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BCHM Mod 3 > Section 1 > Flashcards

Section 1 Flashcards

1
Q

Nucleic acids are composed of chains of ____________

A

nucleotides

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2
Q

What are the functions of DNA?

A
  1. Long-term storage molecule
  2. Template for DNA replication
  3. Coding for proteins and functional RNAs
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3
Q

A short nucleic acid containing 50 or fewer nucleotides is generally called an ____________

A

oligonucleotide

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4
Q

A longer nucleic acid (generally over 50 nucleotides) is called a ___________

A

polynucleotide

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5
Q

Weak forces such as _____________ and ________________ coordinate the self-assembly of nucleic acids into their 3D structure.

A

Watson-crick base pairing and base stacking

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6
Q

What are the components of a nucleotide?

A
  • A heterocyclic base
  • A five-carbon sugar called a pentose
  • A phosphate group
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7
Q

What does heterocyclic mean?

A

A cyclic compound with one or more ring structures that contain atoms of at least two different elements.

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8
Q

Is there always an equal percentage of purines and pyrimidines in double stranded DNA?

A

Yes, since A always pairs with T, and C always pairs with G, according to the Watson-Crick model of DNA

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9
Q

What is the relationship of the number of purines and pyrimidines in DNA?

A

A + G = T + C
(the sum of purine residues = the

This is called Chargaff’s Rule, and is critical for information storage (maintaining nucleotide order) and replication (since it is semi-conservative)

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10
Q

What is the significance of Chargaff’s Rule in DNA?

A

Chargaff’s Rule is critical for information storage in DNA because it helps maintain the order of nucleotides and ensures that there is an equal balance of purines and pyrimidines. It is also essential for DNA replication, as it plays a role in the semi-conservative nature of DNA replication.

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11
Q

What is the Watson-Crick model of DNA?

A

The Watson-Crick model of DNA describes DNA as a double-stranded, helical molecule consisting of two sugar-phosphate backbones held together by hydrogen bonds between pairs of nitrogenous bases. The four nitrogenous bases are adenine (A), cytosine (C), guanine (G), and thymine (T). In this model, hydrogen bonding occurs between A and T, and G and C.

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12
Q

How are the two strands of a DNA molecule held together?

A

The two strands of a DNA molecule are held together via base pairing between the nitrogenous bases. Specifically, adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G) through hydrogen bonds.

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13
Q

What type of bonds are responsible for holding the two DNA strands together?

A

The bonds that hold the two DNA strands together are hydrogen bonds. These are relatively weak interactions that form between the nitrogenous bases of the DNA strands.

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14
Q

WHy is the C-G base pair stronger than the A-T?

A

Because C and G share three hydrogen bonds, while A and T share only two.

The presence of an extra hydrogen bond in the C-G pair contributes to its greater stability.

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15
Q

What elements or groups in the nitrogenous bases are involved in forming hydrogen bonds in DNA base pairing?

A

Hydrogen bonds in DNA base pairing are formed due to the hydrogen-bonding capacity of the ring nitrogens, ring carbonyl groups, and the amino groups located outside the ring structure of the nitrogenous bases. These groups are involved in the interactions that lead to base pairing in DNA.

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16
Q

How does the strength of hydrogen bonding in DNA base pairs relate to the overall stability and structure of the DNA molecule?

A

The strength of hydrogen bonding in DNA base pairs is crucial for the overall stability and structure of the DNA molecule. The differential strength of these bonds contributes to the stability of the double helix and plays a fundamental role in the structural integrity of DNA, ensuring accurate replication and transmission of genetic information.

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17
Q

What is the overall shape of the DNA molecule?

A

The DNA molecule has a right-handed double helix structure.

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18
Q

What is the composition of the backbone of each DNA strand?

A

The backbone of each DNA strand is composed of alternating sugar and phosphate residues, known as the sugar-phosphate backbone. It is highly negatively charged.

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19
Q

Where are the nitrogenous bases of DNA located within the double helix, and what is their role?

A

The nitrogenous bases of DNA are positioned towards the center of the helix. They play a crucial role in hydrogen bonding with complementary bases on the opposing DNA strand, facilitating base pairing.

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20
Q

What is the concept of directionality in the DNA double helix?

A

The DNA double helix exhibits directionality, meaning each strand has opposing directionality. This directionality is based on the linkages formed by carbons at the phosphate and OH groups on the pentose sugar. The two strands run in opposite directions, with one strand having a 5’ → 3’ direction, while the other has a 3’ → 5’ direction.

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21
Q

Why is the antiparallel orientation of DNA more energetically favorable than the parallel orientation?

A

The antiparallel orientation of DNA is more energetically favorable due to the geometry of the component bases. In the antiparallel arrangement, the complementary base pairs align in a way that allows for proper hydrogen bonding. In a parallel orientation, the bases would not align correctly, making it less stable and less suitable for genetic information storage and replication.

22
Q

What is antiparallel vs parallel?

A

Antiparallel: In an antiparallel arrangement, the two DNA strands run in opposite directions along the length of the helix. One strand runs in the 5’ to 3’ direction, meaning the 5’ end of one strand is paired with the 3’ end of the other strand, and vice versa. This arrangement allows for the complementary base pairs (A with T and C with G) to align properly and form hydrogen bonds.

Parallel: In a parallel orientation, both DNA strands run in the same direction along the length of the helix, such as both running from 5’ to 3’ or both running from 3’ to 5’. In this configuration, the bases on the two strands do not align correctly for proper hydrogen bonding. A parallel orientation is not found in the natural structure of DNA because it would result in an unstable and ineffective molecule for genetic information storage and replication.

23
Q

How is a phosphodiester bond in nucleic acids formed?

A

A phosphodiester bond is created when the 5′-phosphate group of one nucleotide unit is linked to the 3′-hydroxyl group of the next nucleotide. This reaction involves the loss of water, and the linked nucleotides are now referred to as ‘residues.’

24
Q

In the DNA double helix, what are the two unequal surfaces formed by the twist of the helix, and what are they called?

A

The twist of the DNA helix forms two unequal surfaces known as the major groove and the minor groove. The major groove is the wider groove found on the outside of the DNA strand and is primarily where the nucleotide sequence is read by DNA-binding proteins, as it is more accessible.

25
Q

Difference between purines and pyrmidines.

A

Purines have dual ring structure with imidazole group (adenine, guanine)

Pyrimidines have one ring structure (cytosine, thymine, uracil)

26
Q

What are Chargaff’s Rules? Won’t be asked to state them, but will be asked to apply them.

A
  1. the base composition of DNA varies from species to species
  2. DNA samples from different tissues of the same species have the same base composition
  3. DNA base composition does not change with age, nutritional state, or environment
  4. I all DNAs, for all species, A=T and G=C
27
Q

How many angstroms or base pairs is one helical turn of the DNA double helix?

A

34 angstroms or roughly 10.5 base pairs

28
Q

You are studying the genome of a new virus and discover that it contains 19% Adenosine and 32% Thymidine. What does that tell you about the virus?

a) Its genome is not composed of nucleic acids
b) Its genome is double stranded DNA
c) Its genome is single stranded DNA
d) Its genome is RNA

A

c) Its genome is single stranded DNA

its not RNA because it doesn’t have uracil. if it was double stranded there would be equal amount of A and T.

29
Q

What are three functions of DNA?

A
  1. Long-term storage of genetic information
  2. Template for DNA replication
  3. Coding for proteins and functional RNAs
30
Q

Describe how DNA is used as an information storage molecule.

A
31
Q

What is hydrophobic stacking in the context of nucleic acids, and why does it occur?

A

Hydrophobic stacking is an interaction between bases within nucleic acids. It occurs because the purines and pyrimidines, which make up the bases, are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. This causes the bases to align with their ring planes in parallel, like a stack of coins, which stabilizes the DNA helix by minimizing contact with water.

32
Q

How do weak bonds contribute to the stability of double-stranded DNA?

A

Weak bonds, including van der Waals interactions, hydrogen bonds, and electrostatic interactions among bases, form a network of interactions within the double-stranded DNA structure. These bonds are arranged so that breaking one bond simultaneously breaks many others. As a result, DNA double helices that are 10 or more base pairs long are quite stable at room temperature.

33
Q

What are the major and minor grooves in DNA, and what role do they play in base pairing interactions?

A

In DNA, the major and minor grooves are unequal surfaces formed by the twist of the helix. Atoms in these grooves can act as hydrogen donors (‘D’) or acceptors (‘A’) in base pairing interactions. These grooves are essential for DNA-binding proteins to interact with the nucleotide sequence, primarily in the major groove, which is more accessible.

34
Q

How does replication fidelity relate to the transmission of genetic information in DNA?

A

Replication fidelity is crucial for the transmission of genetic information in DNA. The double helix structure of DNA allows for the separation of the two strands, and each original strand can serve as a template for synthesizing a complementary strand.

This process is made possible due to base pairing rules, ensuring that the new strand is a precise copy of the original strand. This mechanism of DNA replication confirms the accuracy of genetic information transfer and revolutionizes our understanding of biological inheritance.

35
Q

Why is the inherent stability of DNA important for its role as a repository of genetic information?

A

The inherent stability of DNA is crucial for its role as a repository of genetic information because it ensures long-term storage without alteration. The chemical transformations in DNA are generally slow in the absence of enzyme catalysts. Even minor changes in DNA structure can be physiologically significant. The stability of DNA allows for the preservation of genetic information over time.

36
Q

What is the significance of strand separation in DNA?

A

Strand separation in DNA is essential for processes like replication and transcription. Before DNA can be replicated or transcribed into RNA, the two DNA strands must be separated. This separation is a non-destructive alteration of DNA and is necessary for its function in the replication and expression of genetic information.

37
Q

How can you use organic solvents to separate double stranded DNA?

A

If we want to separate these strands we can use organic solvents like (formamide or urea) and they can form H bonds with the nitrogenous bases of DNA thereby separating the strands hydrogen bonds that hold them together.

38
Q

How do hydrophobic interactions contribute to the stability of the DNA duplex?

A

Hydrophobic interactions stabilize base pairing in the DNA duplex. Bases in DNA are hydrophobic and face the interior of the helix, away from water (H2O), while the sugar-phosphate backbone is hydrophilic and faces the exterior, interacting with water.

39
Q

What are van der Waals interactions, and how do they affect the stability of the DNA duplex?

A

Van der Waals interactions occur between stacked bases in the DNA duplex through their ring structures. These interactions play a role in stabilizing the stacking of bases along the DNA strands.

40
Q

How does hydrogen bonding between paired bases influence the stability of the DNA duplex?

A

Hydrogen bonding occurs between paired bases in the DNA duplex. The stability of the base pairing is determined by the number of hydrogen bonds formed between each pair of bases. For example, G-C bonds are more stable than A-T bonds due to the difference in the number of hydrogen bonds.

41
Q

What role do ionic interactions play in the stability of the DNA duplex?

A

Ionic interactions are important for stabilizing the DNA duplex. The negative charge of the backbone phosphates is neutralized by interactions with cations such as Na+ and Mg++. These interactions help reduce the electrostatic repulsion between the negatively charged DNA strands, contributing to the overall stability of the duplex.

42
Q

How is the stability of the DNA double helix affected by its phosphate backbone and what can counteract this instability?

A

The stability of the DNA double helix is influenced by the negative charges on the phosphate groups of its backbone. These phosphate groups are negatively charged due to their low pKa (2) and are fully deprotonated at neutral pH. This negative charge can cause the DNA backbones to repel each other, leading to destabilization of the double helix. One way to counteract this destabilization is by increasing the salt concentration, with sodium ions being effective at neutralizing the negative charge on the backbone. This interaction with positively charged ions helps stabilize the DNA double helix. This same principle applies to RNA as well, which is also stabilized by positively charged metal ions.

43
Q

Which of the following chemical interactions is NOT involved in stabilizing the transition of single stranded DNA into a double helical structure?

a) Hydrogen bonding between paired bases
b) Hydrophobic interactions
c) Phosphodiester bonds
d) Van der Waals interactions

A

Phosphodiester bonds because these are not involved in the transition of single to double stranded DNA. They are just involved in the backbone of the single stranded DNA

44
Q

What are the four forces that affect duplex stability?

A
  1. Hydrophobic interactions (bases are hydrophobic and face the interior of the helix away from water, and sugar-phosphate backbone is hydrophilic and faces the exterior, interacting with water)
  2. Van der Waals interaction (stacked bases interact through ring structures)
  3. Hydrogen bonding between paired bases
  4. Ionic interactions (the negative charge of backbone phosphates are neutralized by interactions with cations, such as Na+ and Mg2+)
45
Q

What are the external factors that influence DNA stability?

A
  1. Temperature (can cause DNA to unwind, destabilizing DNA)
  2. Salt (increases duplex stability)
  3. DNA binding proteins (which are involved in the compaction of genomes, and can contribute to both the global and local structure of DNA)
  4. Organic solvents (carbon-based solvents) destabilize the DNA helix by disrupting hydrogen bonds and solvating bases
46
Q

What factors allow DNA and RNA to interact with various molecules through electrostatic interactions?

A

Both DNA and RNA can engage in electrostatic interactions with diverse molecules due to the negative charge of their sugar-phosphate backbones.

The hydrophilic nature of the DNA and RNA backbones leads to the formation of hydrogen bonds with water, further facilitating interactions.

Phosphate groups in the DNA and RNA backbones are highly negatively charged at pH 7, with a pKa near 2. These negative charges are typically neutralized through ionic interactions with positively charged proteins, metal ions, or polyamines, which are organic molecules containing multiple amine groups.

Common cations, such as magnesium and potassium ions, are known to bind to the phosphate groups on the RNA backbone, contributing to the stabilization of the folded RNA structure.

47
Q

How can you promote DNA melting?

A
  1. Increase temperature: Raising the temperature can promote DNA melting by providing the necessary thermal energy to break the hydrogen bonds holding the DNA strands together.
  2. Decrease salt concentration: Lowering the salt concentration, particularly monovalent cations like sodium ions, reduces the shielding of the negatively charged DNA backbone, making it easier for the strands to separate.
  3. Use organic solvents (e.g., urea): Organic solvents like urea can disrupt the hydrogen bonds and hydrophobic interactions in DNA, contributing to DNA denaturation.
  4. DNA binding proteins (e.g., helicase): Enzymes like helicase can actively unwind and separate the DNA strands, promoting DNA melting as part of various cellular processes.
48
Q

Which of the following would be a consequence of reducing the salt concentration of a solution of double stranded DNA?
You can respond once
It would melt at a lower temperature
It would melt at a higher temperature
Salt would not influence the melting temperature

A

It would melt at a LOWER temperature because salt stabilizes the DNA backbone and neutralizes the DNA backbone (more salt means more stable DNA helix, less salt means less stable DNA double helix therefore easier to break the bonds and easier to melt)

49
Q

You are studying the genome of a new virus and discover that it contains 19% Adenosine and 32% Thymidine. What does that tell you about the virus?
Poll is full. This poll has received the maximum number of responses allowed.
Its genome is not composed of nucleic acids
Its genome is double stranded DNA
Its genome is single stranded DNA
Its genome is RNA

A

Its genome is single stranded DNA

its not RNA because it doesn’t have uracil. if it was double stranded there would be equal amount of A and T.

50
Q
A

BCHM Mod 3 (9 decks)

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