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
what are miRNA and siRNA?
micro RNA and small interfering RNA, which are two major types of small regulatory RNA molecules. these small regulatory RNA molecules can inhibit translation or cause destruction of an RNA transcript.
in _____, the sequence of bases in an RNA molecule known as mRNA is used to specify the order in which successive ____ ____ are added to a newly synthesized polypeptide chain.
translation.
amino acids
what are the structures called that is made up of RNA and protein that binds with mRNA are the site of translation?
ribosomes. the ribosome consists of a small subunit and a larger subunit, each composed of 1 to 3 types of ribosomal RNA and 20 to 50 types of ribosomal proteins
the large subunit of the ribosome includes 3 binding sites for molecules of transfer RNA (tRNA), what are these binding sites called?
1) aminoacyl (A) site
2) peptidyl (P) site
3) exit (E) site
a major role of the _____ is to ensure that, when the mRNA is in place on the ribosome, the sequence in the mRNA coding for amino acids is read in _____, _______ groups of three nucleotides.
ribosome.
successive, nonoverlapping
each nonoverlapping group of three adjacent nucleotides constitutes a ______ which codes for a single amino acid in the polypeptide chain.
codon
the protein-coding sequence in an mRNA consists of its sequence of bases which can be translated into the correct protein only if it is translated in the proper _______ ______.
reading frame. the ribosome establishes the correct reading frame for the codons.
the actual translation of each codon in the mRNA into one amino acid in the polypeptide chain is carried out by _____
tRNA. transfer RNA, which has 70-90 nucleotides that each has a characteristic self-pairing structure, in which the letters indicate the bases common to all tRNA molecules.
three bases in the anticodon loop make up the ______; these are the three nucleotides that undergo base pairing with the corresponding _____.
anticodon.
codon
enzymes called aminoacyl tRNA synthetases connect specific ____ ____ to specific ___ molecules. these enzymes are directly responsible for actually translating the ____ sequence in a nucleic acid to a specific amino acid in a ______ ______.
amino acids
tRNA.
codon.
polypeptide chain.
the first 5’ base in the ____ in mRNA pairs with the last 3’ base of the anticodon because nucleic acid strands that undergo base pairing must be _____.
codon.
antiparallel
most codons specify an amino acid according to the _____ ____.
genetic code. the genetic code has 64 codons in total, with 61 codons specifying 20 amino acids.
three codons do not specify amino acids, instead they are ___ codons.
stop. the three stop codons are UAA, UAG, and UGA. they’re sometimes called termination codons
stop codons signal where ______ ______ and the protein is released from the ribosome.
translation terminates
because there are a lot more codons than amino acids, many amino acids are specified by ____ _____ ___ codon.
more than one
the codon in which translation begins is called the ____ codon and it is coded by AUG, which specifies the amino acid ____.
initiation. Met
the position of the initiator AUG codon in the mRNA establishes the _____ ____ that determines how the downstream ____ are to be read.
reading frame.
codons
what are the three processes of translation called?
1) initiation
2) elongation
3) termination
what occurs during initiation of translation?
the initiator AUG codon is recognized and Met is established as the first amino acid in the new polypeptide chain
what occurs during elongation of translation?
successive amino acids are added one by one to the growing polypeptide chain
what occurs during termination of translation?
the addition of amino acids stops and the completed polypeptide chain is released from the ribosome.
initiation of translation requires a number of protein _______ ______ that bind to the mRNA. In eukaryotes, one group of initiation factors binds to the __ ____ that is added to the mRNA during processing.
initiation factors.
5’ cap
the initiation complex moves along the mRNA until it encounters the first ____ triplet. the position of this ___ codon establishes the translational ______ _____.
AUG.
AUG.
reading frame
when the complex reaches an AUG, the large _____ _____ joins and the initiation factors are _____.
ribosomal subunit.
released.
in the first step of elongation, when the tRNA(Met) is bound at the P site of the _____, the next tRNA in line (complementary to the next codon) binds to the ______ site.
ribosome.
A (aminoacyl) site
in the second step of elongation, a _____ takes place in which the bond connecting the Met to its tRNA is transferred to the next amino acid group in line, forming a ______ _____ between the two amino acids.
reaction.
peptide bond.
in the third step of elongation, the ribosome moves down one ____, which puts the tRNA carrying the peptide into the P site and the now uncharged tRNA into the E site, where it is _____. A new tRNA complementary to the next codon binds to the A site.
codon
released
in the fourth, last step of elongation, the _____ transfers to the amino acid on the tRNA in the __ site. the polypeptide is elongated by repeating steps 3 and 4.
polypeptide
A site.
ribosome movement along the mRNA and the formation of the peptide bonds require _____, which is obtained with the help of proteins called ______ ______.
energy.
elongation factors.
Elongation factors are bound to GTP molecules and break their high-energy bonds to provide energy for the ______ of the _______.
elongation of the polypeptide
the elongation process proceeds until the ____ encounters one of the _____ ______ (UAA, UAG, or UGA) and when the ribosome encounters a stop codon, a protein ____ ____ binds to its A site.
ribosome
stop codons.
release factor
the release factor causes the ____ connecting the polypeptide to the tRNA to ____ and it creates the carboxyl terminus of the polypeptide which completes the chain.
bond
break
true or false: initiation elongation differs between eukaryotes and prokaryotes
true. in eukaryotes the initiation complex forms at the 5’ cap but in prokaryotic RNA molecules there is no 5’ cap.
in prokaryotes, the initiation complex is formed at one or more _____ ______ present in the mRNA known as a Shine-Dalgarno sequence. Each shine-dalgarno sequence can serve as an _____ ____ for translation, so all of the polypeptides can be translated.
internal sequences.
initiation site
the ability to initiate translation internally allows prokaryotic mRNA’s to code for ___ than ___ protein. such an mRNA is know as a _______ mRNA.
more than one protein.
polycistronic
when drawing an RNA molecule, what do you need to make sure to include?
poly A tail (AAA) at 3’ end, 5’ cap at the 5’ end, and all of the correct exons.
true or false: ribosomes are the RNA component that catalyzes peptide bond formation
true
in eukaryotes, the initiation complex forms at the 5’ cap and scans along the mRNA until the first ____ ______ is encountered
AUG sequence
Each Shine-Dalgarno sequence can serve as an initiation site for translation, what does this mean for translation?
all of the peptides can be translated simultaneously with the different Shine-Dalgarno sequences.
a polycistronic mRNA results from transcription of a group of functionally related genes located in tandem along the DNA and ______ as a single unit from one promoter. this type of gene organization is called an _____.
transcribed
operon.
_____ have many of their genes organized into an operon because the production of a polycistronic mRNA allows all the protein products to be _____ _______wherever they are needed.
prokaryotes.
expressed together
____, the molecule involved in the translating step of translation, may have originally served in ____ synthesis.
tRNA
RNA
amino acid sequences evolve through ______ and ______
mutation and selection
what is a mutation?
a change in the sequence of a gene
mutations effecting proteins occur ______ in regard to their effects on protein _____
randomly.
function
most ____ amino acid mutations impair protein function to some extent. some mutant proteins function just as well as the _____ and a _____ ____ change function.
random.
original
precious few
in a population of organisms, random mutations are retained or eliminated by the process of ______ ______ among individuals on the basis of their ability to ____ and ________.
natural selection.
survive and reproduce
most mutations that impair protein function will be _____ because the individuals carrying these mutations will leave fewer _____ than others.
eliminated
offspring
individuals that carry the occasional mutation that improves protein function will survive and reproduce more ______ than others.
successfully.
what will happen because of the enhanced reproduction of the mutant protein that improves function?
the mutant gene encoding the improved protein will gradually increase in frequency and spread throughout the entire species eventually.
one amino acid sequence may be _____ with another one over the course of ______
replaced.
evolution
the exact order of amino acids in a protein determines the proteins’ _____ and _____
shape and function
what is the general structure of an amino acid?
consists of a central carbon atom, called the a (alpha) carbon, connected by covalent bonds to four different chemical groups
what are the four different chemical groups that form the general structure of an amino acid?
-an amino group (-NH2)
-a carboxyl group (-COOH)
-a hydrogen atom (-H)
-variable R group or side chain
the four covalent bonds formed from an _____ _____ are at _____ angels, forming a tetrahedron, a pyramid with ____ triangular faces.
alpha carbon
equal.
4
which group out of the 4 makes amino acids differ from one another?
the R group
the R groups are chemically diverse and are grouped according to their ______, with a particular emphasis on whether they are _____ or ______
properties.
hydrophobic or hydrophilic
these ______ influence how a polypeptide chain _____ and hence effects the 3-dimensional shape of the protein
properties
folds
____ amino acids do not readily react with water or form _____ bonds.
hydrophobic
hydrogen
most hydrophobic amino acids have nonpolar ___ groups composed of hydrocarbon chains or uncharged _____ ______. the hydrophobic __ _____ tend to aggregate with each other.
R
carbon rings
R groups
true or false: hydrophobic molecules tend to interact with each other, and hydrophilic molecules tend to interact with each other
true
hydrophilic amino acids are ____ molecules and they tend to form hydrogen bonds with each other or with _____ molecules
polar
water
charged groups (+ or -) can form ____ ____ with a negatively charged group or a positively charged group.
ionic bonds
successive amino acids in proteins are connected by ______ ______
peptide bonds
when forming a peptide bond, the ____ group of one amino acids reacts with the amino group of the next amino acid in line, and a molecule of ____ is ______
carboxyl
water
released
in the resulting molecule, the R groups of each amino acid point in _____ ______
different directions
a peptide bond is ____ than a single bond and it is ___ ___to rotate around their central axis.
shorter
not free
a polymer of amino acids connected by _____ ____ is known as a _______, which usually consists of a few hundred amino acids
peptide bonds
polypeptide
one end of a peptide has a free amino group; this is the ____ end of the molecule. the other end has a free carboxyl group; this is the _____ end of the molecule.
-amino end
-carboxyl end
the sequence of amino acids dictates protein folding, which determines protein ______
function
the sequence of amino acids in a protein is its ______ ________. the interactions between stretches of amino acids in a protein form local ______ _______.
primary structure.
secondary structures
longer range interactions between these secondary structures _____ the overall three-dimensional shape of the polypeptide, which is its _______ _______.
supports
tertiary structure. the tertiary structure is made up of several secondary structure elements
some proteins are made up of several individual polypeptides that interact with each other and the resulting ensamble is the _____ _______
quaternary structure
how does a hydrophobic amino acid keep away from water molecules?
buries itself in the interior of folded proteins or by inserting into the cell membrane
no matter what the function of a protein is, the ability to carry out this function depends on the ___ _______ _____ of the protein
3-dimensional shape
how is a sequence of amino acids in a protein represented? does the order matter?
by a series of three letter abbreviations for the amino acids and yes the order matters
the amino acids in a protein are listed from left to right, starting at the ____ end and proceeding to the ____ end.
amino end
carboxyl end
_____ bonds can form between the carboxyl group in one peptide bond the amide group in another peptide bond, thus allowing regions of the polypeptide chain to ____. this folding is the main contribution to the _____ structure of the protein
hydrogen
fold
secondary
what are the two types of secondary structures found in many proteins called?
alpha helix and beta sheet. both of these secondary structures are stabilized by hydrogen bonding along the polypeptide backbone.
what does an alpha helix structure look like?
the polypeptide backbone is tightly twisted into a helical structure with R groups projecting outwards from the alpha helix
what does a beta sheet structure look like?
the polypeptide backbone folds back and forth on itself to form a pleated sheet with the R groups projecting alternately above and below the plane of the beta sheet
hydrogen bonds form between _____ groups in one polypeptide and ____ groups in a different part of the polypeptide
carbonyl groups and amide groups
true or false: in a beta sheet, adjacent strands can run in the same direction (parallel) or in opposite directions (antiparallel)
true.
tertiary structure is defined largely by interactions between the amino acid ___ ______
R groups
tertiary structure is determined by the _____ ______ of hydrophilic and hydrophobic R groups along the molecule, as well as by different types of ______ _____ and interactions that form between various R groups
spatial distribution
chemical bonds
the amino acids whose R groups form bonds with each other may be far apart in the ______ ____ but may end up right next to each other in the ______ protein
polypeptide chain
folded
when you are translating, you always read in the order from ___ to ____
5’ to 3’ end
true or false: the r group or side chain of an amino acid is similar to the base on a nucleotide in that these groups make the monomer unique and are responsible for the chemical and physical properties of each monomer
true
______ structures can have both types of secondary structures, ____ _____ or _____ _____
tertiary
beta sheets or alpha helices
the quaternary structure results from interactions of _______ subunits
polypeptide
tertiary structure is determined by the spatial distribution of ____ and ______ R groups along the molecule, as well as different types of ______ _____ and interactions (ionic, hydrogen, Van de Waals) that form between various R groups.
hydrophobic and hydrophilic.
chemical bonds
tertiary structure usually includes ____ or ____ in the backbone that allows R groups to sit near each other in space or allows R groups to form _____.
loops or turns.
bonds
what determines how a polypeptide chain folds?
the sequence of amino acids
which structure, primary, secondary, tertiary or quaternary, determines the function of the protein?
tertiary structure determines structure because it is the 3 dimensional structure of the molecule
why does the 3 dimensional structure determine the function of a protein?
the contours and distribution of charges of the outside of the molecule and the presence of pockets that might bind with smaller molecules on the inside enable that protein to serve as structural support, membrane channel, enzyme or signaling molecule
what is denaturation?
denaturation is the process in which molecules are unfolded and therefore lose their structure and functional purpose
how can most proteins be denatured?
by chemical treatment or high temperature that disrupts the hydrogen and ionic bonds holding the tertiary structure together.
many proteins are comprised of two or more _______ _____ or subunits with a tertiary structure that come together to form a higher order _____ structure.
polypeptide chains.
quaternary
in a protein with a quaternary structure, can the polypeptide subunits be identical or different or both?
polypeptide subunits can be different or identical.
in a quaternary structure, the subunits can ____ each other in subtle ways and _____ their function.
influence
what determines how a secondary, tertiary and quaternary structure are built?
the amino acid sequence (primary structure of a protein)
cells have evolved proteins called _____ that help protect slow-folding or denatured proteins until they can gain their proper 3 dimensional structure
chaperones
chaperones bind with _____ groups and nonpolar ___ groups to shield them from inappropriate aggregation which can prevent improper folding in proteins
hydrophobic groups
R groups
how do chaperones help prevent improper folding in proteins?
in the repeated cycles of binding and release they give the polypeptide time to find its correct shape
eukaryotic gene regulation can take place during what four processes?
-transcription
-translation
-RNA processing
-through chemical modification of chromatin or histones
the human body contains ~200 major types of cells. why do they look and function differently from one another?
differential expression; expresses a different set of genes at different times
in prokaryotes, why is gene regulation more simple than in eukaryotes?
-DNA is not packaged into chromosomes
-mRNA is not processed
-there is no nuclear membrane separating the process of translation and transcription
_____ ______ is when a regulatory molecule (activator protein) binds to DNA at a site near the gene so that transcription can take place
positive regulation. when the activator protein is not present or not able to bind with the DNA, transcription cannot occur.
when the ____ ______ is present and can bind to the DNA, the ____ _____ complex is recruited to the promoter of the gene.
activator protein
RNA polymerase
sometimes in positive regulation, the activator protein undergoes a change in shape that alters its binding affinity for DNA, this is an example of an ______ _____
allosteric effect
_____ _______ is when a regulatory molecule (repressor protein) binds to DNA at a site near the gene so that transcription can be prevented.
negative regulation. when the repressor protein is present and can bind to the DNA, RNA polymerase cannot bind and therefore there is no transcription
when the _____ ____ is absent or not able to bind with DNA, the DNA itself can recruit the ___ ______ complex and transcription can take place
repressor protein
RNA polymerase
what is the example of a lac operon of a prokaryote preforming gene regulation?
The bacterium E. Coli. It can metabolize or catalyze lactose. the structural genes involved in lactose metabolism are only transcribed when needed, when lactose is present.
what are three examples of regulatory DNA sequences necessary for gene regulation to occur?
-promoter (needed to recruit the RNA polymerase complex)
-operator (the binding site for a negative regulator)
-CRP-cAMP binding site (binding site for a positive regulator)
the lac operon without lactose: the lacl gene (encoding the _____ protein) is expressed constantly at a low level.
repressor
in the _____ of lactose, the repressor binds with the ______, the RNA polymerase is not recruited, and transcription does not take place.
absence
operator (lacO)
the lac operon with lactose: the repressor protein is ____ to bind to the operator, therefore RNA polymerase is recruited and transcription _____.
unable
occurs
lactose acts as an _____ because it prevents binding with the repressor protein, inducing transcription. whenever lactose is present, a small amount of _____ is produced.
inducer.
allolactose
the allolactose binds to the _____ and prevents it from binding with the operator which allows the ___ ____ to bind with operator instead
repressor
RNA polymerase
lacl mutants do not produce a functional ______, lacZ and lacY are expressed in the presence or absence of lactose.
repressor
lacO mutations prevent the repressor protein from ______, so lacZ and lacY are expressed in the presence or absence of lactose
binding
mutations like lacl and lacO are called ______ because the proteins are produced continuously no matter what
constitutive
in cells containing one mutant and one nonmutant copy of lacl (repressor), the lactose genes are expressed only in the ____ of lactose
presence
in cells containing one mutant and one nonmutant copy of ___ (operator), the lactose genes are expressed in the presence or absence of lactose.
lacO
true or false: lacl genes encodes a diffusible protein
true
the ____ is a region of DNA that does not produce a diffusible product.
operator
the CRP-cAMP complex is a _____ regulator of the lac operon and it activates gene expression upon binding to DNA
positive. CRP-cAMP provides another level of control over transcription that is more sensitive to the nutrional needs of the cell
in the absence of glucose cAMP levels are ___ and cAMP binds to CRP, changing the shape of CRP. CRP binds to ___ and activates transcription
high
DNA
in the presence of glucose, cAMP levels are ____, the cAMP-CRP complex doesn’t form and CRP does not bind to the ____ _____
low
lactose operon. even in the presence of lactose, he lactose operon is not transcribed to high levels.
true or false: E. Coli preferentially used lactose when both lactose and glucose are present
false, E. Coli preferentially uses glucose, not lactose
the mechanisms that regulate whether or not transcription occurs in known collectively as ________ ________
transcriptional regulation. lactose utilization in E. Coli is the pioneering example of this phenomenon
lacZ is the gene for the enzyme beta-galactosidase, which cleaves the ______ ______ into its glucose and galactose constituents. how is a functional, nonmutant form of the lacZ denoted?
lactose molecule.
lacZ+
lacY is the gene for the protein lactose permease, which transports lactose from the ______ _____ into the cell. how is a functional, nonmutant form the lacY denoted?
external medium.
lacY+
the region of DNA consisting of the promoter, the operator, and the coding sequence for the genes is called an ______.
operon
lacO is the binding site for the repressor and is called the _______
operator
lacI encodes for a _____ protein
repressor
lacP encodes for a _____, whose function is to recruit the RNA polymerase complex and initiate transcription and an operator
promoter
the phenotype of a cell carrying such a mutation is said to be _______ for production of the proteins. this means that expression occurs continuously
constitutive
______ _______ is when the same primary transcript is spliced in different ways to yield different protein types
alternative splicing
what does a high affinity resemble?
if there is a high affinity then the receptor binds very tightly to something else
what does ORF stand for?
open reading frame
what are the regions on the mature mRNA molecule called that are not translated?
5’ UTR and 3’ UTR. Both untranslated region have regulatory functions
processes and molecules that effect the ______ of mRNA molecules in the cytoplasm can be important _____ of gene expression
lifespan
regulators
where are these elements found that impact stability of mRNA molecules?
the untranslated region of mRNA
the half life of mRNAs is often controlled by ______ elements
instability
instability elements are species sequences of ______ which can be recognized by specific _____ that target mRNA for rapid degradation
nucleotides
proteins
example: AUUU
if an mRNA is degraded, can it be translated?
no
the most common mechanism of translational regulation effects the _______ process
initiation
a base sequence recognized by binding protein can block ________
ribosomes from binding
cAMP has an inverse relationship to ______
glucose
eukaryotic gene regulation can occur during four processes, what are they?
-through chemical modification of chromatin or histones
-during transcription
-during RNA processing
-during translation
what does epigenetics mean?
“over and under” genetic inheritance
does epigenetics change the DNA sequence?
no but it can affect gene expression
epigenetic changes can be ________ through cell division and are often ______ and responsive to changes in the environment
inherited.
reversable
true or false: epigenetic changes include chromatin remodeling, histone modifications and DNA methylation
true
eukaryotic DNA is packaged as ______, a complex of DNA, RNA, and proteins that gives chromosomes their _______
chromatin.
structure
what must happen to the chromatin in order for transcription to be carried out?
the chromatin is a coiled and condensed structure that must undergo chromatin remodeling which allows it to become uncoiled or unraveled. this allows the proteins that carry out transcription to access the DNA.
nucleosomes (consist of DNA and ______) are repositioned to expose different stretches of the DNA
histones
what are histone tails?
structures that protrude from the histone proteins of the nucleosome. they’re made up of individual amino acids
individual amino acids in the histone tails can be _____ by the addition (or removal) of different chemical groups including methyl and ____ groups.
modified
acetyl
generally, how does the methylation of histone tails impact expression?
increases or decreases expression
generally, how does the acetylation of histone tails impact expression?
increases expression and transcription
positively charged amino acid R groups on ______ are attracted to negatively charged _________ backbone of DNA, holding DNA wrapped around histones in place.
histones
phosphodiester
the most common chemical modifications of DNA is the addition of a _____ group to cytosine.
methyl (CH3)
clusters of CG dinucleotides are called ___ _____ and are often near the promoter of genes.
CgP islands
CgP methylation ______ gene expression
decreases. methylation can change over time in response to the environment and be reversed as well.
true or false: one x chromosome is inactivated so you don’t have double the expression of the genes present on the X chromosome
true
in calico cats, one gene for fur color on the paternal X or one gene on the maternal X is inactivated. what is usually expressed?
maternal copy is expressed and orange fur occurs for those cells.
the white patches in calico cats are due to an _______ gene
autosomal
calico cats are _____ because a _____ will either be black or orange because they will have either a paternal or maternal x chromosome, instead of two x chromosomes.
female
male
what is X inactivation mediated by?
Xist noncoding RNA
the process of x inactivation:
-the Xist gene is _______ and spliced, and Xist noncoding RNA binds with the X-chromosome inactivation center (XIC).
-transcription of Xist continues and the X chromosome is eventually _____ by the Xist RNA.
-the presence of the Xist RNA triggers DNA methylation and other changes associated with ______ transcriptional activity.
transcribed
coated
reduced
in later stages of development, as each cell divides, the X chromosome that was _____ in the parental cell remains _____ in the daughter cells.
inactive
