DNA & RNA Replication (Exam III) Flashcards by Annabella Moody

DNA is ___ stranded molecule, while RNA is a _____ stranded molecule

Double; single

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If a 2’ hydroxyl group is present on the pentose sugar the molecule is

Ribose

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If the 2’ hydroxyl group is absent on the pentose sugar (only a hydrogen in this position)

Deoxyribose

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High energy _____ molecules are attached to the 5’ carbon of the pentose sugar in both DNA and RNA

Phosphate

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What are the purines

Pure as Gold

Adenine and Guanine

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What are the pyramidines

Cut the Pie

Cytosine Uracil and Thymine

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Structure of the purines

You would rather have more gold than pie

Double ring structure

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Describe the structure of the pyrimidines

You would rather have more gold than pie

Single ring structure

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Difference between uracil and thymine

Uracil - RNA
Thymine - DNA

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The steps of the staircase when referring to the double helix structure of a DNA molecule are the

Bases

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What is Chargaff’s rule

A=T and G=C

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How many bonds form between adenine and thymine?

How many bonds form between guanine and cytosine?

AT = 2
GC = 3

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What base pairing is more stable and why

G-C because they have an extra hydrogen bond

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What controls the expression of prokaryotic transcription

Promoters and Operons

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In prokaryotic organisms the DNA is organized into a ____ or ____ fashion

Linear or contiguous

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In prokaryotic gene transcription, the RNA copy made is:

Ready for use in translation

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As DNA transcription proceeds in a prokaryotic organism the RNA transcript is described as:

Co-linear

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When we refer to the RNA copy as being “co-linear” what we mean is

It’s an identical copy of the DNA transcript

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In eukaryotic organisms the DNA is broken up into ____ that will give rise to the protein sequence

Coding regions or exons

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The regions that separate exons that do not get coded

Introns

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Regions at the 5’ and 3’ ends that do not encode proteins

Untranslated regions (UTRs)

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In eukaryotic organisms one strand of the DNA is first copied in a linear fashion and then the introns are removed by a process called

Splicing

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In prokaryotic organism the RNA copy made from the DNA copy is a ______ copy that is ready for _____

In eukaryotic organisms, everything in the DNA gets copied to the RNA but ____ and ____ must take place to give rise to the mature RNA, which is transported out of the nucleus for use as the template for protein synthesis

Exact; protein synthesis
Splicing; subsequent modifications

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Translation

Protein synthesis

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In eukaryotic organisms primary transcripts are often spliced in multiple combinations of exons, this process is called

Alternative splicing

Alternative splicing gives rise to a possibility of

Numerous different proteins from the same transcript

A region of DNA that encodes a protein and includes all of the regulatory elements included in it to control its expression

Gene

In order to fit inside a cell or nucleus, linear DNA must be

Condensed

Prokaryotic organisms condense their DNA by a set of ____ and _____ into back and forth loops

Polyamines Proteins

In eukaryotes, DNA is first condensed into ____

Nucleosomes

Each nucleosomes involves around ____ bp of DNA and a set of ____

200 Core histone proteins

As DNA is packaged, it exists in what two forms

Euchromatin Heterochromatin

The slightly more relaxed form of chromatin and transcriptionally active

Euchromatin

Highly condensed and generally not transcriptionally active form of chromatin

Heterochromatin

Chromatin can be further condensed into ___ and ____ ultimately into _____ by function specific sets of proteins

Solenoids Supersolenoids Chromosomes

DNA is broken up into fragments called

Chromosomes

In humans we have 22 chromosomes that are referred to as ____ and each exists as a ____

Autosomes Pair

The gametes contain ____ copy of a chromosome

One

How many protein coding genes in the human genome

20,000-25,000

The average gene is about _____ bp long, contains about _____ exons and a coding sequence of about ____ bp

27,000 9 1340

Estimated that on average each gene gives rise to about ___ isoforms, splice variants, etc.

The human genome contains around ____ bp

3.2 billion

It only takes a single bp change to cause

Disease

Allie and Abbie have a difference of about how many base pairs

1-2 million

Abbie and Chelsea have a difference of about how many base pairs

Six million

Because of the antiparallel orientation of the strains and the fact that the strands are complementary, each strand can

Act as template for synthesis of new DNA strand

When is DNA replicated

During S phase of cell cycle

Central dogma of genetic information flow

DNA ————————> RNA ——————> Protein Transcription Translation

The first and foremost important principle of DNA replication is that its all driven by

base-pairing

You have a strand of DNA that serves as a template, and the nucleotide bases that make up that strand will dictate

What base gets incorporated at that position in the strand being made

Molecule that catalyzes the stepwise addition of deoxyribonucleotide-triphosphate to the 3’ OH end fo a polynucleotide chain

DNA polymerase

The reason the stepwise addition of a deoxyribonucleotide-triphosphate to the 3’ hydroxyl end of the polynucleotide chain is important is because the addition of the next base is driven by the favorable free energy that is released from the:

hydrolysis of the triphosphate molecule to a mono-phosphate phosphodiester bond

DNA synthesis on the strand that is being made ALWAYS proceeds

5’ ——> 3’

For DNA synthesis to occur you need (3)

1. Deoxynucleotide triphosphate 2. A region of double strand of DNA 3. A free 3’ hydroxyl group

DNA polymerase synthesizes the new strand in what direction

5’ ——> 3’

DNA polymerase requires a _____ and a strand to build off of with a _____

Template strand Free 3’ OH

DNA polymerase contains a _______ polymerase activity and a _______ exonuclease activity

5’ to 3’ 3’ to 5’

The free 3’ hydroxyl group on the deoxyribose will form a ____ bond with the next nucleoside-triphosphate that is going to put there

Phoshphodietser

The high fidelity of DNA Replication requires

Proofreading mechanisms

DNA polymerases are a ________ enzyme that remove their own polymerization errors

Self-correcting

DNA polymerase have a 3’ to 5’ _______ activity during DNA synthesis

Exonuclease proofreading

If an incorrect base gets put in it creates a ____ that gets removed by the 3’ to 5’ exonuclease, which will leave a ________to basepair with the correct base

Bulge Free 3’ hydroxyl group

DNA synthesis starts at ____ regions known as origins as replication

A-T rich regions

It is important that the origins of replication are A-T rich because

They have weaker bonds making them easier to separate

Origins of replication from a

Replication fork

Daughter strand that is synthesized continuously towards the replication fork

Leading strand

Daughter strand that is synthesized discontinuously away from replication fork

Lagging strand

DNA synthesis begins following DNA unwinding and _____ synthesis at replication origins

RNA primer

The RNA primers that come into the newly opened up area of double-stranded DNA provide:

A double-stranded template with free 3’ hydroxyl group

What strand do Okazaki fragments get made on

Lagging strand

Begins with synthesis of short RNA primer by a special nucleotide-polymerizing enzyme

Lagging strand DNA synthesis

Enzyme that makes the short RNA primers made on the lagging strand using DNA as a template

DNA primase

Unlike DNA polymerase, the DNA primase _______ by joining two nucleoside triphosphates together

Start a new polynucleotide chain

The primase synthesizes a short polynucleotide in the 5’ to 3’ direction and then stops, making the 3’ end of the primer available for the ______ to produce the Okazaki fragment

DNA polymerase

What is responsible for moving the RNA primers (about 10 nucleotides in length)

5’ to 3’ exonuclease activity of DNA polymerase

Responsible for joining Okazaki fragments together

DNA ligase (doesn’t actually operate in the replication fork)

Lagging strand synthesis is:

Energetically costly (using a lot of ATP and ATP hydrolysis)

Only changes accumulated in the ____ can be inherited

Gametes

Protein that uses the hydrolysis of ATP to change the shape of the protein, and moves rapidly along the DAN strand, if encountering a region of double stranded helix itch will pry the helix apart

DNA helicase

Energetically when you have two single stranded regions of DNA they will want to rapidly rejoin. A protein that doesn’t unwind the double helix itself, but aids helicase by stabilizing this unwound helix is

Single-strand DNA binding proteins (helix-destabilizing proteins)

Anchoring protein that are responsible for holding the DNA polymerase to the replication fork and allow it to move along as the DNA unwinds

Sliding clamp /sliding ring

Premature aging disease with respect to DNA replication process

Werner syndrome

Individuals with Werners syndrome either have:

Cells that divide ore slowly or stop dividing

Werner’s syndrome is caused by a mutation in the

DNA helicase