Exam #4 - DNA structure and DNA replication/Gene Expression Flashcards
What are the two functions of DNA?
1) DNA encodes PROTEINS, and thereby TRAITS
2) DNA must be COPIED
How does the cell synthesize DNA?
Build DNA utilizing base complementarity
How does that happen? (2)
1) Pull apart the two chains, exposing the basis which can then be paired with a complementary base
2) Each strand will then be used as a TEMPLATE to build a new strand
What happens to the old DNA?
Replication is ____-conservative: conserving the chains but independently of one another
It’s still there!
semi-conservative
Each new DNA will contain ___ old strand, and ___ new strand.
one
The DNA is _______…each of the old chains serves as a _______ to build the new chain. That’s the mechanism. We call it a ____-________ mechanism.
One nucleotide at a time is used to build these chains.
unwound
template
semi-conservative
In order for this process to happen ________, replication must happen on many different locations on a chromosome spontaneously.
efficiently
Replication begins at a replication ______.
origin
Replication happens in _____ directions.
both
The __________ ____ is where new DNA is actually made
replication fork
What is needed to make DNA?
1) Templates
2) Nucleotides
3) several enzymes
The enzyme that makes DNA is called ___ ________.
DNA polymerase - makes DNA.
The most important enzyme of DNA replication
DNA polymerase adds ________ to a chain.
ALWAYS the _ prime end of the chain.
nucleotide
3’
DNA polymerase cannot add to the _ prime end.
5’
DNA is constructed in a _ to _ direction
5’ - 3’ direction
DNA polymerase adds nucleotides to a pre-existing chain.
This enzyme does not have the ability to _____ DNA synthesis, it can only _______ it.
begin, continue
Consequences ?
1) If new chains are built from 5’ to 3’ , and the two templates are ANTIPARALLEL…
- synthesis will go in _________ directions along each template
2) If DNA polymerase cannot INITIATE…
- ANOTHER enzyme must make another polynucleotide
- Make an RNA ______
opposite
primer
So you need some ___ to start DNA synthesis
RNA.
This we call an RNA primer, because it primes DNA synthesis
Whenever you make some DNA, you have to make some ___ first. ABSOLUTELY.
RNA
Where is DNA synthesis actually occurring?
The replication fork
What’s the first step of replication?
UNWIND the DNA helix.
EXPOSE the nucleotides that can be then used as a template to build a new chain.
The enzyme that unwinds the DNA helix is called _______.
helicase
Step 1: ______ unwinds the DNA helix
helicase
Now the template chains are exposed.
However, those template chains want nothing more in life than to come back together. They’re attracted to each other.
NOW we must stabilize them and prevent the re-naturing of the nucleotides.
Step 2:
The single strand binding protein binds the chains to prevent them from…?
coming together
Step 3: An enzyme builds a short chain of ___, complementary to the template, which will serve as a primer.
This is called _______.
RNA
primase
______ builds a primer.
Primase
Now can we build DNA?
Absolutely.
We have a primer, we have nucleotides, we have DNA polymerase and there it goes. psskkkjndauidnwiefniefneinfaejnfszjknfjzknef. It’s fast!
We build _’ to _’.
We READ ’ to’.
build 5’ to 3’
READ 3’ to 5’
The ______ strand is the strand that is build toward the fork.
leading
As the ______ continues to unwind DNA, if we’re going to make more DNA…we have to make another primer. And then extend it with DNA.
Along the opposite template, we have DNA synthesis away from the fork, and in a _________ manner.
Unwind more DNA, build a third primer. Primase. Extend with DNA polymerase. Unwind some more. A fourth primer. Primase. Extend with DNA polymerase. Unwind some more. A fifth primer. Primase. It just keeps going.
helicase
discontinuous
Building DNA away from the fork in a _________ fashion.
discontinuous
That’s what we call _______ strand synthesis.
lagging
One chain is build toward the fork in a continuous manner, that’s the _______ strand.
The other strand is build away from the fork in a discontinuous manner, that’s the ______ strand.
leading
lagging
How do we join all the pieces?
1) remove the RNA primer
- we’re building DNA, not RNA
2) fill in the ‘gap’ with DNA
3) join the Okazaki fragments with Ligase
Lagging strands are referred to as ________ fragments.
Okazaki fragments
Leading strand synthesis and lagging strand synthesis are _________.
simultaneous
Both processes require a primer…but the lagging strand synthesis requires _____ of them.
Leading strand synthesis just needs ___.
many
one
The place on a chromosome where DNA synthesis begins is called a _________ ______
replication origin
Every replication bubble contains ___ replication forks.
two
The enzyme that joins the individual deoxyribonucleotides together into a chain of DNA is called ___ ________.
DNA polymerase
Which of the following pertain to or play a role in LEADING STRAND DNA synthesis?
1) complementary base pairing
2) discontinuous DNA synthesis
3) DNA synthesis away from the replication fork
4) a primer is required
5) more than one of these answers are correct
all of these answers are correct
More than one of these are correct
Specifically: complementary base pairing and a primer is required
Which of the following pertain to or play a role in LAGGING STRAND DNA synthesis?
1) complementary base pairing
2) discontinuous DNA synthesis
3) DNA synthesis toward the replication fork
4) more than one of these answers are correct
5) all of these answers are correct
More than one of these are correct
Specifically: complementary base pairing, discontinuous DNA synthesis
The enzyme ligase _____ during replication.
1) joins together the DNA fragments produced by lagging strand synthesis
2) unwinds the double helix
3) stablizes single-stranded DNA
4) builds DNA, nucleotide by nucleotide
5) creates a short polynucleotide chain that will then be extended by another enzyme
joins together the DNA fragments produced by lagging strand synthesis
The main point of DNA is to make _____.
protein.
The DNA is first ______ into RNA, which is then _______ to make protein.
copied, decoded
Important distinction #1
Whereas replication copies ALL the DNA..this copies a ____.
gene
The copy of the gene is called _____.
mRNA
Copying the gene is called __________.
Decoding the mRNA is called __________.
transcription
translation
In eukaryotes, where does transcription happen?
In the nucleus
In eukaryotes, where does translation happen?
In the cytosol
There are 20 different amino acids and DNA contains 4 different nucleotides…
What is the minimum number of nucleotides you need to make 20 different amino acids?
You need atlas 3 different nucleotides to make twenty different words
The code words are 3 nucleotides long, and if you consider all the different possibilities. 4^3 different possibilities. How many different possibilities?
64
What do we call these ‘code words’?
Codons
These codons will occur in ______.
series
61 of the 64 encode amino acids, what do the remaining 3 do?
They serve as STOP codons
T/F: The Aug (start) codon also encodes an amino acid
True
Who uses the genetic code?
All organisms use the genetic code. It’s UNIVERSAL
RNA synthesis
______ are transcribed
GENES
There’s only ___ chain that is used as a template to make RNA
ONE
How is an RNA copy made?
1) The DNA strands are separated
2) ONE strand is used as a template to build an RNA
What enzyme makes RNA?
RNA polymerase
Unlike DNA Polymerase which cannot initiate strand synthesis…RNA Polymerase can ______ polynucleotide synthesis, which means no _______ is required.
begin/initiate
primer/primase
How does the RNA polymerase know where to begin?
Starts at the _______:
A short sequence of ___ recognized and bound to by ___ _______.
-contains a start site (where transcription actually begins)
-determines which strand is the _______ strand
promoter
DNA
RNA Polymerase
template
Transcription ends at the ________.
terminator
The template strand is the one going _’ to _’.
3’ to 5’ because we read 3’ to 5’
As we copy the gene, the DNA ________. So the bubble doesn’t get any bigger. The RNA will come off of the DNA, and when you reach the terminator, you’re done. And the gene has been left as it was.
renatures/reseals
Summary of transcription
1) Catalyzed by ___ _______
2) Begins at the _______
3) ___ template
4) Complementary base pairing
5) 5’ to 3’
6) RNA transcript
RNA polymerase
promotor/start site
ONE
Before translation, eukaryotic mRNAs must be PROCESSED.
Most drastic: ___ ______
RNA splicing
What’s the importance of the start codon?
It tells the ribosome the correct frame
_____ are going to transfer the right amino acid at the right time.
tRNAs
Transfer RNAs recognize codons through __________ base-pairing.
complementary
What are tRNAs?
At one end: have a 3-nucleotide sequence called an _______, that is complementary to a SPECIFIC codon.
At the other end: carry the ______ _____ encoded by the codon they receive
anticodon
amino acid
The ribosome does THREE things:
1) _____ a codon in mRNA and a tRNA’s anticodon.
2) _______ the joining of the amino acids (peptide bond)
3) ________ the ‘frame’ of reading.
Joins
Catalyzes
Maintains
The sequence of nucleotides where RNA polymerase first binds to the gene, and which indicates WHICH strand will be the template is called the ________.
promoter
