Exam #4 - DNA structure and DNA replication/Gene Expression Flashcards by Anthony Kemmer

What are the two functions of DNA?

1) DNA encodes PROTEINS, and thereby TRAITS

2) DNA must be COPIED

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How does the cell synthesize DNA?

Build DNA utilizing base complementarity

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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

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What happens to the old DNA?

Replication is ____-conservative: conserving the chains but independently of one another

It’s still there!

semi-conservative

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Each new DNA will contain ___ old strand, and ___ new strand.

one

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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

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In order for this process to happen ________, replication must happen on many different locations on a chromosome spontaneously.

efficiently

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Replication begins at a replication ______.

origin

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Replication happens in _____ directions.

both

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The __________ ____ is where new DNA is actually made

replication fork

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What is needed to make DNA?

1) Templates
2) Nucleotides
3) several enzymes

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The enzyme that makes DNA is called ___ ________.

DNA polymerase - makes DNA.

The most important enzyme of DNA replication

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DNA polymerase adds ________ to a chain.

ALWAYS the _ prime end of the chain.

nucleotide

3’

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DNA polymerase cannot add to the _ prime end.

5’

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DNA is constructed in a _ to _ direction

5’ - 3’ direction

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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

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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

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So you need some ___ to start DNA synthesis

RNA.

This we call an RNA primer, because it primes DNA synthesis

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Whenever you make some DNA, you have to make some ___ first. ABSOLUTELY.

RNA

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Where is DNA synthesis actually occurring?

The replication fork

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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.

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The enzyme that unwinds the DNA helix is called _______.

helicase

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Step 1: ______ unwinds the DNA helix

helicase

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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

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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?

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