Chapter 3 - Nucleic Acids and Transcription Flashcards
What is the makeup of DNA?
linear polymer of 4 different subunits
double helix structure - 2 strands coiled around each pother - linear backbone strands and paired base units
How does the double helix of DNA give it it’s function? (2 reasons)
DNA stores genetic information that is encoded in the sequence of subunits along its length some of the DNA info encodes proteins that provide structure and do much of the work of the cell. genetic info of DNA organised in form of genes.
DNA transmits genetic information to other molecules and from one generation to the next - maintain identity throughout time
how do genes exist and how are they expressed?
can exist in many different forms in different individuals
genes usually have no effect on the organism unless they are ‘turned on’ and their product is made
What is gene regulation?
whether a gene expression occurs at a given time, in a given cell, or at what level
Who conducted studies on transmission of genetic information in 1928? what did he find?
Frederick Griffiths - showed that macromolecules in extracts from bacteria could transmit genetic information from one bacterial cell to another
What was the name of the process that Frederick Griffiths studied? and how did he do it?
Bacterial Virulence
non virulent bacteria when injected into mice do not cause illness
dead virulent bacteria when injected also didn’t cause illness
but when living non virulent were injected alongside dead virulent, illness was caused
What was Frederick Griffiths conclusion?
dead virulent bacteria somehow caused non virulent bacteria to become virulent
In the early 1940s who identified DNA as molecule responsible for carrying genetic information?
Oswald Avery, Colin Macleod, and Maclyn McCarty
What did Avery, Macleod and McCarty study to find DNA as responsible for carrying genetic information?
virulence in pneumococcal bacteria
killed virulent bacterial cells with heat, then purified the remains of the dead virulent cells to make a solution (control worked)
to identify treated with 3 different enzymes (DNase, RNase, protease) which destroyed one of the 3 types of molecule (DNA, RNA and protein) that they thought might be responsible.
What was the hypothesis of Avery, Macleod, and McCarty’s experiment?
if the molecule responsible for transformation was destroyed it would not occur
What was the result of Avery, Macleod, and McCarty’s experiment?
with RNase and protease still occurred with DNase transformation did not occur
What was the conclusion of Avery, Macleod, and McCarty’s experiment?
DNA was the responsible molecule
How do nucleotides make up DNA molecules?
5 carbon sugar and phosphate group form backbone of molecule
bases give chemical identity and pair with other strand
What is there on a phosphate group? causing?
an ionised hydroxyl group - oxygen’s are negatively charged, therefore DNA is a mild acid
What carbon on the sugar is each base attached too?
1’ carbon
What are the purines?
double ring = adenine and guanine
WHat are the pyrimidines?
single ring = thymine and cytosine
If a nucleotide has 1,2 or 3 phosphates what are they called?
monophosphate, di, or tri
What is the linkage between nucleotides in DNA?
5’ carbon to 3’ carbon
What is the bond between the carbons in DNA nucleotides called?/ look like?
Phosphodiester bonds
C-O-P-O-C
What are the properties of phosphodiester bonds?
relatively stable bond can withstand stresses such as heat and substantial pH changes give strand polarity one end differs from another
Who discovered the double helix shape of DNA?
Watson and Crick - 1953
How many base pairs are there between a complete turn in double helix?
10
what is the diameter of DNA?
2nm
What does the outside of DNA helix consist of?
twisted strands with uneven pairs of grooves called major and minor grooves
What are the 2 strands of DNA in relation to each other?
they are antiparallel (run in opposite directions)
What are the complementary base pair A and T held together by?
2 hydrogen bonds
What are the complementary base pairs C and G held together by?
3 hydrogen bonds
How does a hydrogen bond form in DNA?
when an electronegative atom in the base shares a hydrogen atom with another electron atom across the way
What is the strength of Hydrogen bonds?
relatively weak (5-10% of covalent bonds) but together contribute to stability greatly
What happens between bases in DNA?
base stacking - the non polar flat surfaces of bases group together away from water and hence stuck on top as tightly as possible
What are DNA molecules copied in process of?
Replication
What is RNA an intermediary between?
DNA and proteins
What are most of the active molecules in cells and developmental processes?
proteins
What is transcription?
genetic information in a molecule is used as a template to generate a molecule of RNA, base pairing between a strand of DNA and RNA means that the strand in DNA is transferred to RNA in the same language of nucleic acids
What is translation?
RNA is used as a code for the sequence of amino acids in a protein change of languages from nucleotides to amino acids
Do transcription and translation occur all the time?
no they are regulated
What allows cells to be specialised?
genes can be ‘turned on’ or ‘turned off’
Where do transcription and translation occur in Prokaryotes?
cytoplasm
Where do transcription and translation occur in Eukaryotes?
spatially seprated
transcription in nucleus
translation in cytoplasm
it allows for an extra level of gene regulation
Who supported hypothesis of RNA as intermediary that carries genetic information from DNA to ribosomes in 1961?
Sydney Brenner, Francois Jacob, and Matthew Meselson
how did Brenner, Jacob, and Meselson support RNA as intermediary?
They used T2 virus, which infects cells of bacteria E-Coli and hijacks the cellular machinery to produce it’s own viral proteins
What did research of the T2 virus find?
while T2 DNA never associates with bacterial ribosomes, the bacteria infected with viruses produce a burst of RNA molecules shortly after infection and before they make viral proteins. Therefore
What are the differences between RNA and DNA?
5 carbon sugar in RNA is ribose (in DNA is deoxyribose)
RNA has Uracil instead of Thymine
RNA is shorter than DNA
most RNA is single stranded
some RNA can act as enzymes and serve as catalysts in biochemical reactions
What is the difference between ribose and deoxyribose?
on the 2’ carbon in ribose there is an OH group (in deoxyribose is just a H group)
What is the difference between Uracil and Thymine?
uracil has a H group where Thymine has a CH3 group
How many nucleotides long is RNA typically and DNA?
RNA only a few thousand nucleotides
DNA millions/tens of millions of nucleotides long
What is the RNA world hypothesis?
RNA was original information storage molecule in earliest forms of life on earth.
Who conducted an experiment to show how RNA could have evolved the ability to catalyse a simple reaction?
Jack W. Szostak
What did jack W. Szostak’s experiment involve?
single RNA strand synthesised and replicated
exposed RNA to chemical that induced random changes in identity of some nucleotides
RNA molecules into test tube - variant succesfully catalysed - cleaves a strand of RNA were isolated and cycle was repeated
In each round RNA that functioned best was retained, prelicated, treated (chemical again) and seen if successful again. after a few rounds very effective RNA catalyse produced
What is DNA used as in transcription and how?
as a template to make complementary RNA
DNA duplex unwinds amd strand used as template for synthesis of an RNA transcript, complementary in sequence except from U
what is the enzyme that carries out polymerisation?
RNA polymerase
What strand of DNA is not transcribed?
the non template strand
What are the 3 stages of transcription?
initiation, elongation, and termination
What happens in initiation?
RNA polymerase and other proteins are attracted to double-stranded DNA, the DNA strands are separated, and transcription of the template strand begins
What happens in elongation?
successive nucleotides are added to the 3’ end of the growing RNA transcript the RNA polymerase proceeds along the template strand
What happens in termination?
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?
starts at a promoter and ends at a terminator
what are promoters?
regions of typically a few hundred base pairs where RNA polymerase and associated proteins bind to the DNA duplex
What is the promoter sequence in many Eukaryotes and Archaea?
5’-TATAAA-3’ known as TATA box
What happens when promoters are orientated in opposite direction?
transcription occurs in opposite driections
in bacteria what is promoter recognition mediated by?
a protein called a sigma factor, which associates with RNA polymerase and facilitates its binding to specific promoters
in Eukaryotes what is needed to assemble the promoter of a gene?
general transcription factors = at least 6 proteins
and the presence of 1 or more types of transcriptional activator protein - each of which bind to a specific DNA region called an enhancer
What do transcriptional activator proteins do?
help control when and in which cells transcription of a gene will occur
Once binding to promoters occurs in eukaryotes what is able to occur?
thay can attract a mediator complex of proteins which imn turn recruits the RNA polymerase complex to the promoter
What is Pol II?
RNA polymerase in Eukaryotes responsible for transcription of protein coding genes
what does RNA polymerase do?
adds successive nucleotides to the 3’ end of the transcript
What is the total length of transcription bubble and length of RNA-DNA duplex in bacteria?
about 14 base pairs - transcription bubble
8 base pairs - RNA-DNA duplex
What does polymerisation reaction release?
a phosphate-phosphate group
What does the RNA polymerase complex do?
opens, transcribes, and closes duplex DNA
Whats the transcription process follow?
transcription bubble forms - RNA polymerase separates DNA strands - allows an RNA-DNA duplex to form, elongate the transcription nucleotide by nucleotide, release the finished transcript, and restore the original DNA double helix
What is the primary transcript?
RNA transcript that comes off DNA template
for protein coding genes means primary transcript includes information needed to direct the ribosome to produce protein corresponding to gene
What does mRNA stand for and do?
messenger RNA - molecule that combines with ribosome to direct protein synthesis, carries genetic ‘message’ from DNA to ribosome
In prokaryotes what happens to primary transcripts?
they are translated immediately because prokaryotes have no nuclear envelope to spatially separate transcription from translation
what are molecules that code for multiple proteins called?
polycistronic mRNA
What does the nuclear envelope in eukaryotes allow for in transcription process?
RNA processing to occur - converts the primary transcript into finished mRNA, which can then be translated by the ribosome
WHat is the 5’ cap?
modified nucleotide - that allows for recognition when being transcribed
What is polyadenylation?
addition of a string of 250 consecutive A beam nucleotides to the 3’ end, forming a poly(A)tail
WHat do the 5’ cap and poly(A)tail do?
stabilise RNA transcript - by protecting the 2 ends of the transcript
WHat is the protein coding sequence in RNA called?
exons
What is the non coding sequence in RNA called?
introns
What is the removal of non coding introns called?
splicing
what enzyme allows for removal of non coding introns?
spliceosome
What are introns important for?
gene expression
90% of all human genes have at least 1 intron
most genes 6-9 introns maximum=147
What are the length of most introns?
a few thousand nucleotides (10% > 10,000)
What is alternative splicing?
primary transcripts in same gene can be spliced in different ways yields different mRNA’s and therefore, different protein products >80% of human genes are alternatively spliced
what does rRNA stand for? what does it do?
Ribosomal RNA - makes up the bulk of ribosomes and is essential in translation
what does tRNA stand for? what does it do?
Transfer RNA - carries individual amino acids for use in translation
what does smRNA stand for? what does it do?
small nuclear RNA - essential component of spliceosome required for RNA processing
What are some examples of small regulatory molecules? what do they do?
microRNA (miRNA) and small interfering RNA (siRNA) - can inhibit translation or cause destruction of the transcript
