DNA & RNA Flashcards by Ryan Hewitt

This is found in eukaryotic nuclei, prokaryotic cells, mitochondria and chloroplasts

DNA

How well did you know this?

Not at all

Perfectly

Polymer of deoxyribonucleoside mono-phosphates are linked by…

3’ to 5’ phosphodiester bonds

How well did you know this?

Not at all

Perfectly

Which base pairs have only 2 hydrogen bonds?

Adenine and Thymine

How well did you know this?

Not at all

Perfectly

Which base pairs have 3 hydrogen bonds?

Cytosine and Guanine

How well did you know this?

Not at all

Perfectly

What will break hydrogen bonds?

Heat or extreme pH

How well did you know this?

Not at all

Perfectly

This defines the loss of helical structure

Denaturation

How well did you know this?

Not at all

Perfectly

What is DNA synthesis primarily carried out by?

DNA polymerases

How well did you know this?

Not at all

Perfectly

Initiation of DNA synthesis begins where?

The replication fork

How well did you know this?

Not at all

Perfectly

This requires ATP in order to separate the DNA strands during initiation

dnaA protein

How well did you know this?

Not at all

Perfectly

This binds to ssDNA (single-stranded) to keep the DNA strand unwound and uses ATP in the process

DNA helicase

How well did you know this?

Not at all

Perfectly

This protects unwound singles strand DNA

SSB (single strand binding protein)

How well did you know this?

Not at all

Perfectly

These are used to prevent the DNA from “supercoiling” ahead of the replication fork

Topoisomerases

How well did you know this?

Not at all

Perfectly

These enzymes reversibly cut one strand of the double helix. They have both nuclease (strand-cutting) and ligase (strand-resealing) activities. This process stores energy from the phosphodiester bond they cleave, reusing the energy to reseal the strand.

Type 1 Topoisomerases

How well did you know this?

Not at all

Perfectly

These enzymes bind tightly to the DNA double helix and make transient breaks in both strands. The enzyme then causes a second stretch of the DNA double helix to pass through the break and, finally, reseals the
break. This process requires ATP.

Type 2 Topoisomerases

How well did you know this?

Not at all

Perfectly

The DNA polymerases responsible for copying the DNA templates are only able to “read” the parental nucleotide sequences in what direction?

3’ to 5’

How well did you know this?

Not at all

Perfectly

DNA strands are synthesized in what direction

5’ to 3’

How well did you know this?

Not at all

Perfectly

The strand that is being copied in the direction of the advancing replication fork, and that is synthesized continuously is called

The leading strand

How well did you know this?

Not at all

Perfectly

The strand that is being copied in the direction
away from the replication fork that is synthesized discontinuously, with small fragments of DNA being copied near the replication fork is called

The lagging strand

How well did you know this?

Not at all

Perfectly

These short stretches of discontinuous DNA, are eventually joined (ligated) to become a single, continuous strand. The short stretches are known as

Okazaki fragments

How well did you know this?

Not at all

Perfectly

DNA polymerases cannot initiate synthesis of a complementary strand of DNA on a totally single-stranded template. They require…

An RNA primer

How well did you know this?

Not at all

Perfectly

This builds a short double stranded region of RNA with a free 3’ end

RNA primase

How well did you know this?

Not at all

Perfectly

RNA primase triggers the beginning of this

DNA synthesis

How well did you know this?

Not at all

Perfectly

This begins to add nucleotides along the single-stranded template that
specifies the sequence of bases in the newly synthesized chain.

DNA polymerase III

How well did you know this?

Not at all

Perfectly

The processivity of DNA polymerase III is the result of its β subunit forming a ring that encircles and moves along the
template strand of the DNA, thus serving as

Sliding DNA clamp

How well did you know this?

Not at all

Perfectly

The new strand grows antiparallel to the parent strand. It grows in this direction

5' to 3'

This is released when each new deoxynucleoside monophosphate is added to the growing chain, driving the reaction forward

Pyrophosphate

All of these must be present for DNA elongation to occur

Deoxyribonucleoside triphosphates (dATP, dTTP, dCTP, and dGTP)

This checks to make certain the added | nucleotide is, in fact, correctly matched to its complementary base on the template

DNA polymerase III

DNA polymerase III continues to synthesize DNA on the lagging strand until it is blocked by proximity to an RNA primer. When this occurs, the RNA is excised and the gap filled by

DNA polymerase I

This can remove one nucleotide at a time from a region of DNA that is properly base-paired. The nucleotides it removes can be either ribonucleotides or deoxyribonucleotides. It also removes groups of altered nucleotides

5' to 3' exonuclease

The DNA chain synthesized by DNA polymerase III and the 3'-hydroxyl group on the chain made by DNA polymerase I is catalyzed by

DNA ligase

The joining of these two stretches of | DNA requires energy, which in most organisms is provided by the cleavage of

ATP to AMP + PPi

This is very similar to Prokaryotic DNA replication, has linear chromosomes, and involves 5 different polymerases

Eukaryotic DNA replication

This is a multisubunit enzyme. One subunit has primase activity, which initiates strand synthesis on the leading strand and at the beginning of each Okazaki fragment on the lagging strand.

Pol α

THIS is thought to be recruited to complete DNA synthesis on the leading strand whereas THIS elongates the Okazaki fragments of the lagging strand, each using 3' to 5' exonuclease activity to proofread the newly synthesized DNA.

Pol ε; Pol δ

This is involved in "gap filling" in DNA repair

Pol β

This replicates mitochondrial DNA.

Pol γ

DNA replication is occurring during this phase of Interphase, prior to mitosis

The S (synthesis) phase

DNA replication in the Cell cycle is regulated closely by

Cyclins and cyclin-dependent kinases (cdks)

These are noncoding DNA sequences that protect ends of linear chromosomes, there activity decreases with age

Telomeres

When a telomere sequence shortens over rounds of replication, this is known as

Senescence

These may be viewed as mitotic clocks in | that their length in most cells is inversely related to the number of times the cells have divided.

Telomeres

These are RNA-directed DNA polymerases, used by retroviruses such as HIV to transcribe their DNA elements and randomly insert them into the cell’s genome

Reverse transcriptases

Sugars that lack a free 3’ end will not be able to participate in replication. This can be known as

Inhibition of DNA synthesis

Human cells are this, and are broken down into 46 chromosomes in 23 nearly identical pairs

Diploid

DNA errors can occur during replication, or more likely, through

Mutagens

This repairs insertions, deletions and mis-incorporation of bases that can arise during DNA replication and recombination.

Endonuclease and exonuclease mismatch repair

These are DNA repeats which are frequent in DNA tumor suppressor genes.

Microsatellites

This is an autosomal dominant genetic condition caused by an error in mismatched DNA repair

Lynch syndrome

This occurs between adjacent pyrimidines; most commonly between T-T dimers

Nucleotide excision repair

This is a rare, genetic disease where cells cannot repair damaged DNA. Can be susceptible to extreme sunburn, malignant melanoma, and other skin cancers

Xeroderma pigmentosum (XP)

This is repair of base alterations where bases can slowly or spontaneously change via deamination, or even become lost

Base excision repair

In base excision repair cytosine turns to this

Uracil

In base excision repair adenine turns to this

Hypoxanithine

In base excision repair guanine turns to this

Xanithine

This removes the single residue in base excision repair

Deoxyribose phosphate lyase

This is associated with predisposition to cancer and immunodeficiency syndromes, due to ionizing radiation or oxidative free radicals

Double-strand break repair

This is similar structure to DNA, but single stranded and linear

RNA

This is the message or direction on how to make a protein

mRNA

This matches up amino acids(20) with the RNA message, and accounts for only 5% of total RNA in the cell

tRNA

This is used to bind the mRNA message, and accounts for ~80% of total RNA in the cell

rRNA

This is a multisubunit enzyme that includes both promoter and termination regions that will control RNA transcription

RNA polymerase

RNA is synthesized in what direction compared to the DNA template

5' to 3' antiparallel

This begins with RNA pol holoenzyme binding to upstream, non-transcribed region of DNA usually containing consensus sequences

Initiation of RNA transcription

This is the site of initial DNA unwinding to open transcription bubble in RNA synthesis

Pribnow box

This step in RNA synthesis uses nucleoside triphosphates as substrates, Lacks 3’ to 5’ exonuclease (proofreading) ability, and processes DNA utilizing sliding clamp mechanism

Elongation of RNA Synthesis

This type of termination has a hairpin formation

ρ-Independent termination

This type of termination requires Rho (ρ) protein that uses ATPase activity to release RNA

ρ-Dependent termination

This prevents bacterial cell growth by inhibiting RNA synthesis via inhibiting binding of RNA polymerase

Antibiotics

This term describes genes that are tightly coiled in nucleosomes will not be expressed

Heterochromatin

This type of DNA coiling actively transcribed genes are not condensed

Euchromatin

This is mediated by histone acetyltransferases (HATs) and histone deactylases (HDACs)

DNA coiling

This synthesizes precursors of 28S, 18S, and 5.8S rRNA in nucleolus

RNA polymerase I

This synthesizes precursors of mRNA, some snRNA,

RNA polymerase II

This serves as binding sites for general transcription factor proteins

TATAA box

This signals the binding site for the RNA transcription factor

CAAT box

This binds transcription factors called enhancers

GC box

Transcription factors bind DNA through

Motifs

This synthesizes tRNA, 5s rRNA, some snRNA

RNA polymerase III

This utilizes a single RNA pol more similar to the prokaryotic enzyme

Mitochondrial RNA transcription

Introns removed from anticodon loop by nucleases is an example of

Modifications of tRNA

These are non-coding portions of primary RNA transcription

Introns

These are the coding (expressed) portions of primary RNA transcription

Exons

This is added by polyadenylate polymerase using ATP in eukaryotic mRNA

Poly A tail to 3’ end

This helps stabilize mRNA, facilitates exit from the nucleus, and aids in translation in eukaryotic mRNA

Poly A tail to 3’ end

This protects from nucleases and permits initiation of translation in eukaryotic mRNA

5' capping

This removes Introns, at which points Exons are then joined together

Splicing

This helps to remove introns by forming base pairs with consensus sequences located at the end of introns

Mediate splicing

This allows for a more diverse set of protein products to be produced from the limited set of genes

Alternative splicing

In bacteria, one species of RNA polymerase synthesizes all of the RNA except for the short RNA primers needed for DNA replication

RNA polymerase

This enables RNA polymerase to recognize promoter regions on the DNA.

Holoenzyme

This enzyme lacks specificity, that is, it cannot recognize the promoter region on the DNA template

Core enzyme

This is the initial point of contact for the holo - | enzyme, and a closed complex is formed. It is centered about 35 bases to the left of the transcription start site

-35 sequence

Chromosomal DNA is thought to consist primarily of what DNA structural form?

B-form DNA

The conformation found in DNA–RNA hybrids or RNA–RNA double-stranded regions is probably very close to what DNA structural form?

A-form DNA

Transitions between these two forms of helical | DNA may play a role in regulating gene expression.

B & Z form DNA

Each chromosome in the nucleus of a eukaryote contains one long, linear molecule of this, which is bound to a complex mixture of proteins to form chromatin

dsDNA

The enzymes involved in the DNA | replication process are what?

Template-directed polymerases

When a new deoxynucleoside monophosphate is added to the growing chain this is a product in replication

Pyrophosphate (PPi)

This type of Double strand DNA break repair occurs during interphase in replication

Homologous Recombination

This serves as an “adaptor” molecule that carries its specific amino acid—covalently attached to its 3'-end—to the site of protein synthesis.

tRNA

In eukaryotic transcription RNA polymerase II has a promoter sequence similar to the prokaryotic

Hogness box (TATAAA)

DNA & RNA Flashcards

(102 cards)