ch.5 DNA world Flashcards
Explain why DNA is a better template than RNA and why proteins are better catalysts than RNA
DNA doesn’t have an OH group on its carbon-2 of ribose like RNA does. Instead, it has an H, which makes hydrogen bonds between complementary bases extremely more stable (RNA’s OH group tends to be get attacked by other chemicals while trying to replicate). DNA also has a tendency to remain double stranded and its lack of OH makes it 1000 times more stable. It also tremendously increases the amount of nucleotides that can be replicated (from less than 1000 nucleotides to over 100’s of millions nucleotides long).
Proteins are made of monomers (amino acids) that have a much higher versatility than strings of ribonucleotides because there are 20 different amino acids to choose from. This leads to many more combinations of polymers and the greater range in structure than what was available before with only 4 ribonucleotides to choose from.
During the process of replication, compare and contrast the process by which the leading strand and the lagging strand are formed. How does the direction of travel of the helicase (5’ or 3’) clue you in to which strand is leading and which is lagging?
Leading strand is continuous and provides a template to replicate from 3’ to 5’.
Lagging strand is discontinuous and provides template to replicate from 5’ to 3’.
List the two main functions of DNA
DNA’s 2 main functions are replicating itself and directing protein synthesis.
The figure on p.50 of the Primer depicts the “Central Dogma”. Explain the central dogma in words using the words protein, translation, transcription, DNA.
Central Dogma: order of process from DNA to protein
Transcription is used to transcribe DNA into RNA (both have nucleotides so same language). Translation is then used to translate RNA into proteins (completely different so different languages).
Be able to make a sketch and narrate in detail how replication proceeds on the leading strand using the following words (more or less in order of appearance): helicase, primase, 3’ vs 5’ carbon, RNA, DNA polymerase III, DNA polymerase I, DNA ligase.
First, you start with 2 strands of DNA. Then 2 helicases binds to DNA at origin of replication and starts to split up the strands by breaking the hydrogen bonds between the complementary bases as they move apart. Helicase continues to move further apart. Primase then binds to the single stranded DNA to RNA nucleotides one at a time from 5’ to 3’. DNA polymerase III then binds to the primer that is made because it can’t find where to attach without the primer. DNA polymerase III adds DNA nucleotides one at a time from 5’ to 3’. While all this is happening, DNA polymerase I attaches to the RNA primer to remove and replace the RNA nucleotides that its made of with DNA. After all of them are replaced, ligase combines the ends of the DNA polymers, completing the covalent bonds in the sugar-phosphate backbone.
Be able to make a sketch and narrate in detail how replication proceeds on the leading strand at the level of the individual nucleotide using the following words (more or less in order of appearance): primase, 3’ vs 5’ carbon, RNA nucleotide, DNA polymerase III DNA nucleotide, DNA polymerase I, DNA ligase. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step.
First, primase bonds to the single DNA strand and facilitates hydrogen bonding of RNA nucleotides to DNA nucleotides. A covalent bond is formed between the 2 RNA nucleotides when two phosphates are broken off of the triphosphate. Primase continues to add RNA nucleotides. DNA polymerase III then binds and adds DNA nucleotides one at a time, which makes hydrogen bonds with its DNA complement on the template strand and covalent bonds with the 3’ end of the previous nucleotide. DNA polymerase continues to add DNA nucleotides one at a time. DNA polymerase I then binds to the primer and removes RNA nucleotides one at a time to replace them with DNA. After the primer is completely replaced with DNA, ligase binds to make a covalent bond between the newly attached DNA with the DNA attached already to complete the sugar-phosphate backbone.
Be able to clearly sketch where and how Okazaki fragments are made. Use the words, polymerization, 3’ vs 5’ carbon, primer, DNA polymerase 3, ligase, anti-parallel, Okazaki fragment, leading strand, lagging strand.
During DNA polymerization, after a primer is made, DNA polymerase III binds and adds DNA nucleotides one at a time. DNA polymerase III continues to bind DNA nucleotides to the primer of the leading strand. Once the lagging strands primer is done, primase is then able to bind to lagging strands. DNA polymerase III is still adding DNA nucleotides to the leading strand, while primase can still add more primers to lagging strands as the replication bubble expands. DNA polymerase I then binds and removes RNA nucleotides and replaces then with DNA one at a time from 5’ to 3’. This leaves a lot of gaps between the newly replaced DNA and the DNA already laid out. However, lagging strands have many more than leading strands which only have one gap. The gaps between the lagging strands are called Okazaki fragments. Ligase fixes all the gaps and Okazaki fragments by binding to DNA segments to finish the sugar-phosphate backbone.
Be able to make a sketch and narrate how transcription proceeds, using the following words (more or less in order of appearance): Promoter region, RNA polymerase, template strand, RNA triphosphate nucleotide, non-template strand, GC hairpin. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step.
Initiation starts off with a 5’ to 3’ non-template strand antiparallel to a 3’ to 5’ template strand. RNA polymerase is bound the the promoter region of DNA and unwinds DNA at the start site. RNA polymerase adds RNA nucleotides one at a time from 5’ to 3’ to create a primer. The RNA strand eventually falls off of the DNA template while RNA polymerase keeps adding RNA. DNA reconnects behind RNA polymerase (hydrogen bonds between DNA is stronger than hydrogen bonds between RNA). Transcription continues until it reaches the GC hairpin which is formed by internal hydrogen bonds made between the RNA nucleotides as well as the poly U tail. Lastly, RNA polymerase and the RNA strand are released from DNA and DNA is able to repeat the process again.
Describe 3 different ways that RNA has maintained its role as “middle-man” in the overall process of protein synthesis.
RNA is used as a template, placer, and as a catalyst in protein synthesis. mRNA is used to create polypeptide chains, which are used to make proteins. tRNA is used to carry amino acids to the ribosome and match them to codons (using anticodons). rRNA is inside the ribosomes and carries out the actual function of translating mRNA.
mRNA (messenger RNA): in between DNA template strand and process of protein translation where proteins are made
tRNA (transfer RNA): in between “charger” enzyme and ribosomes (ribosomal subunits) since it takes amino acids and attaches them to growing peptide chain
rRNA (ribosomal RNA): is part of ribosome itself along with protein and helps read mRNA and translates it into a protein
In simple terms that your parents, and Dr Rowland-Goldsmith and Dr. Hsu would understand, explain the important difference in function between transcription and replication? Given those differences, why do students often get them confused? In other words, even though they serve entirely different purposes, what is similar about transcription and replication?
Transcription: transcribes DNA to RNA to create mRNA so proteins can be made (making of completely new thing)
Replication: duplication of DNA through polymerization (cell division and making of same thing)
