Pharm 411: DNA structure, synthesis, and repair Flashcards Preview

Pharm 411: fundamentals of molecular bio > Pharm 411: DNA structure, synthesis, and repair > Flashcards

Flashcards in Pharm 411: DNA structure, synthesis, and repair Deck (65)
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What does DNA stand for and what does it do?

Deoxyribonucleic acid
and it encodes the genetic makeup of a cell


How are the strands of DNA composed?

two antiparallel strands wound around each other in a right-handed helix
-The bases on one strand are complementary to, and hydrogen bond to, the bases on the opposite strand


What are the ingredients of nucleic acids?

1. purine or pyrimidine bases
2. pentose sugar (either ribose or deoxyribose)
3. phosphate groups


What is DNA composed of?

deoxyribonucleotides, which are composed of purine and pyrimidine bases, deoxyribose, and phosphate


What is a nucleoside?

A base + pentose sugar
- deoxyribonucleoside


What is a nucleotide?

Base+ pentose+ phosphate


What does it mean if the nucleic acid ends with -ine?

Means its a nucleoside


What does it mean if the nucleic acid ends with -ylate

Means its a nucleotide


What is a phosphodiester bond?

The linkage with the phosphate linking 5' hydroxyl of one nucleotide to the 3' hydroxyl of another


What does it mean when they say DNA has directionality?

As the DNA molecule grows, the strand always has an unreacted 5' phosphate group while the other has an unreacted 3'
hydroxyl group
**DNA is always synthesized 5' to 3'


What is the secondary structure of DNA?

Formed by the hydrogen bonding between complementary bases
- the acidic hydrophilic phosphate backbone is on the outside
- the hydrophobic bases stack inside
-they are coiled around axis of symmetry
-This nature causes it to form major and minor grooves


What must two strands of DNA be in order to pair?

They must be complementary


What does it mean if DNA is complementary?

1. the sequences must be appropriately paired
- Sequences must be paired AGCT must match TCGA
2. the strands must be in opposite directions
- 3' end of one strand will pair with the 5' end of the other (antiparallel)


What does it mean if DNA can reanneal?

Complementary strands combine upon meeting, and refrom double-stranded DNA


Can DNA be denaturated?

It separated into single strands by breaking apart hydrogen bonds
-Change pH
-Inc heat
- proteins involved in replication


What is the melting temp (Tm) of DNA?

The temp needed to separate the strands of the DNA
- higher Tm means DNA strands are more stable


What does the melting temp (Tm) depend on?

The relative amount of purine-pyrimidine pairs
- G-C pairs have 3 hydrogen bonds
- A-T pairs have 2 hydrogen bonds
** the more G-C pairs in the DNA the higher the Tm


What areas of DNA that open for replication or synthesis of RNA usually have?

more A-T content, meaning a lower melting point and easier to separate


How many chromosomes does a human have?

23 pairs or 46 total chromosomes
- has 3.2 x10^9 base pairs


What are histones?

They are proteins that bind to the DNA and coil it into compact structures called nucleosomes


What happens if DNA in not condensed into chromosomes?

Cell division cannot occur


What is replication?

DNA synthesis


What are the steps in DNA replication?

1. identification of the origin of replication at a specific base pair sequence
2. Unwinding (denaturation) of the double strand to provide two single strand templates forming the replication fork
3. initiation of DNA synthesis on each side of the fork
4. elongation, and ligation of newly synthesized DNA segments


What does it mean by DNA is semi-conservative?

Each new DNA molecule contains one strand from the parent, and one newly synthesized strand


What direction does DNA replication proceed?

In a 5' to 3' direction on both strands


Where can DNA polymerase add nucleotides?

To the 3' hydroxyl on an existing chain of nucleotides (CAN NOT initiate a new chain)


What are RNA primers?

They are synthesized by an enzyme called primase (RNA polymerase) which provide a starting point for DNA synthesis


What is DNA helicase?

An enzyme that binds single-stranded DNA at the origin of DNA replication and "unzips" the DNA


What is single-stranded DNA binding protein?

Enzyme that stabilizes the single-stranded DNA so that it stays unwound


What is Toposiomerase?

Enzyme that cuts one or both strands of DNA to remove coils and knots in the DNA