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118 Cards in this Set

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Bacteria
One of two prokaryotic domains, the other being Archaea.
bacteriophage
A virus that infects bacteria
bacterium
Member of the prokaryotic domain Bacteria.
chromatin
The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.
deoxyribose
The sugar component of DNA nucleotides, having one fewer hydroxyl group than ribose, the sugar component of RNA nucleotides.
DNA ligase
A linking enzyme essential for DNA replication
DNA polymerase
An enzyme that catalyzes the elongation of new DNA (for example, at a replication fork) by the addition of nucleotides to the 3' end of an existing chain. There are several different DNA polymerases
double helix
The form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape.
euchromatin
The less condensed form of eukaryotic chromatin that is available for transcription.
helicase
An enzyme that untwists the double helix of DNA at the replication forks, separating the two strands and making them available as template strands.
heterochromatin
Eukaryotic chromatin that remains highly compacted during interphase and is generally not transcribed.
histone
A small protein with a high proportion of positively charged amino acids that binds to the negatively charged DNA and plays a key role in chromatin structure.
lagging strand
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' -3' direction away from the replication fork.
leading strand
The new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5'?3' direction.
mismatch repair
The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.
nuclease
An enzyme that cuts DNA or RNA, either removing one or a few bases or hydrolyzing the DNA or RNA completely into its component nucleotides.
nucleoid
A dense region of DNA in a prokaryotic cell.
nucleoid region
A dense region of DNA in a prokaryotic cell.
nucleosome
The basic, bead-like unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone.
nucleotide excision repair
A repair system that removes and then correctly replaces a damaged segment of DNA using the undamaged strand as a guide.
Okazaki fragment
A short segment of DNA synthesized away from the replication fork on a template strand during DNA replication, many of which are joined together to make up the lagging strand of newly synthesized DNA.
origin of replication
Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
phage
A virus that infects bacteria
primase
An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.
primer
A short stretch of RNA with a free 3' end, bound by complementary base pairing to the template strand, that is elongated with DNA nucleotides during DNA replication.
pyrimidine
One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring. Cytosine (C), thymine (T), and uracil (U) are pyrimidines.
radioactive isotope
An isotope (an atomic form of a chemical element) that is unstable
repetitive DNA
Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome.
replication fork
A Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are growing.
semiconservative model
Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand.
single-strand DNA-binding protein (SSBPs)
A protein that binds to the unpaired DNA strands during DNA replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands of DNA.
telomerase
An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells.
telomere
The tandemly repetitive DNA at the end of a eukaryotic chromosome’s DNA molecule that protects the organism’s genes from being eroded during successive rounds of replication. See also repetitive DNA.
template strand
The DNA strand that provides the pattern, or template, for ordering the sequence of nucleotides in an RNA transcript.
topoisomerase
A protein that breaks, swivels, and rejoins DNA strands. During DNA replication, topoisomerase helps to relieve strain in the double helix ahead of the replication fork.
transformation
(1) The conversion of a normal animal cell to a cancerous cell. (2) A change in genotype and phenotype due to the assimilation of external DNA by a cell.
X-ray crystallography
A technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.
Watson & Crick, April 1953
Present scientific world with double-helical model for the structure of deoxyribohucleic acid (DNA).
Genetic endowment
is the DNA contained in the 46 chromosomes inherited from parents and in the mitochondria passed along by mother.
Heredity information
is encoded in the chemical language of DNA and reproduced in all the cells of body.
Genes
are located along chromosomes, the two chemical components of chromosomes: DNA & Protein.
Griffith, 1928
Studying streptococcus pneumonia, bacterium that causes pneumonia in mammals. Used two strains of the bacterium, one pathogenic (disease causing) and one nonpathogenic (harmless). Killed the pathogenic strain with head, mixed the remains with living bacteria of the nonpathogenic strain, some of the living cells became pathogenic. Newly acquired trait of pathogenicity was inherited by all the descendants of the transformed bacteria. Some chemical component of the dead pathogenic cells caused the inheritable change, although the identify of the substance was unknown. American bacteriologist, Avery, searched for that substance for 14 years – announced the transforming agent was DNA.
Transformation
was what Griffith called the phenomenon, now is defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell.
Viruses are simpler than cells
is little more than DNA (or sometimes RNA) enclosed by a protective coat, which is often simply protein. To reproduce, a virus must infect a cell and take over the cell’s metabolic machinery.
Hershey & Chase, 1952
performed experements showing that DNA is the genetic material of a phage known as T2, one of many phages that infect E. Coli – the bacterium that normally lives in the intestines of mammals.
DNA
a polymer of nucleotides, each consisting of three components: nitrogenous (nitrogen containing) base, pentose sugar called deoxyribose, and phosphate group.
Base composition of DNA can be
adenine (A), thymine (T), guanine (G), or cytosine (C).
Chargaff, 1950
reported that base composition varies from one species to another, example – 30.3% of human DNA nucleotides have the base A, and E. coli have only 26.0% A.
Chargaff’s Rule
The equivalences for any given species between the number of A and T bases and the number of G and C bases. Also noticed the peculiar regularity in the ratios of nucleotide bases within a single species – DNA studied, the number of A approximately equaled the number of T, and the number of G approximately equaled the number of C.
In human DNA
the four bases are present in the percentages: A = 30.3% and T + 30.3%, G = 19.5% and C = 19.9%.
Structure of a DNA strand
each nucleotide monomer consists of a nitrogenous base (T, A, C, or G), the sugar deoxyribose, and a phosphate group. The phosphate of one nucleotide is attached to the sugar of the next, resulting in a “backbone” of alternating phosphates and sugars from which the bases project. The polynucleotide strand has directionality, from the 5’ end (with the phosphate group) to the 3’ end (with the –OH group). 5’ and 3’ refer to the numbers assigned to the carbons in the sugar ring.
DNA Structure
Key features, the double helix – “ribbons” represent the sugar phosphate backbones of the two DNA strands – helix is “right-handed”, curving up to the right. The two strands are held together by hydrogen bonds between the bases, which are paired in the interior of the double helix. Partial chemical structure, the strands are antiparallel, meaning that they are oriented in the opposite directions. Van der Waals attractions between the stacked pairs paly a major role in holding the molecule together.
Purines
Adenine and guanine, nitrogenous bases with two organic rings.
Pyrimidines
Cytosine and thymine, nitrogenous bases with a single ring.
Watson & Crick ended their paper with the statement
“It has not escaped our notice that the specific pairing we have postulated immediately suggest a possible copying mechanism for the genetic material.”
Semiconservative model can be distinguished from a conservative model of replication
in which the two parent strands somehow come back together after the process (that is, the parent molecule is conserved).
The bacterium E. coli has a single chromosome of about
4.6 million nucleotide pairs and can copy all the DNA and divide to form two genetically identical daughter cells in less than an hour.
Human cells have
46 DNA molecules in its nucleus, one long double-helical molecule per chromosome. In all, that represents about 6 billion base pairs or over a thousand times more DNA than is found in bacterial cell.
The replication of a DNA molecule begins at special sites called
origins of replication, short stretches of DNA having a specific sequence of nucleotides – eukaryotic chromosome may have hundreds or even a few thousand replication origins.
At each end of a replication bubble is a
replication fork, a Y-shaped region where the parental strands of DNA are being unwound.
Several kinds of proteins participate in the unwinding
Helicases are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands.
After parental strand separation
single strand binding proteins bind to the unpaired DNA strands stabilizing them.
The untwisting of the double helix causes together twisting and strain ahead of the replication fork
Topoisomerase helps relieve this strain by breaking swiveling and rejoining DNA strands.
Enzymes that synthesize DNA cannot initiate the synthesis of a polynucleotide
they can only add nucleotides to the end of an already existing chain that is base paired with the template strand.
The initial nucleotide chain that is produced during DNA synthesis is actually a short stretch of
RNA, not DNA. This RNA chain is called a primer and is synthesized by the enzyme primase.
Primase starts an RNA chain
from a single RNA nucleotide, adding RNA nucleotides one at a time, using the parental DNA strand as a template.
The completed primer
generally 5 to 10 nucleotides long, is thus base paired to the template strand. The new DNA strand will start from the 3’ end of the RNA primer.
Enzymes called DNA polymerases
catalyze the synthesis of new DNA by adding nucleotides to a preexisting chain. Eukaryotes have at least 11 different DNA polymerases discovered so far.
Most DNA polymerase require a
primer and a DNA template strand, along which complementary DNA nucleotides line up. The rate of elongation is about 50 per second in human cells.
Each nucleotide added to a growing DNA strand comes from
a nucleoside triphosphate, which is a nucleoside (a sugar and a base) with three phosphate groups.
The only difference between the ATP of energy metabolism and dATP, the nucleoside triphosphate that supplies an adenine nucleotide to DNA
is the sugar compound which is deoxyribose in the building block of DNA, but ribose in ATP.
Like ATP, the dATP used for DNA synthesis are chemically reactive because
their triphosphate tails have an unstable cluster of negative charge.
As each monomer joins the growing end of DNA strand, two phosphate groups
are lost as a molecule of pyrophosphate. Subsequently hydrolysis of the pyrophosphate to two molecules of inorganic phosphate is a coupled exergonic reaction that helps drive the polymerization reaction.
Two strands of DNA in a double helix are antiparallel, meaning
that they are oriented in opposite directions to each other.
The antiparallel arrangement of the double helix affects replication, because of their structure. DNA polymerases can add nucleotides only to
the free 3’ end of a primer or growing DNA strand, never to the 5’ end.
A new DNA strand can elongate only in the
5’ → 3’ direction.
Along one template strand
DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5’ → 3’ DNA pol III nestles in the replication fork on the template strand and continuously adds nucleotides to the new complementary strand as the fork progresses. The DNA strand made by this mechanism is called the leading strand.
To elongate the other new strand of DNA in the mandatory 5’ → 3’ direction
DNA pol III must work along the other template strand in the direction away from the replication fork. The DNA strand elongating tin this direction is called the lagging strand.
Contrast to the leading strand, the lagging strands is synthesized
discontinuously, as a series of segments. Theses segments of the lagging strand are called Okazaki fragments, which are about 200 nucleotides long in eukaryotes.
Each Okazaki fragment on the lagging strand must be
primed separately. another DNA polymerase, DNA polymerase 1 (DNA pol I), replaces the RNA nucleotides of the primers with DNA versions, adding them one by one onto the 3’ end of the adjacent Okazaki fragment.
DNA pol I cannot joining the final nucleotide of this replacement DNA segment to the first DNA nucleotide of the Okazaki fragment whose primer was just replace.
Another enzyme, DNA ligase, accomplishes this task, joining the sugar phosphate backbones of all the Okazaki fragments into a continuous DNA strand.
The various proteins that participate in DNA replication actually from a single large complex, a “DNA replication machine.” For example, by interacting with other proteins at the fork
primase apparently acts as a molecular brake, slowing progress of the replication fork and coordinating the rate of replication on the leading and lagging strands.
Second, the DNA replication complex does not move along the DNA: rather
the DNA moves through the complex during the replication process.
In eukaryotic cells, multiple copies of the complex, perhaps grouped into “factories,” may
anchored to the nuclear matrix, a framework of fibers extending through the interior of the nucleus.
Recent studies support a model in which
two DNA polymerase molecules, one on each template strand, “reel in” the parental DNA and extrude newly made daughter DNA molecules. Additional evidence suggests that the lagging strand is looped back through the complex, so that when a DNA polymers completes synthesis of an Okazaki fragment and dissociates, it doesn’t have far to travel to reach the primer for the next fragment, near the replication fork. This looping of the lagging strand enables more Okazaki fragments to be synthesized in less time.
Errors in the completed DNA molecule amount to only one in 10 billion nucleotides, initial pairing errors between incoming nucleotides and those in the template strand are
100,000 times more common – an error rate of one in 100,000 nucleotides.
During DNA replication
DNA polymerases proofread each nucleotide against its template as soon as it is added to the growing strand.
Upon finding an incorrectly paired nucleotide
the polymerase removes the nucleotide and then resumes synthesis. Mismatched nucleotides sometimes evade proofreading by a DNA polymerase.
In mismatch repair
enzymes remove and replace incorrectly paired nucleotides that have resulted from replication errors.
Reactive chemicals (in the environment and occurring naturally in cells)
radioactive emissions, X-rays, ultraviolet light, and certain molecules in cigarette smoke can change nucleotides in ways that affect encoded genetic information.
Many different DNA repair enzymes have evolved, about
130 have been identified so far in humans.
A segment of the strand containing the damage is cut out (excised) by a
DNA cutting enzyme – a nuclease – and the resulting gap is then filled in with nucleotides, using the undamaged strand as a template.
The enzymes involved in filling the gap are a
DNA polymerase and DNA ligase. One such DNA repair systems is called nucleotide excision repair.
The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands. Even if an Okazaki fragment can be started with an RNA primer bound to the very end of the template strand, once that primer is removed
it cannot be replaced with DNA because there is no 3’ end available for nucleotide addition.
Eukaryotic chromosomal DNA molecules have special nucleotide sequence called
telomeres at their ends. Telomeres do not contain genes, instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence.
In each human telomere, for example, the
six nucleotide sequence TTAGGG is repeated between 100 and 1,000 times. Telomere DNA protects the organism’s genes. In addition, specific proteins associated with telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell’s systems for monitoring DNA damage.
Staggered ends of a DNA molecule, which often result from double strand breaks
can trigger signal transduction pathways leading to cell cycle arrest or cell death.
Telomeres do not prevent the shortening of DNA molecules due to successive rounds of replication
they just postpone the erosion of genes near the ends of DNA molecules.
An enzyme called telomerase
catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication.
Telomerase is not active in most human somatic cells, but its activity in
germ cells results in telomeres of maximum length in the zygote.
Eukaryotic chromosomes consists of one linear DNA molecule associated with
a large amount of protein. Each chromosome contain a single linear DNA double helix, in humans averages about 1.5 x 108 nucleotide pairs.
Together this complex of DNA and protein, called
chromatin, fits into the nucleus through an elaborate, multilevel system of DNA packing.
Dense region of DNA in a bacterium, called the
nucleoid is not bounded by a membrane.
DNA, the double helix
the phosphate groups along the backbone contribute a negative charge along the outside of each strand.
Histones
are proteins responsible for the first level of DNA packing in chromatin, small (containing about 100 amino acids).

More than a fifth of a histone’s amino acids are positively charge (lysine and arginine) and bind tightly to the negatively charged DNA.
Four types of histones common in chromatin
H2A, H2B, H3, and H4, all four main types of histones are critical in the next level of DNA packing.
Fifth type of histone, called
H1, is involved in a further stage of packing.
Nucleosomes, or “beads on a string” (10 nm fiber)
unfolded chromatin, each bead is a nucleosome, the basic unit of DNA packing the “string” between beads is called linker DNA.
Nucleosome consists of DNA wound twice around a protein core composed of two molecules each of the four main histone types. The amino end
(N-terminus) of each histone (histone tail) extends outward from the nucleosome.
Next level of packing is due to
interactions between the histone tails of one nucleosome and the linker DNA and nucleosomes on either side, H1 (fifth histone) is involved at this level.
Interactions cause the extended 10 nm fiber to coil or folded, forming a chromatin fiber is prevalent in
the interphase nucleus.
Loops called
loop domains attached to a chromosome scaffold made of proteins.
The scaffold is rich in one type of
topoisomerase, and H1 molecules also appear to be present.
In mitotic chromosomes, the looped domains themselves coil and fold, further compacting all the chromatin to produce the characteristic
metaphase chromosome.
Particular genes always end up located at the
same places in metaphase chromosomes, indicating that the packing steps are highly specific can precise.
During interphase, the centromeres and telomeres of chromosomes, as well as other chromosomal regions in some cells, exist in a highly condensed state similar to that seen in a metaphase chromosome, visible as irregular clumps with a light microscope, is called
heterochromatin.
Distinguished from the less compacted more dispersed
euchromatin (true chromatin). Genes present in euchromatin can be expressed.
Phosphorylation of a specific amino acid on histone tail plays a crucial role in chromosomes behavior during
prophase 1 of meiosis. Other chemical modifications of histones also have multiple effects on gene activity.