Nucleotides And Nucleic Acids Flashcards by Hector Arredondo

What is transformation?

A transfer of genetic material from one organism to another

E.g. Griffit bacteria mouse experiment

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What is a bacteriophage?

A virus that infects bacteria

These virus’s transfer genetic material into host, which then replicate the virus

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What is transcription?

DNA is copied into RNA

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What is translation

Nucleic acid information is used to synthesize proteins

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What do nucleotides play a role in?

Building blocks of nucleic acids (DNA/RNA)

Energy currency (ATP/GTP)

Mediator in signaling (GDP/GTP)

Structural component of many enzyme con factors and metabolic intermediates (NAD+. FADH2, UDP-glucose)

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Nucleotides consist of:

A nitrogenous base (a purine or pyrimidine)

A pentode sugar (ribose or deoxyribose)

1 to 3 phosphates

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How do you distinguish a Nucleoside from a nucleotide?

They lack phosphates

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What are the pyrimidines?

Cytosine
Thymine
Uracil

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What are the Purines?

Adenine and Guanine

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How do you know a structure is a purine?

How do you know which is guanine?

Two rings

It has a carbonyl and a amino group while the adenine has an amino group where the carbonyl is at

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How do you distinguish the pyrimidines?

One ring

Cytosine: has an amino group

Thymine: has a methyl group

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How do you name the nucleotides?

Start with the nucleoside name
If it’s a deoxyribose, use the deoxy prefix
Invite the number of phosphates as 5’ mono-, di- or tri- phosphates

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How are nucleotides joined together?

A 3’-5’ phosphodiester bond

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What are the two distinct ends of a nucleic acid?

3’ hydroxyl

5’ phosphate

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In which direction are nucleic acids written?

In the 5’ to 3’ direction

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What happens to RNA and DNA in basic solutions?

RNA is degraded to individual nucleotides
-2’ or 3’ monophosphates

DNA is stable since it lacks the 2’ OH

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What methylated base do eukaryotes use?

Only methylcytosine

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What do bacteria use to methylate base?

5-methycytosine

N6-metyhadeosine

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When are bases methylated?

Only C’s followed by G’s can be methylated

Only A’s in the sequence GATC can be methylated

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When can a cytosine be methylated?

When it is followed by a G

-60-90% of CpG’s are methylated

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When can Adenosines be methylated?

When in the sequence GATC

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What produces methylated bases?

Methylase

Bacteria: DAM (deoxyadenosine methylase)

Eukaryote: DNMT (DNA methytransferase )

Recognition site are palindromic!

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What does palindromic mean?

Sequence is the same forwards no backwards

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Why does methylation occur bacteria?

Controlling initiation of replication
Discrimination of self DNA (methylated) from foreign DNA (non-methylated)
Discriminate old and new strands in mismatch repair
Regulation of gene expression

-All DNA based

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Why do eukaryotes methylate?

Regulation of chromatin structure and gene expression

What kind of gene expression does methylation allow?

Gene silencing An epigenetic mechanism E.g. Imprinting and X-chromosome inactivation

In what order is the DNA double helix stranded?

2 antiparallel strands - one 5'-3' The other 3'-5'

What complementary bases pair in a DNA helix?

G pairs with C A pairs with T - Through hydrogen bonds (the number of bonds differs) - A purine way pairs with a pyrimidine

In DNA what side is oriented outward and what side is oriented inward?

Hydrophilic sugar-phosphate backbone is oriented outward Hydrophobic bases stacked in the interior

How many bonds do the A-T and G-C complementary bases have?

AT:2 GC: 3

About how much stronger is a GC bond than an AT bond?

50% stronger

What is base stacking?

Interactions between stacked bases above and below through: Van der walls Hydrophobic

What does base stacking contribute to?

Major contribution to helical stability

What bases have the strongest and weakest base stacking?

Stacked GC bases are strongest Stacked AT bases are weakest

What are Chargaff's Rules?

A always = T C always = G Pyrimidines nucleotides (T+C) always = total amount of purine nucleotides (A+G) (A+G)=(C+T) *More AT than GC*

What is G-quadrupled DNA?

``` Guanine tetrads: 4 G's in a plane connected by hydrogen bonding Stabilized by a cation (k+) Stacks of 2 or more guanine tetrads Found physiologically in G-rich region E.g. Telomeres ```

Where can you find G-quadruplex DNA?

Telomeres

What kind of DNA is found physiologically?

B-form DNA

Which side contains the minor grove?

The side with the glycosidic bond

Where do DNA binding proteins bind?

Bind in the grooves making specific interactions with these atom -usually the major groove

What do the bases in DNA provide for binding proteins?

H-bond donors (N-H0 Acceptors (N,O) Methyl groups for hydrophobic interactions

How can you tell if DNA is plindromic DNA?

Reads the same 5' to 3' on complimentary strands

What's an example of palindromic DNA?t

GACGTC

Why are DNA palindromes important?

They are recognition sequences for restriction endonucleases and some transcription factors

What is the difference between DNA palindromes in restriction endonucleases and transcription factors?

Restriction: palindrome not interrupted Transcription: palindrome is often interrupted by a few bases

What is the recognition sequence for EcoRI (restriction endonuclease)

5' GAATTC 3'

What is the recognition sequence for transcription factors such as Glucocotiocoid receptor binding site?

5'AGAACAnnnTGTTCT3' The nnn is the interruption

What are inverted repeats?

When single-stranded may form a hairpin or a stem-loop structure

What are mirror repeats in DNA?

Repeats that are not repeats in the 5' to 3' direction

Why are mirror repeats important?

For the formation of triple stranded DNA | -aka Hoogsteen or H-DNA

What repeats facilitates in the H-DNA formation?

Repeat of a poly-purine:polypyrimidine tract

With what strand does the third strand interact with?

Major groove via base-specific hydrogen bonds

What are Direct repeats and inverted repeats are often involved in?

Structural chromosomal abnormalities

What are direct repeats DNA inverted repeats?

Direct repeats = deletion and duplications Inverted repeats= inversions

Trinucleotide repeat expansions such are hungtintons Disease are associated with what kind of elemental symmetry?

Direct repeats

How re direct repeats and inverted repeats formed?

Unequal crossing-over in meiosis

How can we denature DNA?

(Def: bases are broken down) Heat, high ph AKA: melting

What tool can we use to follow denturation and renaturation of DNA?

UV spectrometry

What light does ssDNA absorb?

260 nm

How does the melting temperature of DNA increase?

With a higher content of GC

Does denaturation cause an increase in absorbance?

Yes

What is DNA hybridization?

Annealing of single-strand of DNA to a complementary strand of different DNA molecule

What is demination?

Loss of an exocyclic amino group

What is usually deaminated? How often does this occur?

Cytosine into uracil 1 every 10Mb per 24h

What enhance deamination?

Nitrous acid (HNO2)

What is depurination?

Los of the base from a nucleotide (usually a purine)

What does depurination lead to?

An apurinic site (AP site )

What are mutagens?

Physical, chemical, or biological agents that increase the rate of mutations -may be carcinogens or teratogens

What are alkylating agents? What do they cause?

They add alkyl groups (methyl or ethyl) to bases Cause mispairing E.g. O6-methylguanine pairs with T instead of C

What are the addition of bulky group do to DNA? Reword this q....

Benzo(a)Pyrenees's Found in col tar, tobacco smoke, charred food Oxidized in cels and binds covalently to guanine, distorting the double helix

What are intercalating agents?

Flat, planar molecules that slide between the stacked bases of the double helix

What do intercalating agents do?

Distort double helix and increases separation of bases - cause insertions and deletions during DNA replication - frameshift mutations

What are some examples of radiation-induced DNA damage

X rays | UV

What do X-rays do to DNA?

Generate free radicals that cause DNA double-stranded breaks

What does UV generate?

Pyrimidine diners (thymidine diners) -covalent bonds between adjacent pyrimidines in the same strand

What is the main example for oxidative damage?

Reactive oxygen species (ROS) | -Hydrogen peroxide (H2O2), Hydroxyl radicals (OH*), and superoxide radicals (O2-)

How are ROS generated?

Irradiation and from oxidative phosphorylation in the mitochondria

What are the main differences between RNA and DNA?

1. Ribose 2. Uracil instead of Thymine 3. Single-stranded 4. Intramolecular base-pairing 5. Unstable 6. Unusual bases may occur (tRNA)

What does intramolecular base pairing create in RNA?

Partially double-stranded structures Either Watson-crick or Hoogsteen base-pairing

Wha is Inosine?

A deaminated adenosine

IS inosine a purine or pyrimidine?

Purine

What will inverted repeats form in RN?

A hairpin or stem-loop

How are complex RNA structures generated?

H-bonds and base stacking

Nucleotides And Nucleic Acids Flashcards

(83 cards)