EXAM #2 Flashcards
what is the name of the molecule that hereditary information is transmitted from generation to generation?
DNA–deoxyribonucleic acid.
DNA is a linear ____ made up of ____ different subunits.
polymer, 4
a DNA strand consists of subunits called: _____
nucleotides. each strand of DNA consists of an enormous number of nucleotides linked on to the next.
Nucleotides consist of 3 components, what are the 3? how do they aid in maintaining the structure of DNA?
1) a 5-carbon sugar
2) one or more phosphate groups
(1&2 both form the backbone of the molecule, with each sugar being linked to the phosphate group of the neighboring nucleotide)
3) a base (gives each nucleotide its chemical identity)
a nucleotide normally consists of one of ___ types of bases. How are they denoted?
- A, G, T, and C is how the bases are denoted
two of the bases are double-ring structures known as _____. These are the bases A: _____ and G: _______.
purines.
A: adenine
G: guanine
the other two bases are single-ring structures known as _________. These are bases T: ______ and C: ______.
pyrimidines
T: thymine
C: cytosine
the combination of sugar and base is known as a ______.
nucleoside
a nucleoside that has one or more phosphate groups is termed a ______.
nucleotide.
a nucleotide with one phosphate group is called a ______ _________, with two phosphate groups is called a _____ ________, and with three phosphate groups it is called a ______ ___________.
nucleoside monophosphate.
nucleoside diphosphate.
nucleoside triphosphate.
DNA is composed of nucleotides that are linked by _______ bonds.
phosphodiester bonds. has a C-O-P-O-C linkage. in DNA, it is a stable bond that can withstand stress such as heat and larger changes in pH that would break apart weaker bonds.
the phosphodiester bonds in a DNA strand give it _____, which means that one end differs from the other.
polarity. because each end has polarity you must specify which end is which (3’ or 5’ end).
when a base sequence is stated without specifying which end is which (3’ or 5’), the end at the left side is always the ____ end.
5’
cellular DNA molecules have what type of form?
a double helix strand
what is true about the relative number of molecules found in each type of base (A, T, G, C)?
the number of molecules of the nucleotide base adenine (A) always equals the number of molecules of thymine (T). the number of molecules of guanine (G) always equals the number of molecules of cytosine (C).
within the double helix strand, the outside contours of the twisted strands form an uneven pair of grooves. what are the names of the two grooves?
the major groove and the minor groove. proteins that interact with DNA often recognize a particular sequence of bases by making contact with the bases by the major or minor groove or both.
the individual DNA strands in the double helix are _____, which means that they run in opposite directions.
antiparallel. at each end you will have a 3’ paired with a 5’.
because they form specific pairs, the bases A and T are said to be _____, as well as the bases G and C.
complementary
the paired strands forming a double stranded DNA helix must have (different or the same) base sequences?
different.
T or F: because of the A-T and G-C base pairing, knowing the base sequence of one strand tells you the base sequence of its partner sequence?
true
base stacking within a strand contributes to the ____ of the DNA double helix.
stability.
why does base stacking occur?
base stacking occurs because the nonpolar, flat surfaces of the bases tend to group together away from water molecules, and hence stack on top of one another as tightly as possible.
in a DNA structure, there is no restriction on the ____ of bases along the DNA.
sequence. for example, an A can be followed by a T, C, G or another A.
what does this lack of sequence constraint imply?
the genetic information carrying capacity of a single DNA molecule is unimaginable.
DNA molecules are copied in the process of replication, which relies on what?
base pairing
describe what DNA replication is
the unique ability of DNA molecules to create exact copies of itself containing the same base pair sequence.
describe the process of DNA replication
-the two strands of a parental double helix unwind and separate into two single strands.
-each of the parental strands serves as a template/pattern for the synthesis of a complementary daughter strand
-the synthesis of a new strand of DNA is carried out
what is the result of DNA replication?
when the process of replication is complete there are two molecules, each containing one parental strand and one daughter strand. the two parental and daughter strands are identical in sequence, with the exception of errors.
what is the enzyme called that carries out the synthesis of a new strand of DNA?
DNA polymerase
how can someone predict what the daughter strand of a double helix will look like based off a parental strand?
the sequence of the parental strand determines the sequence of the daughter strand. wherever one strand carries an A, the other needs a T, and where there is a G, the other has a C.
what is a mutation? what is it a result from?
a mutation is a change in the genetic information in DNA. it results from an unrepaired error in DNA replication
most mutations in genes are ______, but in some cases mutations can be ______ why?
harmful.
positive.
rare favorable mutations are essential in the process of evolution because they allow populations of organisms to change through time and adapt to their environment.
RNA (ribonucleic acid) is an _____ between DNA and the amino acid sequence of proteins.
intermediary
most of the active molecules in cells and development processes are _____, including ____ that convert energy into usable forms and the _____ that provide structural support for the cell.
proteins.
enzymes.
proteins
what is one of the central dogmas of molecular biology?
DNA –> RNA (transcription)
RNA –> proteins (translation)
describe the process of transcription
genetic information in a DNA molecule is used as a “template” to transcribe or copy an RNA molecule, using the same language of nucleic acid.
describe the process of translation
a molecule of RNA is used as a code for the sequence of amino acids in a protein. translation is used to indicate a change of languages, from nucleotides that make up nucleic acids to amino acids that make up proteins.
transcription and translation are two steps in the process of ___ ______, which is a production of a functional gene product.
gene expression.
when a gene is ____, it is turned ___. when a gene in not ____ it is not turned ___.
expressed. on. genes are expressed only at specific times and places, and are not expressed at other times and places.
Gene expression is _____, meaning that it does not occur at all times in all cells, even though all cells in an individual contain the same ___.
regulated.
DNA.
cells are specialized for certain functions and these certain functions depend on which genes are turned off in specific cells.
the timing of ___ _____ is carefully ______.
gene expression.
controlled.
nucleic acids are _____ made up of ______.
polymers.
monomers
what type of bond forms between A and T and C and G in DNA?
Hydrogen bonds. H bonds are weak and can be disrupted by pH and heat.
electronegative atoms such as O and N share a H atom with another _________ _____.
electronegative atom
what is Chargaff’s rule?
the amount of one base (A and T, G and C) is equal to the amount of the complementary base.
what is a phosphodiester bond?
3’ C-O-P-O-C 5’ linkage. these types of bonds give DNA polarity (asymmetry) and directionality (5’ to 3’ from top to bottom in this case).
what is denaturation?
the separation of paired, complementary strands of nucleic acids
if you disrupt the ______ ______ holding together secondary structure, it will denature.
noncovalent interactions
what can disrupt the non-covalent interactions (includes base stacking and H bonding)?
high temperatures and high pH
what is RNA?
RNA is a polymer of nucleotides linked by phosphodiester bonds. each RNA has a polarity determined by which end is 3’ and 5’.
what are the two main differences between RNA and DNA?
RNA contains the sugar ribose rather than deoxyribose.
RNA has the base uracil (U) rather than thymine (T).
Ribose carries a _____ group on the 2’ carbon and these groups are reactive functional groups which in part explains why RNA molecules are less stable than DNA molecules.
hydroxyl
while the 5’ end of a DNA strand is typically a monophosphate, the 5’ end of an RNA strand is typically a _______
triphosphate
in RNA the base ____ replaces the base thymine in DNA.
uracil (U).
the groups that participate in hydrogen bonding are identical, so what does the base uracil pair with in RNA?
uracil pairs with adenine (U-A) in the same way that thymine pairs with adenine in DNA (T-A).
what molecules are shorter, RNA or DNA?
RNA is much shorter than DNA molecules as they contain only a few thousand nucleotides compared to millions of nucleotides
what is the main physical difference between RNA and DNA?
most RNA molecules are single stranded, whereas most DNA molecules are double stranded.
although most RNA molecules are synthesized as single stranded, they can fold into complex, three dimensional structures containing one or more ____ _______ regions where the RNA forms ______ _____ ______ by folding upon itself like a hairpin.
double-stranded regions.
complementary base pairs.
RNA stores its genetic information in its sequence of _____.
nucleotides.
true or false: some RNA molecules can actually act as enzymes that facilitate chemical reactions (catalyze)
true
what is the RNA world hypothesis?
RNA, not DNA was the original information/genetic storage molecule in the earliest forms of life on earth because RNA has properties of both DNA and proteins (enzymes). RNA was a key molecule in the very first forms of life
as a region of DNA unwinds, one strand is used as a _____ for the synthesis of an RNA transcript that is _____ in sequence to the template according to the base pairing rules. what is one the exception to this rule?
template.
complementary.
the exception is that the RNA transcript contains U (uracil) where the template contains A (adenine)
the DNA -> RNA transcript is produced by _____ of nucleoside triphosphates
polymerization
how many template strands are transcribed from a DNA helix?
only 1, which is called the template strand. its partner, the non template strand is not transcribed.
what is the enzyme called that carries out polymerization?
RNA polymerase, which acts by adding successive nucleotides to the 3’ end of the growing transcript.
is reverse transcription a thing??
yes, some viruses have RNA genomes that are reversed transcribed into DNA
What is the process called when DNA or genetic material is passed between bacteria and its surrounding environment?
transformation
promoters of many genes have mostly adenines and thymine’s. what is most likely the reason for this high proportion of adenines and thymines?
this is the region where template and nontemplate strands separate, and A-T bases require less energy to separate than G-C base pairs.
which DNA molecules would be more stable under increasing temperature?
a DNA molecule that has more guanine and cytosine nucleotides
a polymerization reaction is made irreversible by what?
hydrolysis of a pyrophosphate group
what are the three stages in transcription called?
initiation, elongation, and termination
what happens at the first stage of transcription?
RNA polymerase and other proteins are attracted to double stranded DNA, the DNA strands are separated, and transcription of the template strand actually begins.
what happens at the second stage of transcription?
successive nucleotides are added to the 3’ end of the growing RNA transcript as the RNA polymerase proceeds along the template strand
what happens at the last stage of transcription?
the RNA polymerase encounters a sequence in the template strand that causes transcription to stop and the RNA transcript to be released.
where does transcription start and end?
transcription starts at a promoter and ends at a terminator
the DNA template runs in the opposite direction from the RNA template, meaning they’re ________
antiparallel
true or false: the RNA transcript is synthesized in the 5’ to 3’ direction and the DNA template is read in the opposite direction (3’ to 5’).
true
what is a promoter?
regions of typically a few hundred base pairs where RNA polymerase and associated proteins bind to DNA.
is transcription initiated in one or both strands on a double stranded DNA helix?
only one strand of the double helix because both strands are needed to recruit these proteins
what is a TATA box?
a promoter sequence of 5’ -T-A-T-A-3’ for many eukaryotic and archaeal promoters
transcription takes place about 25 ______ downstream of the ____ ____.
nucleotides.
TATA box
transcription occurs until the RNA polymerase encounters a sequence known as a ______ and then the transcript is ____.
terminator.
released
which DNA strand in a double helix is transcribed depends on the orientation of the _____
promoter
for genes whose products are needed by the cell 247, transcription takes place ______. most genes however are transcribed only at ____ times, under certain conditions or in certain cell types.
continually.
specific
for such genes, regulation of transcription often depends on whether the RNA polymerase and associated proteins are able to ___ with the ____
bind with the promoter
in bacteria, promoter recognition is mediated by a protein called ____ ____
sigma factor
in eukaryotes, transcription requires the combined action of at least 6 proteins known as ____ _____ _____ that assemble the promoter of a gene
general transcription factors. assembly of these general transcription factors is necessary for transcription to occur
in eukaryotes, transcription also requires the presence of one or more types of _____ _____ _____, each of which binds to a specific DNA sequence known as an _______.
transcriptional activator proteins.
enhancer.
these transcriptional activator proteins are necessary for transcription to begin in any eukaryotic cell
transcriptional activator proteins help control when and in which cells _____ of a ___ will occur. they are able to bind with _____ DNA sequences as well as with proteins that allow transcription to begin,
transcription of a gene.
enhancer
once transcriptional activator proteins have bound to enhancer DNA sequences, they attract or recruit a ____ ______ of proteins, which in turn recruits the RNA polymerase complex to the ______.
mediator complex.
promoter
once transcriptional activation takes place, successive nucleotides are added to grow the transcript in the process of ______. transcription takes place in a sort of bubble in which the two strands of DNA are separated and the growing end of the RNA transcript is _____ with the ______ ______
elongation.
paired with the template strand
the RNA polymerase complex is a molecular machine that opens, _____ and _____ DNA
transcribes and closes
does transcription take place spontaneously?
no, it requires template DNA, a supply of ribonucleoside triphosphates, and RNA polymerase, the large multiprotein complex in which transcription occurs.
does DNA or RNA polymerase have a higher error rate?
RNA polymerase because it doesn’t have an error-correcting (proofreading) function like DNA polymerase does
what is a primary transcript?
a primary transcript is the RNA transcript that comes off the DNA strand and contains the complement of every base that was transcribed from the DNA template.
for protein coding genes, this means that the primary transcript includes the information needed to direct the _______ to produce the ____ corresponding to the gene.
ribosome.
protein
what is messenger RNA or mRNA?
mRNA is the RNA molecule that combines with the ribosome to direct protein synthesis. it carries the genetic “message” from DNA to the ribosome
in prokaryotes, the primary transcript is the ____ and they are translated immediately from _____ binding with special sequences near the ___ end and beginning the process of protein synthesis.
mRNA.
ribosomes.
5’
in prokaryotes, transcription and transcription are _____, translation begins even before transcription is completed.
coupled, they’re connected in space and time
(in prokaryotes) molecules of ___ that contain the genetic information for the _____ of two or more different proteins are known as polycistronic _____.
RNA
synthesis
mRNA
in eukaryotes, the process of transcription occurs in the ____ and translation occurs in the ____.
nucleus.
cytoplasm.
the nuclear envelope is a barrier between the two processes
the separation of the two processes allows for a complex chemical _____ of the primary transcript, known as ____ _______.
modifications
RNA processing
what is RNA processing?
converting the primary transcript into the finished mRNA, which can be translated by the ribosome.
RNA processing consists of ___ types of chemical modifications. what are they?
3
1) the 5’ end is modified by a special nucleotide called the 5’ cap
2) polyadenylation adds a poly(A) tail to the 3’ end.
3) introns are excised from the RNA strand and exons are spliced together
the 5’ cap is essential for ____ in eukaryotes because the _____recognizes the mRNA by its 5’ cap. without the cap, the ribosome would not attach to the mRNA and ____ would not occur.
translation.
ribosomes.
translation
in eukaryotes, the 5’ end and the poly A tail protect the two ends of the transcript and increase the ____ of the RNA transcript until it is translated in the ______
stability.
cytoplasm
transcripts in eukaryotes often contain regions of protein- coding sequence that are expressed, called ____, as well as noncoding regions that are interspersed called ____.
exons.
introns.
the 3rd modification in eukaryotes is the ____ of the noncoding introns.
removal
the process of joining ____ and removing introns is called ____ _____ and is catalyzed by a complex of RNA and proteins know as the ________.
exons
RNA splicing.
spliceosome
the presence of multiple introns in most genes allows for a process known as _____ _____, in which primary transcripts from the same ____ can be ____ in different ways to yield different mRNA’s and therefore different _____ ______.
alternative splicing.
gene; spliced.
protein products
some noncoding ____ _____ are processed differently from protein coding ____ and they have their own functions.
RNA transcripts
transcripts
what is rRNA?
Ribosomal RNA, which makes up the bulk of ribosomes and is essential in translation.
what is tRNA?
Transfer RNA, which carries individual amino acids for use in translation
what is snRNA?
small nuclear RNA, which is an essential component of the spliceosome required for some RNA processing
