Unit 6 - Gene Expression and Regulation Flashcards
What is the chemical composition of nucleic acids?
CHONP
What are examples of nucleic acids?
RNA and DNA
What is the function of nucleic acids?
store and transmit genetic information and are the primary source of inheritable information
Where is the genetic information actually stored in nucleic acids?
its stored in the sequence of nucleotides
How is the continuity of genetics in cells ensured?
through complimentary base pairs
Whats a nucleotide?
monomer of nucleic acids
What is the composition of nucleotides?
a nitrogenous base, a sugar molecule (either ribose or deoxyribose), and a phosphate group
What is the shape of DNA and RNA
DNA is double stranded and RNA is single stranded
What do DNA and RNA have in common?
- both made of nucleotides
- both have 5 and 3 prime
- both have a sugar phosphate backbone
How do nucleotide monomers join together to form a polymer?
through hydrogen bonds at the bases
Purines
A and G and these are double ringed
Pyrimadines
C and T these are single ringed
When C and G bond how many bonds are there?
3
When A and T bond how many bonds are there
2
What are the bonds between the sugar and phosphate?
covalent bonds called phosphodiester bond
What does it mean that DNA is antiparallel?
DNA strands run in opposite directions
How is DNA built and how do we add bases to a DNA strand?
bases are added 5’ to 3’ so the new nucleotide is added to the 3’ end
How do we build our nucleic acids?
1) nucleotides arrive with 3 phosphate groups
2) DNA polymerase 3 uses the energy from phosphates to bind nucleotides
DNA Polymerase 3 in building nucleic acids
uses the energy from phosphates to bind nucleotides together (through energy coupling the exergonic reaction powers the endergonic reaction)
How does energy coupling work with DNA Polymerase 3?
when the 2 phosphate groups are broken off, that is an exergonic reaction. That energy is used to build the phosodiester bond and power the endergonic reaction
DNA Polymerase 3 definiton
is the enzyme that adds nucleotides to the growing strand (must be 5’ to 3’)
What about when you get to the last phosodiester bond?
then an enzyme called ligase is used
Ligase
an enzyme that comes and builds the phosphodiester bond between the 2 nucleotides
Why does DNA replicate?
DNA replicates for reproduction, to make new cells, for repair, and for growth
When does DNA replicate
during the S-phase
Topoisomerase
an enzyme that looses and unwinds the DNA during DNA replication
Helicase
an enzyme that unzips the double helix by breaking the hydrogen bonds between the nitrogenous base pairs
Replication Fork
made by the helicase which helps to unzip the DNA
What will we have by the end of DNA replication?
two identical double helics (sister chromatids)
Primase
because DNA polymerase 3 cannot stat adding bases, primase is an RNA enzyme that adds RNA primers to start replication
Template Strand
the original strand that runs 3’ to 5’; this the template for the new strand that is built from 5’ to 3’
Lagging Strand
opposite direction of the replication fork; okazaki fragments are here
Leading Strand
replicated in the direction of the replication fork
Okazaki Fragments
the strand that was built in fragments, those fragments are called okazaki fragments
DNA polymerase 1
removes the RNA nucleotide and replaces them with DNA nucletoides; cannot add nucelotides to the 5’
What about the RNA primers?
- RNA primers are removed by DNA polymerase 1 \
- lagging strand has a lot of primers so DNA polymerase 1 adds nucleotides to the primer sites on lagging strand
What about the first RNA primers on the leading strand?
- they are removed not replaced
- DNA strands get shorter with each round of replication
Telomeres
everytime our cells divide, our chromosomes get shorter. therefore, we have these protective caps called telomeres made of repeating TTAAGG nucleotides
What shape is DNA in prokaryotes?
circular
Semi Conservative Replication
in replicated DNA you will always have 1 single parent strand
Protein Synthesis
is how we get the directions about how to make proteins from DNA and bring them to the ribosome so that the ribosome can join amino acids in a specific order to synthesize a protein
How do we get the directions from our genes into an actual protein?
through translation and transcription
Where does transcription take place in eukaryotes?
in the nucleus
Where does translation take place in eukaryotes?
in the cytoplasm
Where does translation and transcription take place in prokaryotes?
in the cytoplasm at the same time
Transcription
carrying the code from DNA into RNA
RNA
- single - stranded
- has a 5 carbon sugar called ribose
- four nitrogenous bases (A, U, G, C)
- built in the 5’ to 3’ direction
What are the different types of RNA?
- mRNA (messanger)
- tRNA (transfer)
- rRNA (ribsomal)
- snRNA (small nuclear)
- miRNA (micro)
How is RNA produced?
the enzyme RNA polymerase synthesizes messenger RNA by reading one strand of the DNA and follows base pairing rules to build the mRNA
Transcription Bubble
the enzyme RNA polymerase only unwinds the DNA where transcription occurs. This is called the transcription bubble.
which direction is mRNA synthesized?
5’ to 3’ and therefore the strand of DNA that runs in the 3’ to 5’ is the template strand. The template strand is the DNA strand that is copied in mRNA
What happens when the mRNA is synthesized?
RNA polymerase continues down, and as it moves, the double helix winds back up and the mRNA is processed and then leaves the nucleus
Which strand would be used to build our RNA?
whatever strand is 3’ to 5’ and runs anti-parallel to DNA
Coding Strand
untranscribed DNA that codes for the protein; 5’ to 3’
The DNA strand acting as the template strand is also referred to as the
noncoding strand, minus strand, or antisense strand
How does RNA polymerase know where to attach to begin transcription?
because of the promotor region, the RNA polymerase attaches and begins transcription
How does RNA polymerase know where the promoter is?
through the TATA box that is a repeating sequence of TATA nucleotides; every promotor has a TATA box which is a recognition site for transcription factors
How does RNA polymerase know where to stop transcription?
in prokaryotes, RNA polymerase stops at a terminator sequence
Regulation - Transcription Factors
proteins that attach to the promoter sequence, turning on or off transcription
Transcription Initiation Complex
where transcription factors, promotor, and RNA polymerase bind to start transcription
In eukaryotes there is an extra step called RNA processing? what happens?
we edit the RNA before it reaches a ribosome in the nucleus
3 events that happen in RNA processing. What is the goal?
to make mature mRNA
pre mRNA
freshly made by RNA polymerase in the nucleus
What are the 3 things that happen in RNA processing?
1) a modified quinine is added as a 5’ cap
2) introns (in the way) are removed and exon are spliced together to make a shorter mRNA
3) poly A tail is added (many Adenines are added to the 3’ end ) 50-250
Introns
non coding regions of the mRNA
How are introns cut-out?
through an enzyme called SnRNP
Exons
coding regions of the mRNA (amino acids)
SNRPS
small nuclear RNAS and proteins that cut introns out and attach exons
What are groups of SnRNP’s called?
spliceosomes
Why can several proteins be produced at a time?
because you can use different combinations of exons to express different proteins
Okay mature RNA is made now what?
in eukaryotes, the mature RNA leaves the nucleus through a nuclear pore to the cytoplasm or the Rough ER to find a ribosome. In prokaryotes, translation occurs simultaneously with transcription
Now that we have the directions for how to build a protein, how does the ribosome actually build
ribosomes will “read” the mRNA in groups of three. Three nucleotides are called a codon. Each codon codes for one amino acid.
Initiation
- the mRNA will bind to the small ribosomal sub-unit
- ribosome is going to call a tRNA (transfer the amino acid )
- tRNA will bind with the mRNA (so the anti-codon with codon)
Elongation
- polypeptide is formed making peptide bonds through the process of dehydration synthesis
Termination
- stop codn that releases the polypeptide (mutations)
What are the 3 steps of translation?
Initiation, Elongation, and Termination
What is tRNA?
- transfer RNA
- bring the amino acid to the ribosome
- Anti-codon binds to the codon
Translation in Prokaryotes
prokaryotes do not have a nucleus and do not undergo RNA processing. Therefore, as soon as mRNA is produced, ribosomes can attach and begin translating the mRNA code into amino acids
phosphodiester Bonds
The bond that forms between nucleotides
Transcription in eukaryotes
1) Initiation: RNA polymerase binds to the promoter and opens up the DNA to form a transcription bubble.
2) Elongation: RNA polymerase reads the template DNA strand and creates a complementary RNA strand.
3) Termination: RNA polymerase reaches the termination signal and releases the mRNA.
What happens if introns are not removed?
there will be more amino acids then needed
