Unit 3 Flashcards
nucleic acid polymer
nucleic acid
nucleic acid monomer
nucleotide
nucleotide structure
CHONP
- phosphate group
- 5 carbon sugar (pentose. in RNA it is ribose sugar. DNA is deoxyribose sugar. It has the oxygen removed)
- nitrogenous base (called that because it has nitrogen. this is the one thing that varies in nucleotides)
DNA Nucleotides
- Adenine (2 rings therefore purine)
- cytosine (1 ring therefore pyramidine)
- guanine (2 rings therefore purine)
- thymine (1 ring therefore pyramidine)
RNA Nucleotides
- Adenine (2 rings therefore purine)
- cytosine (1 ring therefore pyramidine)
- guanine (2 rings therefore purine)
- uracil (1 ring therefore pyramidine)
phosphodiester bond
O-phosphate – O
RNA vs DNA
- DNA is more stable
- RNA has a pyramidine base called uracil while DNA has a pyramidine base called thymine
o thymine has better hydrogen bond linkage to create a tighter double stranded structure - RNA is single strand, DNA is double helix
- RNA is found everywhere while DNA can be found only in nucleus
- sugar name: RNA ribose (C#2 OH), DNA deoxyribose (C#2 H)
DNA structure
A and T form 2 hydrogen bonds
o G and C form 3 hydrogen bonds
- alternates phosphate and ribose. then the nitrogenous base sticks out
- condensation synthesis keep the molecules together so the bases stick out. this creates hydrogen bonding between the two chains which keeps them together
“acid” since the phosphate groups are oriented outwards while the basic parts form the rungs of the ladder. overall, molecule acts acidic.
Nitrogenous Base
The nitrogenous bases form an alphabet for coding. Words in DNA language are all 3 letters long, this creates 64 possible combinations of nucleotides for 20 amino acids. 3 possible combinates that exist for one same protein. This helps to protect you if your DNA mutates since there is a chance that it makes the same code as was before.
hydrogen bonding and protein
involved in both secondary and tertiary levels of protein structure
the alpha helices and btal pleated sheets of secondary structure are stabilized by hydrogen bond formation between the amino and carbonyl groups of the amino acid backbone. hydrogen bond formation between r-groups helps stabilize the three dimensional folding of the protein at the tertiary level of structure
nucleic acid and hydrogen bonding
hydrogen bonds are important for complementary base-pairing between the two strands of nucleic acid that make up an molecule of DNA. complementary base-pairing can also occur within the single nucleic acid strand of an RNA molecule
complementary base pairing
the A and T (or U), C and T. these bases are complementary in size and this configuration is the most stable hydrogen bonding configuration
thymine and adenine
have 2 hydrogen bonds
cytosine and guanine
have 3 hydrogen bonds
“Purines always glow”
purines are Adenine and Guanine
replication
when you want to duplicate a cell
- splitting of DNA in half
- then you create another right hand side to match the original left hand split DNA and same thing for right side
- you now have two identical copies of the DNA
transcription
- how genes turn from just DNA instructions to actual proteins
- how DNA goes to mRNA (messenger RNA)
- first step is the same for replication. you first copy one half of the DNA
- insteaded of Adenine with Thymine, Adenine pairs with Uracil.
- this new mRNA can leave the nucleus, attach to a ribosome and code for a protein
translation
- how the mRNA turns into an amino acid sequence to turn into a protein
- this sequence from transcription is used. now every three bases codes for a specific amino acid. three bases together are called a codon
- you can have 1 of 4 bases in 3 different places which creates 64 different codons
o this allows you to account for the 20 different amino acids and reduces the danger of mutation - tRNA attaches to amino acids and then matches them to a mRNA to create a sequence of amino acids which create the right protein.
uracil vs thymine
Uracil is a little less stable than thymine and can make errors more easily. this means that the body would rather have errors in the protein that instructs rather than the instructions themselves because then only some proteins will be wrong, not the instructions itself. Also, mRNA should not be stable because then they would last forever and they are supposed to be messengers.
“purines
Always Glow”
- 2 rings
Replication steps
initiation, elongation, termination/completio, post-processing
initiation replication
In prokaryotic cells like, E. coli there is one single origin of replication (replicon) as the chromosomes are circular. The replication then proceeds until there are two separate chromosomes. In Eukaryotic cells their chromosomes are linear (and much larger - 4.7 million base pairs compared to anywhere from 51-245 million base pairs) and thus have several origins of replication. A large multienzyme complex called a replisome is the machine that carries out DNA systhesis.
First, replication bubbles are opened up by enzyme __. Replication forks are opened further by an enzyme called helices, which uses energy from ATP to unwind the two parent DNA strands. Single stranded binding proteins (SSBs) then attach to the open parts of the helix to keep the parent strands from reattaching. Another enzyme, called DNA gyrase will bind upstream of the replication fork to reduce torsional strain caused by the unwinding strands. This enzyme is an example of a topoisomerase, in which Eukaryotic cells use several types to reduce torsion.
Once the DNA is unwound, the enzyme DNA polymerase will be able to replicate the DNA strand. However, this enzyme can only assemble DNA if there is something to add to. The start of the sequence will be initiated by the enzyme DNA primase, which will create a short sequence (about 16 bases) of RNA that DNA polymerase can add to.
elongation replication
- Deoxyribonucleoside triphosphates hydrogen bond to the exposed bases on the single stranded DNA according to the base pairing rules, with an accuracy of about 99.99%
- A collection of enzymes [called a replisomes] containing DNA Polymerase III removes two phosphates from the 5’ end of the nucleotide and uses the energy to bind it to the 3’ carbon of the previous nucleotide. The new DNA chains thus grow in the 5’ to 3’ direction.[The DNA polymerases in Eukaryotes are called Pol δ and Pol ε. Their role is similar to Pol III..]
- At each replication fork, one new chain can grow continuously from a single RNA primer, as the fork is extending in its 5’ to 3’ direction. - This is called the leading strand.
- For the other new chain, however, the fork is extending in the 3’ to 5’ direction. Numerous primers must be started, and this chain must grow in short sections that elongate back toward the origin. These short sections of DNA, called Okazaki fragments, are typically a few thousand bases long.
- When adjacent replication forks meet, the entire DNA molecule has been copied, but each new strand has alternating long continuous stretches (leading strands) and stretches of short Okazaki fragments (lagging strands). Each leading strand and each Okazaki fragment has a short stretch of RNA where it started.
A multi subunit protein complex called the DNA Pol III remains attached to the template strand and continually synthesizes DNA. It is held in place by a subunit of the protein called the β-subunit, β-clamp or sliding clamp.
termination/completion replication
- An enzyme called DNA Polymerase I (an exonuclease) begins removing RNA nucleotides from one section and adding the appropriate DNA nucleotides to the end of the adjacent strand.
- All the RNA nucleotides are replaced, but the last nucleotide cannot be bonded by polymerase because it no longer has a triphosphate to provide the required energy. Another enzyme, called DNA ligase, finally links all the fragments together.
- Now each daughter strand of DNA is a complete complement for its parent strand.
When replication is complete, DNA gyrase will separate the two chromosomes.
Post-processing replication
- Pol III (or Pol ε and Pol δ) in the replisome proofreads the new DNA as it adds bases, checking for appropriate width of the helix. If it finds mistakes, it backs up, removes the newly added bases, and replaces them with bases that properly complement the parent strand.
- Many other proofing enzymes check DNA constantly and attempt to repair any damage done by radiation, free radicals or other mistakes. These include:
Mismatch repair enzymes that detect shape irregularities in the double helix and replace mismatched bases with complementary pairs. - Because eukaryotic chromosomes are linear, there is always a little section on each lagging strand that cannot be replicated, because it lies beyond the last RNA priming site. Thus, eukaryotic chromosomes tend to become slightly shorter at each division. This slow erosion of the chromosomes may be a major factor in cell and tissue aging. Single celled eukaryotes and the germ cells of multicellular ones produce an enzyme called telomerase.
- Telomerase contains a short stretch of RNA, which it uses as a template to add multiple repeats of DNA to the end of the chromosome. Once telomerase is shut down in specialized cells, the telomers shorten with each division. The initial length of these “telomeres” may determine the number of divisions a cell can make before it dies. Cells with active telomerase are essentially immortal.
lagging strand
has the okazaki fragments
why 5’ to 3’
It builds in a 5’ to 3’ direction, because DNA Pol. III can only synthesize DNA in the 5’ to 3’ direction. Cells build this way, because the energy for the synthesis is provided by deoxynucleoside triphosphates. If it were in the other direction, the energy would have to come from the 5’ end of the growing molecule.
During what two natural cell processes would DNA replication occur?(1)
Mitosis and Meiosis
Why is the structure of the DNA double helix important to replication?
It allows two copies to be produced at once.
RNA transcription steps
initiation, elongation, termination, post-processing
initiation (RNA transcription)
- Each gene has a promoter region “upstream” that must be activated to start transcription. Promoters can be turned on or off by signals from the cell. [Bacteria have many of their genes arranged in operons that contain the genes for several related enzymes. An operon requires only one promoter.]
- A transcription factor (usually protein) must first bind to the promoter before the gene can be read. [In many eukaryotic genes, the transcription factor binds to a region called a TATA box, a stretch of DNA containing the sequence TATAAA, approximately 25 bases upstream from the area to be transcribed. In bacteria, the area is usually rich in T and A, but less uniform.]
- Other transcription factors and enzymes then bind to the activated promoter to form an RNA Polymerase holoenzyme. These additional transcription factors allow the cell control over which genes are active at any time.
elongation (RNA transcription)
As transcription begins, the enzyme will change shape, leave the promoter region and then proceed along the template strand. The enzyme covers a large span of the DNA, but only unwinds about 10 bases at a time. This is called the transcription bubble. It then synthesizes a single stranded RNA molecule that is complementary to the template strand in a 5’ to 3’ direction. As the polymerase passes, the DNA is rewound.
Termination (RNA transcription)
DNA transcription will complete when the RNA polymerase reaches a specific nucleotide sequence in the DNA. This will cause the enzyme to detach from the DNA strand. As the mRNA is released from the DNA, the DNA double helix is reformed.
This sequence usually has many guanine and cytosine pairs and is followed by a sequence of adenine and thymine pairs. The GC pairs twist and hydrogen bond, forming a hairpin. At this point the RNA polymerase has bonded a series of uracil bases to the adenine in the template strand. This puts pressure on the weak intermolecular forces between U and A and the RNA dissociates from the strand.
Termination in eukaryotic cells is recognized by a specific sequence called a polyadenylation sequence which codes for AAUAAA. About 10-35 nucleotides downstream from this, the RNA Pol II dissociates from the DNA.
post processing (RNA transcription)
prokaryotic is ready to be translated right after it is transcribed. It will bind to ribosomes straight away (even sometimes before transcription is complete) and the protein will be produced.
- In eukaryotes, the mRNA must be processed before it can leave the nucleus and produce a protein. The mRNA that is produced by RNA Pol II is referred to as the primary transcript or precursor mRNA (pre-mRNA). The processed mRNA is called mature mRNA. The processing that occurs includes:
Addition of a 5’ cap - this consists of a methylated GTP molecule
that is attached to the 5’ end of the transcript via the phosphate (5’-
5’ bond). The purpose of this protects the RNA and helps it to bind
to a ribosome. makes it resistant to degrading enzymes in the cytoplasm.
Addition of a 3’ poly-A tail - an enzyme adds a series of adenine
nucleotides, which makes the mRNA more stable and allows it to
exist longer in the cytoplasm. The length of poly-A tail determines how long the mRNA will be active before it becomes degraded.
RNA splicing - eukaryotic genes contain non-coding regions called
introns, which are interspersed inbetween coding regions called
exons.
How does RNA differ from DNA (three major differences)
single stranded
ribose sugar
uracil instead of thymine
How did the DNA determine the structure of the mRNA?
The mRNA is produced in the 5’ to 3’ direction and is written complementary to the template strand.
Why is RNA required as a messenger? Why can’t the DNA simply carry information where it is needed? Think of as many advantages of using mRNA as you can.
mRNA is produced from DNA, because there is only one DNA molecule. If this molecule is damaged or digested, it could result in the death of the cell. DNA is also a much longer molecule, which would be difficult to transport and attach to the site of protein synthesis. Another advantage of mRNA is that it can remain active producing protein as long as required by the cell. This would be more efficient than if you had to use energy to unwind the DNA every time you need to produce a polypeptide.
How would the RNA transcribed in a real cell differ from your simple string of codons. How would it have to be changed before translation if this was a real Eukaryotic cell?
It would have a methylated GTP 5’ cap and it would have a poly-A tail at the 3’ end. It would need to have had the introns spliced out before translation.
translation
Once the mRNA transcript is produced, it is then translated in to a protein the second stage of the central dogma. In this process, codons are read to produce the primary confirmation of a polypeptide. The interpretation of codons is done by transfer RNA or tRNA. A tRNA molecule is a single stranded RNA molecule, which is folded into a characteristic clover-leaf shape. The stems of the looped areas are held together by intramolecular base pairing. There are two funcitonal regions of the tRNA molecule. One contains the anticodon loop, which is a stretch of nucleotides that is complimentary to the mRNA codon. The other is at the 3’ single- stranded end of the molecule, where the amino acid is attached and is called the acceptor end.
the charging reaction
The enzyme that attaches the appropriate amino acid to the corresponding tRNA molecule is called aminoacyl-tRNA synthetase. There are 45 enzymes and 45 tRNAs that carry the 20 amino acids. The amino acid is added to the tRNA using the energy from ATP. This produces a charged tRNA, which will not require anymore energy when being added to the growing polypeptide chain.
ribosomes in translation
All three steps of translation take place on the ribosome, which is a large molecule made of two subunits that consist of protein and rRNA (ribosomal RNA). The ribosome will bind two charged tRNA molecules so that a peptide bond can be formed between the amino acid units. Ribosomes have 3 binding sites:
P site (peptidyl) - binds the tRNA that attaches to the growing polypeptide chain.
A site (aminoacyl) - binds the tRNA carrying the next amino acid.
E site (exit) - binds the tRNA that carried the previous amino acid.
tRNA molecules will proceed during elongation from site A to P to E.
initiation translation
In both prokaryotic cells and eukaryotic cells, initiation involves a series of proteins called initiation factors. The exact mechanism and types of proteins are different, but the key aspects of the process are similar.
rRNA in the small subunit of the ribosome will bind to the mRNA, near the start codon (AUG on the mRNA) along with the initiator tRNA-met (carries methionine and has an anticodon UAC). The large subunit of the ribosome is then added, positioning the initiator tRNA at the P site.
elongation translation
The elongation of a polypeptide chain starts with the binding of a new tRNA to the A site on the ribosome. Once bonded to the A site, the ribosome catalyzes a reaction that forms a peptide bond between the open amino end of the amino acid in the A site and carboxyl end of the amino acid in the P site. The mRNA then moves one codon forward so that the tRNA with the growing polypeptide chain is now in the P site. The ‘empty’ tRNA is now in the E (exit) site and the A site is open, ready for the next charged tRNA to bind. This process is called translocation. The tRNA in the E site leaves and another tRNA binds repeating the process and adding another amino acid to the polypeptide chain.
termination translation
Elongation will continue until one of the stop codons is reached. These codons do not bind tRNA, but instead bind proteins called release factors or termination factors. Binding of one of these factors to the A site, causes an enzyme to break the bond between the polypeptide chain and the tRNA in the P site. The ribosomal complex then dissociates from the mRNA, which will remain around to be translated again until it is degraded by ribonuclease enzymes.
RNA polymerase
RNA polemerase (prokaryotic) is quaternary structure
- help the enzyme bind to the DNA
- must face in a way that it can build in a way of 5’ to 3’
- there are promoters that are always 10 bases and 35 bases upstream from the start of the gene
- the unique 3d shape of promoter regions helps enzyme bind
- the promoter region helps the enzyme bind facing the right way and help identify the gene that it is working with
- the -10 always has an alternating adenine and thymine pattern (TATA box) must be a TATA pattern!
eukaryotic transcription
- only one TATA box promoter
- it faces the right way because it binds to the transcription factors which make sure that it is facing 5’ to 3’
termination transcription prokaryotic
o to recognize when it stops, you develop the hairpin loop
o there is an alternation sequence of guanine and cytosines, the loop isn’t that sequence, then it follows with more guanine and cytoseine
• formation happens because the molecule bends around and the bases will line up and hydrogen bond with each other forming a hairpin loop
- formation of hairpin causes the polymerase enzyme to pause as the hairpin gets caught in the enzyme
- when it gets stuck, the mRNA sequence in the enzyme is a series of uracil-adenine pars which is weak hydrogen bonding which separates the mRNA molecule from the DNA molecule
o this also makes the enzyme dissociate from the DNA
termination transcription eukaryotic
o when it reaches the sequence AAUAA which signals the enzyme to stop and break off
post processing transcription prokaryotes
- prokaryotic cells don’t need to further process their mRNA
o that is because we have an nucleus while everything is happening in the cytoplasm
o they overlap the process of translation
o they start translation before transcription even finishes
o ribosomes do this transcription
o sometimes there is more than one ribosome. instead of one gene coding for one protein, multiple genes can be produced by one mRNA and produce like three polypeptides at the same time
