Lecture 3: Nucleic Acids Flashcards by Deanice Cruz

Chemical name for 1 phosphate?

Label the structure!

Monophosphate

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Monomeric units w/ phosphates?

Nucleotides

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Monomeric units that lack phosphates

Nucleosides

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Label the Nucleotide!

How would it be different for DNA vs RNA?

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Two ______ bases: DNA and RNA contain A & G.

Two Purine bases: DNA and RNA contain A & G.

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Name the base.

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Name the base.

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3 _______ bases: DNA and RNA contain C;

mainly T in DNA;

mainly U in RNA.

3 Pyrimidine bases: DNA and RNA contain C;

mainly T in DNA;

mainly U in RNA.

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Name the base.

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Name the base.

DNA/RNA?

DNA

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Name the base.

DNA/RNA?

RNA

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Where does the Glycosidic Bond attach for Purines?

Pyrimidines?

Purines: At N9 to sugar at C1’

Pyrimidines: At N1 to sugar at C1

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Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

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Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

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Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

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Name the Deoxyribonucleotide.

Symbols?

Nucleoside?

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Name the Ribonucleotide.

Symbols?

Nucleoside?

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Name the Ribonucleotide.

Symbols?

Nucleoside?

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Name the Ribonucleotide.

Symbols?

Nucleoside?

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Name the Ribonucleotide.

Symbols?

Nucleoside?

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What is this compound?

Nucleoside?

Nucleotides?

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Adenosine Triphosphate

Nucleoside: Adenosine

Nucelotides: AMP, ADP, ATP

Name the structure and phosphate.

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Adenosine (Adenosine diphosphate, ADP)

Inorganic Phosphate

Name the structure and phosphate.

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Adenosine (Adenosine monophosphate, AMP)

Inorganic Pyrophosphate

What types of substrates does DNA & RNA require?

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dNTP, NTP

DNA Secondary Structure was founded by whom and when?

Chargaff, 1950

Chargaff's Rules for DNA Secondary Structure: 1. All ______ in the ______ species have the ___ mol-% of all _ nucleotides. 2. mol-% of _____ = mol-% of \_\_\_\_\_ 3. %A = %\_\_\_ and %G =%\_\_\_ * i.e. A+G =\_\_\_+\_\_\_\_\_ * W-C MODEL: A pairs w/ ___ and G pairs w/ \_\_\_, and same ____ in all cells

Chargaff's Rules for DNA Secondary Structure: 1. All **tissues** in the **same** species have the **same** mol-% of all **4** nucleotides. 2. mol-% of **Purines** = mol-% of **Pyrimidines** 3. %A = %**T** and %G =%**C** * i.e. A+G =**T**+**C** * W-C MODEL: A pairs w/ **T** and G pairs w/ **C**, and same **DNA** in all cells

What is the backbone of DNA Secondary Structure according to Chargaff and where does new dNTP and NTP get added?

**Phosphate-deoxyribose backbone** **3' end of growing polynucleotide chain**

According to the Watson-Crick Model, what type of backbone encompasses the nucleotides? \_\_\_\_\_\_\_\_ bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes ____ to the helix axis.

**Hydrophilic phosphate-deoxyribose backbone** **Hydrophobic** bases (paired by H-Bonding) on the inside – base-pairs are stacked on one another with planes **perpendicular** to the helix axis.

According to the Watson-Crick Model, complimentary strands run \_\_\_\_\_\_\_\_. A-T has __ H-Bonds. G-C has __ H-Bonds. Which complimentary pair is is stronger?

According to the Watson-Crick Model, complimentary strands run **antiparallel**. A-T has **2** H-Bonds. G-C has **3** H-Bonds, hence **the stronger bond.**

What form of DNA is a right-handed double helix, forms when fully hydrated and under conditions *in vivo* w. majority of proteins recognizing the major groove?

B-Form

The B-form of DNA is a highly (+/-) molecule and every base needs __ phosphodiester bond(s).

The B-form of DNA is a highly **-** molecule and every base needs **1** phosphodiester bond.

The B-form of DNA us a right-handed double helix model that is stabilized by: 1. ________ interactions: base stacking 2. \_\_-Bonding between Pu---Py 3. \_\_\_\_\_\_: neutralize the (-) on the phosphates along the helix of DNA

The B-form of DNA us a right-handed double helix model that is stabilized by: 1. **Hydrophobic** interactions: base stacking 2. **H**-Bonding between Pu---Py 3. **Cations**: neutralize the (-) on the phosphates along the helix of DNA

What form of DNA forms under dehydrated, non-physiological conditions; right-handed helix?

**A-DNA**

What form of DNA is rich in GC content, left-handed, and is important in protein recognition & gene regulation?

**Z-DNA**

Why does DNA need to be condensed and how does it fold?

**To fit into cells,** **Linearly**

in eukaryotic cells, DNA is wrapped around proteins called ________ to help package it in cells.

in eukaryotic cells, DNA is wrapped around proteins called **histones** to help package it in cells.

DNA bases can be modified to provide additonal level to the "code" = \_\_\_\_\_\_\_

DNA bases can be modified to provide additonal level to the "code" = **epigenetics**

What is the loss of structure of DNA & proteins by melting w/ high heat, causing interaction of H-bonds and the chains to come apart?

**Denaturation**

In what does the duplex melt (no covalent bonds break)? 1. ? 2. ? 3. ?

In what does the duplex melt (no covalent bonds break)? 1. **Acid** 2. **Alkali** 3. **Heat**

Stability/melting temperature (T_m) a function of \_/\_ content because they contain _ H-bonds.

Stability/melting temperature a function of **G**/**C** content because they contain **3** H-bonds.

What is the reassociation of denatured DNA strands? And at what temp stability/melting temp is ideal?

**Annealing** **~25º C below T_m**

High ____ stabilizes the duplex, increasing T_m, due to * __________ interactions (bp's) * ________ shielding

High **salt** stabilizes the duplex, increasing T_m, due to * **Hydrophobic** interactions (bp's) * **Phosphate** shielding

What determines the DNA and melting temperature (denaturation) for a molecule and why?

**Amount of G/C content, due to the amount of H-bonds (3 in GC)**

What type of group is RNA secondary structure?

**2' OH group**

T/F: Does RNA have a simple, regular secondary structure?

**False**

What are the most common secondary structures for RNA?

**A-form double helices and hairpins**

Ribose 2' OH of RNA causes _____ interactions in base stacking that prevent _____ of more than 10-12 bp's.

Ribose 2' OH of RNA causes **steric** interactions in base stacking that prevent **coils** of more than 10-12 bp's.

Steps of DNA duplication: 1. ____ copies 3 nucleotide codon (\_RNA) 2. \_RNA reads encoded gene information from \_RNA 3. \_RNA transfers appropriate ____ \_\_\_\_ to a growing polypeptide chain for protein synthesis

Steps of DNA duplication: 1. **DNA** copies 3 nucleotide codon (**m**RNA) 2. **t**RNA reads encoded gene information from **m**RNA 3. **t**RNA transfers appropriate **amino acid** to a growing polypeptide chain for protein synthesis

Lecture 3: Nucleic Acids Flashcards

(48 cards)