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MCAT-Biochemistry > DNA and Biotechnology > Flashcards

DNA and Biotechnology Flashcards

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MCAT flashcards
1
Q

Describe a nucleoside

A

Composed of a five carbon sugar bonded to a nitrogenous base and are formed by covalently linking the base to C-1’ of the sugar

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2
Q

Describe nucleotides

A

When one or more phosphate groups are attached to C-5’ of a nucleoside.

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3
Q

Why are nucleotides such ATP and ADP high energy compounds?

A

This is because of the energy associated with the repulsion between closely associated negative charges on the phosphate groups,

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4
Q

In what way is ATP formation an exception to a chemical rule?

A

Usually bond breaking is exothermic while bond making is usually endothermic

In ATP, due to all the negative charges in close proximity, removing the terminal phosphate from ATP actually release energy, which powers our cells

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5
Q

Differentiate the sugars in RNA and DNA

A

DNA- deoxyribose

RNA- ribose

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6
Q

Name the nucleoside and the nucleotides of the base, Adenine

A

Nucleoside- Adenosine (Deoxyadenosine)

Nucleosides- AMP( dAMP), ADP(dADP) , ATP(dATP)

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7
Q

Name the nucleoside and nucleotides of the base, Guanine

A

Nucleoside -Guanosine( deoxygysnosine)

Nucleotides- GMP( dGMP), GDP(dGDP) , GTP(dGTP)

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8
Q

What is the name of the nucleoside and nucleotides of the base, Cytosine?

A

Nucleoside- Cytidine (Deoxycytidine)

Nucleosides- CMP(dCMP), CDP(dCDP), CTP(dCTP)

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9
Q

What are the names of the nucleoside and nucleotides of the bases, uracil?

A

Nucleoside- Uridine(deoxyuridine)

Nucleotides - UMP( dUMP), UDP(dUDP), UTP(dUTP)

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10
Q

What are the nucleoside and nucleotides of the base, thymine?

A

Nucleoside- Deoxythimidine

Nucleotides- dTMP, dTDP, dTTP

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11
Q

What is the sugar phosphate backbone comprised of?

A

Nucleotides are joined by 3’-5’ phosphodiester bonds

Thus joins alternating sugars and phosphate groups

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12
Q

Why does DNA and RNA have an overall negative charge?

A

Phosphates of the sugar-phosphate backbone carry a negative charge

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13
Q

What is the function of the sugar-phosphate backbone?

A

Determines the directionality of the DNA and is always read from 5’ to 3’

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14
Q

What are purines? Give the 2 examples.

A

Purines contain two rings in the structure

Adenine and Guanine

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15
Q

How can DNA be written ?

A

5’— ATG—3’(or simply ATG, this is how DNA is read)

If written backwards- 3’—GTA—5’

The position of the phosphates may be shown pApTpG

The “d” may be used for deoxyribose : dAdTdG

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16
Q

What are Pyrimidines? Give the 3 examples

A

Three ring structures

Cytosine, thymine, uracil

17
Q

Purines and pyrimidines are aromatic heterocyclic. What are the four specific rules of being aromatic ?

A

The compound is cyclic

The compound is planar

The compound is conjugated (has alternating single and multiple bonds, or lone pairs, creating atleast one unhybridized p-orbital for each atom in the ring)

The compound has 4n+2 (where n is any integer) pi electrons. This is Hückel’s rule

18
Q

Why does benzene specifically, have the delocalization characteristic of aromatic compounds?

A

Carbon atoms in benzene are sp2 hybridized and each orbital overlaps equally with its two neighbors

This causes delocalised electrons to form to pi electron clouds, one above and below the plane of the ring

19
Q

Why are aromatic molecules fairly unreactive?

A

The delocalisation of pi electrons of all aromatic rings

20
Q

What are heterocyclic?

A

Structures that contain atleast two different structures in the ring

21
Q

What are the key features of the Watson-Crick Model?

A
  • The two DNA strands are anti parallel
  • the sugar phosphate backbone is on the outside of the helix with the nitrogenous bases on the inside
  • Complementary base pairing rules, the hydrogen bonds, hydrophobic interactions between bases, provides stability to the double helix structure
  • Properties of Chargaff’s rules state that since the amount of A = the amount of T and amount of C= Amount of G, the number of purines = number of pyrimidines
22
Q

What is B-DNA?

A

When the double helix DNA is a right-handed helix(most DNA)

23
Q

Describe the turn and residues of B-DNA

A

B-DNA makes a turn every 3.4 Na and contains about 10 bases with that span

24
Q

What are major and minor grooves in B-DNA?

A

They can be identified between interlocking strands and are often the site of protein building

25
Q

Describe Z-DNA

A

It has a zigzag appearance, it is a left handed helix that has a turn every 4.6 nm and contains 12 bases within that turn

26
Q

In replication and transcription, access to the DNA is needed. How is this carried out?

A

The DNA is denatured by conditions that disrupt hydrogen bonding and base pairing, resulting in the melting of the double helix strand from each other

27
Q

What is the importance of annealing DNA?

A

Important in many lab processes such as PCR and is brought back together after replication and transcription

28
Q

Describe briefly hybridization

A

Probe DNA is added to mixture of target DNA sequences. When probe DNA binds to target DNA, this may provide evidence of the gene interest

29
Q

What is the real world application of DNA hybridization ?

A

PCR and detection of specific DNA sequences

30
Q

What are histones and their purpose?

A

DNA is wound around a group of proteins called histones, forming chromatin

31
Q

What are the histones proteins and how many are there?

A

There are 5 histone proteins in eukaryotic cells.

Two copies of each protein

H2A, H2B, H3 and H4 to form a histone core

32
Q

What is a nucleosome ?

A

About 200 pairs of DNA are wrapped around the histone protein complex

33
Q

What are nucleoproteins? Give an example

A

Proteins that associate with DNA, histones

34
Q

What is heterochromatin?

A

Chromatin that remains compacted during interphase in which the S phase has DNA replicated

Is transcriptionally silent

35
Q

How does heterochromatin appear under a microscope?

A

Appears dark under light microscopy

36
Q

What is euchromatin?

A

Chromatin that is dispersed

Contains genetically active DNA

37
Q

How does euchromatin appear under microscope?

A

Appears light under light microscope

MCAT-Biochemistry (3 decks)

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