Nucleic acid structure

Question 1

Components of nucleic acids

Answer 1

• Sugar (S)- Ribose in RNA or Deoxy-ribose in DNA
• Phosphate (P) that joins sugar molecules to make a chain
• Bases (B) adenine, guanine, cytosine and thymine (in DNA) or Uracil (in RNA) that are attached to the sugar molecule

Question 2

Purine bases

Answer 2

Adenine and Guanine

Question 3

Pyrimidine bases

Answer 3

Thymine OR uracil and cytosine

Question 4

Differences between DNA and RNA- sugar type

Answer 4

DNA: Contains deoxyribose.
RNA: Contains ribose.

Question 5

Differences between DNA and RNA- bases

Answer 5

DNA: Has thymine.
RNA: Has uracil (no thymine)

Question 6

Differences between DNA and RNA- strand structure

Answer 6

DNA: Typically double-stranded.
RNA: Usually single-stranded

Question 7

Purines vs pyrimidines

Answer 7

Purines: Consist of two rings made of carbon and nitrogen.
Pyrimidines: Have just one such ring.

Question 8

Difference between ribose and deoxy-ribose

Answer 8

• Two sugars differ from each other by an OH group at the 2’ carbon
• Ribose has extra OH group

Question 9

Nucleoside

Answer 9

A base linked to a sugar molecule

Question 10

Nucleotide

Answer 10

A nucleoside with phosphates attached to its sugar’s 5’ carbon

Question 11

Chargaff’s rules

Answer 11

• Balance of Bases: The number of purine bases (A and G) is equal to the number of pyrimidine bases (C and T).
• Matching Pairs: The amount of adenine (A) matches thymine (T), and the amount of guanine (G) matches cytosine (C) ie A=T and G=C
• Significance: These matching pairs are key to the base pairing in DNA and its double-helix structure.

Question 12

Nucleic acids

Answer 12

long chains made up of nucleotides

Question 13

How nucleotides connect

Answer 13

connect end-to-end: a phosphate joins the 5’ end (imagine the top of one link) to the 3’ end (the bottom of the next link)

Question 14

Direction of the chain

Answer 14

• Has a direction, just like a one-way street
• It starts at the 5’ end and ends at the 3’ end- tells us which way the information is read.

Question 15

Sugars and there connections

Answer 15

• The 1’ spot is where the ‘name tag’ (the base) is attached.
• The 3’ and 5’ spots are like the arms of the sugar, reaching out to connect to other sugars with the help of a phosphate bridge.

Question 16

DNA structure

Answer 16

• DNA is like a twisted ladder or a spiral staircase, known as a double helix.
• It is made up of two strands that fit together because they are complementary

Question 17

Antiparallel strands

Answer 17

• These two strands run in opposite directions
• One goes from top to bottom (5’ to 3’), and the other goes from bottom to top (3’ to 5’)- what we mean by ‘antiparallel’

Question 18

DNA spiral

Answer 18

• For every complete twist of this ‘ladder,’ there are about 10.4 rungs, which represent the bases.
• Each twist or turn of the spiral is 3.4 nm long

Question 19

Base pairing

Answer 19

The rungs of the ladder are pairs of bases held together by hydrogen bonds, like a snap button, ensuring the strands fit perfectly

Question 20

5’ end

Answer 20

has a free phosphate group

Question 21

3’ end

Answer 21

has a free OH group

Question 22

Types of DNA sequences in eukaryotes

Answer 22

• Unique sequences
• Moderately repetitive sequences
• Highly repetitive sequences

Question 23

Unique sequences

Answer 23

Presently only once or only a few times: usually protein encoding regions

Question 24

Moderately repetitive sequences

Answer 24

• Usually 150-300 bp sequences repeated many thousand times.
• Examples include rRNA and tRNA genes.
• Tandem repeats
• Interspersed repeats
• Short interspersed elements
• Long interspersed elements

Question 25

Short Interspersed Elements (SINEs)

Answer 25

* usually <500 bp long and >105 copies * Example: Alu elements, ~300 bp, >million copies, comprised of 11 % of the human genome

Question 26

Long Interspersed Elements (LINEs)

Answer 26

* usually <500 bp long and >105 copies * Example: Alu elements, ~300 bp, >million copies, comprised of 11 % of the human genome

Question 27

Highly repetitive sequences

Answer 27

* These sequences are 10 bp or less in length * Repeated in tandems in hundreds of thousands to millions of copies * Clustered in certain regions, around centromeres and telomeres * Also called as satellite DNA

Question 28

Hairpin structure- single strand folding

Answer 28

single strand of nucleic acids (DNA or RNA) can fold onto itself.

Question 29

Hairpin structure- inverted sequences

Answer 29

This folding occurs because a sequence of nucleotides is followed, further along the strand, by its inverted complement (a sequence that matches the original but in the opposite order)

Question 30

Hairpin structure- hairpin formation

Answer 30

When these inverted sequences pair up, they create a structure that resembles a hairpin or a bobby pin with a loop at the top and a double-stranded stem at the bottom

Question 31

Hairpin structure- biological significance

Answer 31

Hairpin structures are important in gene regulation and can have various biological functions

Question 32

Stem

Answer 32

When the complementary sequences are contiguous, the hairpin has a stem but no loop

Question 33

RNA complex structures

Answer 33

RNA molecules may contain numerous hairpins, allowing them to fold up into complex structures

Question 34

Melting temperature (Tm) quantitative measurement

Answer 34

A spectrophotometer is used to measure nucleic acids quantitatively

Question 35

Melting temperature (Tm) absorption characterstics

Answer 35

At 260 nm wavelength, single-stranded DNA (ssDNA) absorbs more light than double-stranded DNA (dsDNA)

Question 36

Melting temperature (Tm) heat denaturation

Answer 36

Heating DNA breaks the hydrogen bonds between bases, turning it from double-stranded to single-stranded. As DNA denatures, its absorption at 260 nm increases until all of it becomes single-stranded

Question 37

Melting temperature (Tm)

Answer 37

The Tm is the temperature at which 50% of the DNA has changed from double-stranded to single-stranded

Question 38

G-C bond strength

Answer 38

GC (Guanine-Cytosine) base pairs are connected by three hydrogen bonds, which are stronger compared to the two hydrogen bonds in AT (Adenine-Thymine) base pairs

Question 39

Melting energy

Answer 39

More energy (heat) is needed to separate GC pairs due to their triple hydrogen bonding

Question 40

Tm and GC content

Answer 40

* The Tm, or melting temperature, is the temperature at which half of the DNA helix unwinds into single strands. * A higher percentage of GC pairs in DNA increases the Tm because more heat is required to break the additional hydrogen bonds