7 nucleic acids Flashcards
which nucleic acids are purines
guanine and adenine
which nucleic acids are pyramidines
thymine
cytosine
which nucleic acids have double rings
guanine and adenine
which nucleic acids have single rings
thymine
cytosine
which part of the carbon is the phosphate on
5’
which part of the carbon is the OH on
3’
which bases have 3 hydrogen bonds between them
cytosine to guanine and vice versa
which bases have 2 hydrogen bonds between them
adenine to guanine and vice versa
what does antiparallel mean
go in different directions
describe supercoiling
the first structure in the supercoiling in dna is called a nucelosome
8 histones proteins make a core
dna wraps around the core twice
a 9th histone protein completes the structure
what is inside the nuclues
chromatin
what are supercoils made of
2 coils of dna and 9 histone proteins
where does transcription take place
nucelus
what direction does transcription ocur in
5’ to 3’ direction
what direction does rna polymerase read
3’ to 5’
what does the rna polymerase add
the 5’ end (phosphate) of the free rna nucleotide to the 3’ end of the growing mrna molecule
why can dna in nucleosomes not be transcriped
the 9th histone protein is in the way. however these can be removed. it can also be regulated by addition of methyl groups which are almost like 10th blocker histone proteins that stop gene expression
what is methylation
process where methyl groups are added to some cytosine bases, and stops the epxression of genes
changes to dna methylation patterns have seen in
differentiation of stem cells
activation of lymphocytes during infection
imprinting behaviour
weightlessness in space
what are exons
sequences of mrna expressed as proteins
what are introns
sections of mrna not expressed as proteins in translation
what does splicing of mrna after transcriptuon do
remove the introns
change the number of exons, maing a different polypeptide and increasing the number of different proteins in an organism
what does polymerase do
makes a copy
what does helicase do
unzips the dna strand
what does ligase do
glue together dna
how many hydrogen bonds between c and g
3
how many hydrogen bonds between a and t
2
a dna nucleotide has the deoxyribose on the …
5’ carbon
a dna nucleotide has the OH group on the …
3’ carbon
how many histone proteins in a nucleosome
8 with one to secure it on top
how many times does dna wrap around the histone protein
twice
what are promoter dna base sequences
non-coding dna with a function, to help gene expression
what are regulator proteins
bind to promoter sequences in dna
changes in dna methylation patterns due to
differentiation of stem cells
activation of lymphocytes during infection
imprinting behaviour
weightlessness in space
what is dna gyrase also known as
topoisomerase
dna gyrase/topoisomerase function
unwinds dna
dna helicase function
unzipper
SSB’s funciton
stops reannealing
dna polymerase III
copies the leading strand
rna primer
primase
dna polymerase III function
copies the leading and lagging strands
rna primer function
initates dna synthesis
what does primase do
In bacteria, primase binds to the DNA helicase forming a complex called the primosome. Primase is activated by the helicase where it then synthesizes a short RNA primer approximately 11 ±1 nucleotides long, to which new nucleotides can be added by DNA polymerase.
ssb’s are
single stranded binding proteins
what does dna polymerase I do
replace rna
what does ligase do
joins fragments
what are ozaki fragments
the short strands of dna that are replicated on the lagging strand as it goes from 5’ to 3’ when the dna polymerase reads 3’ to 5’
which way does dna polymerase III read
3’ to 5’
which way does dna polymerase I produce
5’ to 3’
what does ligase do
glue fragments together
why are the newly formed dna strands called semi conservative
one strand is old and one is new
what does exonuclease/dna polymerase I do
get rid of rna primers
ssb function
keep the two strands apart
which directon does the leading strand go
3’ to 5’
which direction does the lagging strand go
5’ to 3’
how many times is an rna primer needed on the leaing strand
once
how many times is an rna primer needed on the lagging strand
every ogasaki fragment
what is exonuclease also known as
dna polymerase I
when does dna replication occur
interphase, S (synthesis)
what is the replicated dna double helix called
replication fork (numerous throughout the double helix)
are histones alkali or acidic
alkali (and positively charged)
what has histones eukaryotic or prokaryotic dna
eukaryotic
what does a nucleosome consist of
a length of DNA of about 150 base pairs, wrapped around a core of eight histones (which are actually four pairs of four different histones) and a special histone named H1
describe dna properties that make the bonding with histone neutralise it
acidic and negatively charged
how are nucleosomes linked
the DNA strand from one nucleosome flows directly into the next nucleosome. This section of DNA is called a DNA linker. The overall appearance of DNA in this form has been called a string of ‘beads’.
how does base paring allow such stability of the double helix
The hydrogen bonding between the purine and the pyrimidines (see Be aware box below). Two hydrogen bonds occur between adenine (A) and thymine (T), and three hydrogen bonds occur between guanine (G) and cytosine (C).
The slightly positive charge on T and a slightly negative charge on A, allow the two bases to bond together during complementary base pairing.
purines:
adenine and guanine
2 rings in structure
pyramidines are
thymine and cytosine
1 ring in structure
how many replication forks are required in dna replication
2
helicase does what
binds to the origin of replication and breaks hydrogen bonds between base pairs to unwind the DNA double helix. Single-strand binding proteins then bind to the single strands formed to keep them apart to allow time for the DNA sequence to be copied. The two separated strands act as templates for the replication process. As helicase moves along the DNA molecule, it causes supercoiling and tension on the region ahead.
what happens when a free nucleotide triphosphates bind to the template
they lose their two extra phosphate groups to generate energy which is used to add the nucleotide to the growing polynucleotide chain
which one is the leading strand
is the strand of DNA that is being replicated continuously in the 5’ to 3’ direction by continuous polymerisation at the 3’ growing tip.
which one is the lagging strand
the strand of DNA that is replicated discontinuously in small fragments in the 5’ to 3’ direction away from the replication fork.
what can dna polymerase III add dna nucleotides to
the 3’ OH group of the deoxyribose
why can dna polymerase III not work normally on the lagging strand
the last nucleotide ends with a 5’ phosphate group
what happens instead on the lagging strand due to the last nucleotide endingwith a 5’ phosphate group
a DNA primase first makes short RNA primers (these primers are later removed by DNA polymerase I and substituted with a short DNA segment), which allow the DNA polymerase III to add DNA nucleotides to the 3’ OH of the RNA primer. Many such primers are made as a scaffold for the DNA polymerase III. It synthesises short DNA fragments called Okazaki fragments, which are joined together by DNA ligase to form a complete DNA strand. The result is two new strands, both based on the template of the old DNA molecule.
non coding dna
DNA sequences within a genome that do not consist of the information to make a protein
non coding dna includes
regualtors of gene expressin
introns
telomeres
genes for trna
regualtors of gene expression
These are DNA sequences that regulate gene expression in various ways. For instance, promoters are sequences that occur just before genes and act as a binding point for the RNA polymerase enzymes that catalyse the transcription process. Other DNA sequences may act as binding sites for proteins that either increase or decrease the rate of transcription; these are known as enhancers and silencers, respectively.
introns
These are DNA base sequences found within eukaryotic genes that get removed at the end of transcription. They do not contribute to the amino acid sequence of the polypeptide made from the gene.
telomeres
These are repetitive sequences that protect the ends of the chromosome. Telomeres help ensure that DNA is replicated correctly. With every cell division, short stretches of DNA are lost from the telomeres.
genes for trna’s
These genes code for RNA molecules that do not get translated into proteins, but instead fold to form tRNA molecules that play an important role in translation.
what is a tandem repeat
a sequence of two or more dna base paris that is repeated in such a way that the repeats lie end-to-end on the chromosome. generally forms part of non coding dna
what does dna profiling involve
Collection of samples and extraction of DNA
Amplification (copying) of the DNA region containing tandem repeats by PCR
Separation of the DNA fragments using gel electrophoresis .
what is dna sequencing
the method used for deducing the precise order of nucleotides within a DNA molecule. Since all DNA molecules have the same sugar phosphate backbone, the main role of DNA sequencing is to determine the order of the four bases (adenine, guanine, cytosine and thymine) in a DNA strand.
dna sequencing is used for
DNA profiling, paternity suits, forensics, cancer analysis and genome studies
how does dna sequencing work
dye labeled segment sof dna copied from the template with unknown sequence
four seperate reaction mixtures as shown above for C (primers for each nucleotide are attached to dye label of different colour
the products of the four reactions are mixed and all dye labelled segments are applied to a single lane of the gel.
dna migration
the sequence information is fed
what is x ray diffraction
based on the principle that X-rays are scattered when they pass through different material. The scattering is called diffraction, and patterns in diffraction indicate properties of the crystals. Since X-rays affect photographic film in the same way as visible light (turning it black), the scattering pattern can be visualised (shown) on a radiogram. Biological material, such as DNA, can be used in this technique.
what did hershey and chase find
When bacteriophages containing radioactive phosphorus ( 32 P) were allowed to infect nonradioactive bacteria, all the infected cells became radioactive. Additionally, the next generation of bacteriophages, produced from the infected bacteria, were all radioactive.
However, when the bacteria were infected with bacteriophages labelled with radioactive sulfur ( 35 S) and the virus coats removed (by agitating them in an electric blender), almost no radioactivity could be detected in the infected cells.
These findings suggest that the DNA component of the bacteriophages is injected into the bacterial cell, while the protein component remains outside. Since the DNA entered the bacteria and caused the formation of radioactive bacteriophages, it showed that DNA was the genetic material.
stages of transcription
initiation
elongation
termination
what is initiation
when RNA polymerase binds to the dna at the promoter region and the double helix unwinds
what is elongation
when mRNA becomes longer as nucleotides are added to the 3’ OH group.
what is termination
when the mRNA synthesis is complete and the complex of dna, rna polymerase and mrna dissassembles
what is post transcriptional modification
In prokaryotes, there is no nucleus or nuclear membrane. Once the mRNA has been synthesised, translation begins immediately. In eukaryotes, the mRNA that is produced needs to be prepared for translation. this is for introns and exons
introns
are DNA sequences in eukaryotic genes that contain no coding information. Sometimes they contain controlling sequences that regulate the transcription of the gene.
exons
the DNA sequences that code for a polypeptide.
what is a spliceosome
a large ribonucleoprotein (RNP) complex made up of five small nuclear ribonucleoproteins (snRNPs) and several proteins. It acts as an enzyme in the splicing process to remove introns and bind exons together. (You are not expected to know this definition for the exam.)
what does splicing allow
several proteins to be synthesised from the same gene
what does the promoter do
directly affects transcription by controlling whether or not RNA polymerase can access the gene.
what is the role of the promoter
the regulation of transcription
what is an operon
a set of genes all linked to a single promoter
LACTOSE THING
7.2
when lactose is present…
the active repressor protein, a protein that stops transcription, binds to the operator next to the promoter. An operator is a sequence of DNA in prokaryotes that allows a cell to regulate whether a gene is transcribed or not. This stops the binding of RNA polymerase with the promoter. Thus, the genes of the lac operon are not transcribed.
what does transcriptional regulation ensure
that certian genes are transcribed and others remain silent, meaning that they are not transcribed
what charge do histones have
positie
what does prokaryotic dna lack that eukaryotic dna has
histones
how are nucleosomes linked
because the dna strand from one nucleosome flows directly into the next one (dna linker)
purpose of nucleosomes
to supercoil dna
What type of cells have DNA associated with histones?
eukaryotic
how many hydrogen bonds between a and t
two
how many hydrogen bonds between c and g
three
purines
a and g
pyramidines
c and t
functions of non coding dna
regulators of gene expression
introns
telomeres
genes for trnas
what is a tandem repeat
a sequence of two or more dna base pairs that is repeated in such a way that the repeats lie end to end on the chromosome.
generally non coding dna
uses of tandem repeats
dna profiling
steps of dna profiling
collection of samples and extraction of dna
Amplification (copying) of the DNA region containing tandem repeats by PCR
Separation of the DNA fragments using gel electrophoresis
what must happen for a dna profile
all dna fragments for one to indetified must match to at least one of the parents
what is dna sequencing
the method used for deducing the precise order of nucleotides within a DNA molecule. Since all DNA molecules have the same sugar phosphate backbone, the main role of DNA sequencing is to determine the order of the four bases (adenine, guanine, cytosine and thymine) in a DNA strand.
to sequene a piece of dna you need:
template dna
short dna primer
dna polymerse
four nucleotides
dideoxynucleotides (slightly different to normal nucleotides and can be recognised by a sequencer)
what do you do in dna sequencing
heat mixture so two strands of dna seperate
lower temperature so short primer sequence finds its complementary sequence in template dna
raise temp slightly allowing enzyme to bind to dna and create a new strand (which is complementary
each time ddNTP is incorporatd, synthesis stops
transfer mix into a lane of a polyacrylamide gel
place into sequencer for electrophoresis and analysis
fragments migrate according to size and each is detected as it passes a laser beam at the bottom of the gel
each type of dioxynucleotide emits coloured light of a certain wavelength and is recorded.
computer generates an electropherogram with coloured peaks for each letter/nucleotide.
the simulated gel image is read from bottom to top starting with smallest fragment.
Gene expression might be altered at the level of post-transcriptional processing in eukaryotes and not in prokaryotes because of which of the following?
Eukaryotic exons may be spliced in alternative patterns.
when does post transcriptional regulation of mrna not occur
in prokaryotes
what happens instead of post transcriptional regulation of mrna in eurkaryotes
transcripton generates a pre mrna which is modified by splicing out the intron sequences, adding a cap and a poly a tail
what happens instead of post transcriptional regulation of mrna in eurkaryotes
transcripton generates a pre mrna which is modified by splicing out the intron sequences, adding a cap and a poly a tail
In which direction does transcription occur?
5’ to 3’
Which statement correctly describes the elongation stage of transcription?
RNA polymerase adds nucleotides to the 3’ end of the RNA molecule.
are exons found in dna
no
Alternative splicing of exons increases the
diversity of proteins that can be made.
what is an operon
a set of genes all linked to a single promoter
what is a promoter
controls whether or not rna polymerase can access the gene
a short DNA sequence situated just before a gene, which acts as a binding point for the RNA polymerase enzyme. The promoter is a good example of non-coding DNA with a function.
what is an active repressor protein
stops transcription
what happens in the presence of lactose
the active repressor binds to lactose instead of attaching to the operator. As a result, RNA polymerase can bind to the promoter and transcribe the genes of the lac operon. The genes are thus switched on. The genes that are transcribed and translated enable the bacterium to break down lactose as a food source. Thus the bacterium only expends the energy to produce these enzymes when their substrate is present in the environment.
what is transcriptuonal regulation
ensures that certain genes are transcribed and others remains silent, meaning they are not transcribed.
what do actiator proteins bind to
enhancers to increase the rate of transcription
what do represser proteins bind to
silencers to increase and decrease the rate of transcription
why do histones have a direct influence on transcription
when they bind to dna they block access to rna polymerase
what does acetylated mean
to add an acetyl group (–CH 3 COO - )
why does acetylation happen
prevents binding between nucleosomes. this partially unwinds the dna. This partially unwinds the DNA, allowing the enzymes involved in transcription to access it. As a result, acetylation of histones generally keeps the genes active while deacetylation, removal of the acetyl group, silences the gene.
what is methylation
adding a methyl group (-CH3)
effect of methylation
positive or negative depending on where the histones are located on the genome
dna that is methylates is usually
not expressed (cytosine nucleotides are shut down)
what is epigenetics
the study of heritable changes in organisms that are brought about by changes in gene expression rather than by modification of the genetic code.
CpG what does the p stand for
phosphate
what is the CpG
epigenetic tag that can be passed to daughter cells during mitosis in the body (copied during DNA replication)
what affects methylation
pollution, diet, temperature or stress
does methylation of dna change with dna replication
no
stages of translation
initiation
elongation
termination
what happens at initiaion
the mRNA binds to a small ribsomal subunit. Next, the anticodon of the initiator tRNA binds to the codon of the mRNA. Finally, the large ribosomal subunit joins to complete the assembly of the translation complex. Now that each component is in its correct location, the process of translation can start.
what is an aminoacyl-tRNA
When a tRNA molecule binds to its corresponding amino acid it forms a complex
elongation
Elongation involves a repeated cycle of events. A new aminoacyl-tRNA comes in and binds to the A site ( step 1 ). This aminoacyl-tRNA carries a specific amino acid that matches the codon on the mRNA and the anticodon of the tRNA.
In step 2 , the new amino acid is joined to the existing polypeptide chain by a peptide bond.
In step 3 , the tRNA that was bound to the polypeptide chain is now ready to be recycled as it is no longer bound to an amino acid.
In step 4 , the ribosome translocates (moves) the tRNA holding the growing amino acid chain from the A site to the P site. This shifts the ‘empty’ tRNA to the E site, where it can leave the ribosome and be recycled. Now the whole process can start again until the ribosome reaches the termination codons: UAG, UAA or UGA.
termination
Once the termination codon is reached, a release factor binds in the A site and causes the disassembly of the components of the translation complex. All of these components can be reused for another translation complex.
what do e p and a stand for
exit
peptidyl-trna binding
aminoacyl-trna binding site
describe the moving between e p a sites
the E site is where the tRNA moves after transferring its amino acid to the growing polypeptide chain, ready to exit the ribosome. The A site is where the incoming tRNA with its attached amino acid binds, while the P site is where tRNA from the A site moves after its amino acid forms a peptide bond with the growing polypeptide chain. Therefore the P site is where the tRNA holding the growing polypeptide chain is found.
During which stage of translation does a release factor bind to the ribosome?
termination
describe trna
a single-stranded RNA molecule that folds on itself to form a cloverleaf-shaped structure with double-stranded regions and three hairpin loops. One of these loops contains a sequence called the anticodon, which can decode and bind to an mRNA codon. Each tRNA has its corresponding amino acid attached to the 3’ end of CCA (read 5’ to 3’). When a tRNA recognises and binds to its corresponding codon of mRNA in the ribosome, the tRNA transfers the appropriate amino acid to the end of the growing polypeptide. The ribosome acts as an enzyme to catalyse this reaction.
The triplet of bases at the amino acid binding site of tRNA is:
5’ CCA 3’
where does the enzyme attach the amino acid
to the 3’ end of trna
trna is read
3’ to 5’
mrna is read
5’ to 3’
waht is a charged trna
when its attatched to an amino acid
how many aminoacyl-trna synthases are there
20 (one for each amino acid)
What will be the consequence if a mutation alters the formation of a single tRNA such that it still attaches to the same amino acid (phe), but its anticodon loop has the sequence AAU so it binds to the mRNA codon UUA (that usually specifies leucine)?
One mutated tRNA molecule will be relatively inconsequential because it will compete with many ‘normal’ ones.
when does translation start
once the mrna attaches itself to the ribosome
In bacteria, there is no separation between areas of the cell where transcription and translation take place, due to the absence of a nuclear membrane. THEREFORE once the mRNA is produced, and even before the whole molecule has been synthesised,
small and large ribosomal subunits attach themselves to the beginning of the mRNA and translation starts immediately.
Which of the following is a function of the signal recognition particle (SRP)?
To help translocate polypeptides across the ER membrane because an SRP attaches to the signal sequence (on the growing polypeptide chain) and initiates the binding with the ER so the protein can be translocated into the lumen of the ER.
what is a polysome
A group of ribosomes working on the same mRNA moleucle. To allow the production of polypeptides and hence proteins at a faster rate, multiple ribosomes can attach to the same mRNA. The structure formed is called a polysome
biund ribosome synthesise proteins…
mainly meant for secretion or for use in lysosomes
free ribosoms produce proteins
for use mainly within the cell
translation in prokaryotes can occur
immediately after transcription due to the absence of a nuclear membrane
primary structure:
order, identity and number of aminoa cids
peptide bonds
secondary structure
when polypeptide chain folds.
alpha helixes or beta pleated sheets
hydrogen bonds between -NH groups (from the peptide bonds)
and -C=O groups on anothe rpeptide bond further along in the same chain
tertiary structure
folding of alpha helixes or beta pleated sheets, stablised by interactions between r groups.
covalent (disulphride) bonds
will fold according to enevioenemnt (for one incytoplasm, hydrophilic aa will be on outside)
quateranry structure
multiple polypeptide chains
each is called a subunit joined by strong bonds like in teritary structure.
2 a chains
2 b chains
4 heme groups
Quaternary proteins often also have a non-protein molecular unit, called a co-factor or prosthetic group that is tightly attached to their polypeptides. (like heme)
What aspects of protein structure are stabilised or assisted by hydrogen bonds?
Secondary, tertiary, and quaternary structures, but not primary structures
When a protein associates with a prosthetic group as in this example, what is it called?
conjugated protein
