and the product (P + E)
substrates bind to enzymes at a specific region of the enzyme called the ____ ___ where the substrate and the enzyme form transient ____ bonds, weak noncovalent interactions or both.
active site
covalent
enzymes are folded into 3-dimensional shapes that bring particular _____ _____ into close proximity to form the active site.
amino acids
catalytic amino acids are typically spaced ___ apart in the linear sequence of amino acids (_____ structure) of the enzyme, but brought close together by protein ______.
far
linear
folding
enzymes are specific for certain substrates (reactants) as keys…..
are specific for certain locks
true or false: enzymes only interact with substrates that have a complimentary structure
true
some enzymes rely on ______ for their activity.
cofactors. cofactors can be organic or inorganic
breaking a chemical bond requires the ____ of energy. forming a chemical bond is associated with the ______ of energy.
input
release
the hydrolysis of ATP is spontaneous and ______ ____ ____ that can be used to drive other reactions
produces free energy
when the activation energy is low, chemical reactions occur _____
faster
there is a number of inhibitors that ____ ____ _____ when their products are not needed.
“turn off” enzymes
reversible inhibitors form ____ bonds with the enzyme
weak
irreversible inhibitors form ______ bonds with the enzyme
covalent
enzymes that are regulated by allosteric regulators are called _______ _______
allosteric enzymes
DNA replication is the molecular basis for ______
inheritance
describe how DNA replicates (simple)
DNA double helix unwinds and separates into two single strands at the replication fork. then each individual strand of DNA acts as a template for the synthesis of a daughter strand.
DNA replicates _________, which means that each new DNA molecule consists of one strand that was part of the parental molecule and one newly synthesized strand.
semi conservatively
what enzyme separates the two strands of the parental double helix by breaking hydrogen bonds holding the base pairs together?
helicase
what enzyme binds to these single stranded regions to prevent them from coming back together?
single-strand binding protein
true or false: topoisomerases are a family of enzymes that wind or unwind DNA to help relieve stress that occurs during both replication and replication and transcription
true
how many types of topoisomerases are there?
2; type I- cut one strand of DNA
type 2- cut both strands of DNA
what is the enzyme that is a critical component in DNA replication that synthesizes a new DNA strand from an existing template.
DNA polymerase
what are DNA polymerase’s two main properties?
-it can only attach a nucleotide to another nucleotide
-it can only add nucleotides to the 3’ (hydroxyl) end of another nucleotide
true or false: each new DNA strand must begin with a short stretch of RNA on their 5’ end that serves as a primer or starter for DNA synthesis
true
what is the enzyme called that forms a primer which synthesizes a short piece of RNA complementary to the DNA parental strand?
RNA primase.
in DNA replication, one daughter strand is synthesized _________ and the other strand in a series of ____ ______
continuously
short pieces
the ______ strand is synthesized continuously into one long polymer (daughter strand grows towards the replication fork)
leading
the _______ strand is synthesized in small discontinuous pieces that’re later joined together (daughter strand grows away from the replication fork)
lagging
what are the short pieces in the lagging daughter strand of DNA called?
Okazaki fragments
what is the enzyme that will join or ligate adjacent Okazaki fragments together?
DNA ligase
true or false: the DNA polymerase complexes in each daughter strand don’t communicate with each other
false; the DNA polymerase complexes in each daughter strand stay in contact with each other so that the synthesis of the leading and lagging strands is coordinated to occur at the same time/rate
most DNA polymerases can correct an incorrect nucleotide sequence immediately in a process called _______, which is a separate enzymatic process from elongation (synthesis).
proofreading
how frequently is an incorrect nucleotide added?
very rarely
in proofreading, is the correct nucleotide added to replace the incorrect one?
yes
mispairing two bases activates a DNA _____ _____ of DNA polymerase that removes the incorrect nucleotide and inserts a correct one in its place
cleavage function
if the proofreading function fails and two bases are incorrectly paired, what can happen?
mutations can result from errors in nucleotide pairing and be copied and passed down to future daughter cells
replication of DNA in chromosomes starts at many places almost ___________
simultaneously
what is each point at which DNA synthesis is initiated called?
an origin of replication
the opening of the double helix at each origin of replication forms a ________ _______
replication bubble
DNA synthesis takes place at each replication fork. as the replication fork moves in opposite directions, what happens to the replication bubble?
the replication bubble increases in size
true or false: all DNA molecules have a double stranded helical structure
false, most of the DNA molecules in bacteria and in mitochondria and chloroplasts are small circles, not long linear molecules.
such circular DNA molecules typically only have ___ origin of replication
one
each end of a eukaryotic chromosome is capped by a repeating sequence called the ______
telomere
in the chromosomes of humans (differs for other organisms), the telomere consists of the sequence 3’ GGGATT 5’ repeated over and over again in about _____ to ____ copies.
1500 to 3000
what enzyme restores tips of linear chromosomes that were shortened during DNA replication?
telomerase, which contains an RNA molecule complementary to the telomere sequence
telomerase replaces the lost telomere repeats by using its ____ _______ as a guide to add successive nucleotides to the 3’ end of the template strand
RNA molecule
telomerase activity differs from one cell type to another. Telomerase is fully active in what two types of cells?
-germ cells (produce sperm or eggs)
-stem cells (undifferentiated cells that can undergo an unlimited number of mitotic divisions and can differentiate into specialized cell types).
true or false: telomerase is active in most cells in the human body
false, telomerase is mostly inactive in more cells in the human body
DNA polymerase requires an ____ _______ for replication to occur
RNA primer (primase)
___ _____ can cause breaks in the sugar phosphate backbone, in either one strand or both strands on DNA
x-rays
___ ____ can cause adjacent pyrimidines to cross-link, which commonly leads to the formation of thymine (T) dimers that warp the backbone
UV light
_______ _____ such as hydrogen peroxide can oxidize bases such as guanine which can cause improper base pairing
oxidizing agents
______ ____ can add bulky side groups to the bases that hinder proper base pairing
tobacco smoke
true or false: DNA damage can effect both the backbone and the bases
true
_____ are agents that increase the probability of mutation
mutagens
spontaneous loss of a ______ ____ is one of the most common types of DNA damage, resulting from the interaction between DNA and normal metabolic byproducts.
purine base
true or false: most DNA damage cannot be corrected
false; most DNA damage is corrected by specialized repair enzymes
what is the enzyme called that can repair a break in the sugar-phosphate backbone by using the energy in ATP to join the 3’ hydroxyl group of one end to the 5’ phosphate group of the other end
DNA ligase
how many different types of DNA ligase are there?
there can be multiple different types of DNA ligase. one type seals single-stranded breaks in DNA and a different type seals double-stranded breaks in DNA
DNA ligases also allow DNA molecules from different sources to be joined together to produce ________ ____
recombinant DNA
in _______ ______, the segment of a DNA strand containing a nucleotide mismatch is removed and then resynthesized
mismatch repair
______ recognizes mismatched bases in DNA and initiates the repair process by binding to the site of mismatch. _____ and ______ proteins are then recruited to the site and ____ breaks the backbone
Mut S.
Mut L and Mut H.
Mut H
____ determines which DNA backbone will be cleaved
Mut L
_____ cleaves the backbone in the vicinity of the mismatch
Mut H
an _______ removes successive nucleotides, including the one with the mismatched base
exonuclease
a ____ ______ fills in the missing nucleotides, and a DNA _____ rejoins the backbones
DNA polymerase
ligase
does mismatch repair usually cleave the parental or the daughter strand?
mismatch repair usually cleaves the daughter strand, so the correct strand matches the parental/template strand
in ____ ______ _____, a damaged or improperly modified base in DNA and its deoxyribose sugar are both removed, and then the resulting gap is then repaired
base excision repair
what is the first step in base excision repair?
an abnormal or damaged base is cleaved from the sugar in the DNA backbone
what is the second step in base excision repair?
the baseless sugar is removed from the backbone, leaving a gap of one nucleotide
what is the final step in base excision repair?
a repair polymerase inserts the correct nucleotide into the gap (uses the intact nucleotide opposite the gap as a template)
in _______ _______ _______, a damaged or mismatched segment of a DNA strand is removed at one time (not nucleotide by nucleotide) and resynthesized using the undamaged partner strand as a template
nucleotide excision repair
nucleotide excision repair is also used to remove nucleotides with bulky side groups (tobacco smoke), as well as ______ _____ resulting from UV light
thymine dimers
describe the first two steps of nucleotide excision repair
-one or more damaged bases signal the repair process
-enzymes cleave the DNA backbone at sites flanking the damage
describe the last two steps of nucleotide excision repair
-the entire region with damaged bases is removed
-the gap is filled by new DNA synthesis, using the ungapped strand as a template
_____ mutations are changes in a single nucleotide
point
a nucleotide substitution that creates a stop codon is called a __________ _________
nonsense mutation
the disease ________ ____ anemia results from nonsynonymous mutation
sickle-cell
__________ mutations can result in the disruption/shifting of the reading frame
frameshift
__ ______ _________ are a small deletion or insertion that is an exact multiple of 3 nucleotides results in a polypeptide with fewer (in the case of deletion) or more (in the case of insertion) amino acids
in-frame mutations
a common method for making copies of a piece of DNA is the _______ ______ _________, which allows researchers to _______ or ________ a targeted region of a DNA molecule into as many copies as desired.
polymerase chain reactions (PCR)
amplify or replicate
is there a restriction on the amount of starting DNA sample necessary for a PCR to work properly?
the starting sample can be as small as a single molecule of DNA
because the PCR reaction is essentially a DNA synthesis reaction, what four components must be present for the reaction to occur?
-at least one molecule of double-stranded DNA containing the region to be amplified which serves as a template
-the enzyme DNA polymerase for replicate the DNA
-all four nucleotide bases (A,T, G and C) that serve as building blocks for the new DNA
-two primers: short sequences of single-stranded DNA are required for the DNA polymerase to start synthesis
what are the three steps of PCR called?
-denaturation
-annealing
-extension
during denaturation: a solution containing double-stranded DNA (template DNA) is ______ to _________ or denature the DNA into two individual strands (hydrogen bonds between complementary bases are broken).
heated (just short of boiling temp) to separate
during denaturation, the role of ______ is replaced by heat
helicase
during annealing: when the solution has cooled, the two _______ _____ or bind to their ________ sequence on the 3’ ends of the individual strands of the template DNA
primers anneal
complementary
the two primers act as the ______ point for DNA synthesis and occur on the ____ end of the newly synthesized DNA strand.
starting
5’
during extension: ______ ________ synthesizes new DNA strands (complementary to the template strands) by extending the _______ in a 5’ to 3’ direction.
DNA polymerase
primers
the three steps of PCR may be repeated over many times, resulting in ___________ of a target DNA sequence
amplification
each round of amplification _______ the number of DNA molecules
doubles
the primer sequences are called __________ and they’re usually around 2-30 nucleotides long.
oligonucleotides
true or false: oligonucleotides have base sequences that are chosen to be complementary to the ends of the region of DNA to be amplified.
true
what is one challenge associated with PCR?
the DNA polymerase enzymes from humans irreversibly lose both structure and function at the high temperature requires to separate the DNA strands
how have scientists been able to combat the problem associated with DNA polymerase?
we now use DNA polymerase enzymes that are heat-stable from the bacterial species Thermus aquaticus (lives in hot springs). It’s polymerase: Taq polymerase, remains active and functional at high temperatures
how could one determine the size of a DNA fragment?
through gel electrophoresis, a procedure in which DNA fragments are separated by size as they migrate through a porous substance in response to an electric field
in gel electrophoresis: DNA samples are ______ into slots or wells near the edge of a rectangular slab of ______ material that resembles agar (the gel)
inserted
porous
the gel is inserted into an apparatus and immersed in a solution that allows an ________ ______ to be passed through it from ______ at the top where the DNA samples were originally placed to ______ at the bottom of the gel.
electric current
negative
positive
the electric field is what causes the DNA to ______ through the porous gel because the double stranded DNA is negatively charged and will be attracted to the ______ ____ of the electric field
migrate
positive pole
in gel electrophoresis: ______ molecules will move faster through the porous gel than _______ molecules because they take longer to work their way through the pores in the gel
smaller
larger
how can you see the different sizes from a gel electrophoresis experiment?
dyes that bind to DNA and glow or fluoresce under UV light
cutting or cleaving DNA molecules is also a common practice that allows pieces from the same or different organisms to be brought together in recombinant DNA technology. what else does this allow?
cutting DNA allows whole genomes to be broken into smaller pieces for further analysis, such as DNA sequencing
__________ ________ recognize specific, short nucleotide sequences in double stranded DNA and cleave the DNA at these sites
restriction enzymes (there are abt 1000 different kinds and can cut DNA from any organism)
the recognition sequences that the enzymes cleave, called _______ ______, are typically 4 or 6 base pairs long and is where (or near where) the double stranded DNA is typically cleaved
restriction sites
when reading from the 5’ to 3’ end, if the sequence of the top strand is exactly the same as the sequence of the bottom strand, then it is symmetrical and is called _________.
palindromic
are palindromic sequences common for restriction sites?
yes, it is typical for restriction sites to be palindromic
some restriction enzymes cleave their restriction site to produce ___ ______, others produce ___ ______ and some cleave in the middle and leave _____ ends with no _______.
5’ overhang
3’ overhang
blunt
overhang
true or false: DNA strands can be separated but not brought back together again
false; DNA strands be separated and brought back together again
the base pairing of complementary single-stranded nucleic acids is known as ________ or hybridization and the process is ________ from denaturation.
renaturation
opposite
denatured DNA strands from one species can renature with DNA strands from a different species if their sequences are precisely or mostly ___________
complementary
in general, the more closely two species are related, the more perfectly their bases will match up and thus have more _______ _____ holding them together. so, the more closely two species are related, the more similar their ____ _________
hydrogen bonds
DNA sequences
very closely related sequences renature at a _________ temperature than less closely related sequences
higher
renaturation makes it possible to use a small DNA fragment as a _____ which can be used to determine whether or not a sample of double-stranded DNA molecules contains sequences that are _________ to it.
probe
complementary
recombinant DNA combines DNA molecules from two or more different sources into a ______ _________
single molecule
recombinant DNA methods require a fragment of double-stranded DNA that serves as the ______.
donor
reserve transcriptase is an enzyme that produces a double-stranded DNA molecule from a _______-_______ ____ template
single-stranded RNA
to obtain a DNA fragment that contains only the protein-coding region of the gene, researchers use ________ ____________
reverse transcriptase
a DNA molecule produced with reverse transcriptase is known as ____________ ____.
complementary DNA (cDNA)
once a molecule of donor DNA has been ______, a ______ ________ in which the donor fragment can be inserted into is necessary
isolated
vector sequence
the vector sequence is the carrier of the donor fragment and it must have the ability to be _______ in bacterial cells.
maintained
what is an example of a frequently used vector?
a bacterial plasmid
what are kinases?
enzymes that phosphorylate other proteins
