Lecture 1 - DNA Structure

Question 1

why are nucleic acids useful in forensics

Answer 1

they are found in everyone and can have identifiable features for specific individuals within the base pair sequence

Question 2

what is DNA

Answer 2

a polymer made of two polynucleotide chains that coil around one another

Question 3

what are the three core components of nucleic acids in DNA

Answer 3

bases
deoxyribose sugar
phosphate groups - these make phosphodiester bonds with the sugar

Question 4

name the 4 types of bases

what is the base seen in RNA but not DNA

Answer 4

thymine
guanine
cytosine
adenine

uracil

Question 5

what bases are purines

Answer 5

adenine
guanine

AG

Question 6

what bases are pyrimidines

Answer 6

cytosine
thymine
uracil

CUT

Question 7

which bases pair together and how many hydrogen bonds do they form

Answer 7

AT = 2 hydrogen bonds
CG = 3 hydrogen bonds

Question 8

why does a deoxyribose sugar come from

Answer 8

from a ribose sugar that has undergone deoxygenation by an enzyme called ribonucleotide reductase

Question 9

what is a phosphate group

Answer 9

PO4 - one oxygen is double bonded to phosphorus

there is an overall negative charge

Question 10

what are the two possible structures of ribose

Answer 10

linear or cyclic

an equilibrium lies between the two as it can exist in either form

Question 11

where do the phosphate groups attach to the deoxyribose sugar

what does this linkage drive

Answer 11

at carbon 3 and 5

the helical structure of DNA, this asymmetric linkage gives DNA a direction and if more stable in a twisted form

Question 12

what is the difference between a nucleobase, nucleoside and nucleotide

Answer 12

nucleobase = the base alone
nucleoside = the base + sugar
nucleotide = base, sugar + phosphate

Question 13

how is the anti-parallel structure of DNA formed

Answer 13

the two strands are connected via hydrogen bonds between the bases

the strands run 5’-3’ so as there are two of them in order to connect the bases they need to run anti parallel to one another

Question 14

what is the primary structure of DNA

Answer 14

the nucleotide sequence

Question 15

is the CG or AT base paring more stable

Answer 15

CG due to their being more hydrogen bonds between them

Question 16

name 3 features that DNA has in a double helix

Answer 16

a major groove
a minor groove
right handed twist

Question 17

why does DNA form a double helix (4 reasons)

Answer 17

1- to allow hydrogen bonding between the complimentary bases
2 - the negatively charged phosphate groups repel each other so they are furthest apart in the helix (reducing electrostatic repulsion)
3 - pi pi stacking is seen for the rings of the bases (hydrophobic and Van der Waals interactions) allowing a tight helix
4 - the bases being closely packed prevent water getting in and causing the hydrogen bonds to break and the structure to fall = entropically favourable

Question 18

what are the three structure the double helix could be and where are they commonly seen

Answer 18

1. B-DNA - right handed = most common and seen in cells
2. A-DNA - right handed = seen in dehydrated conditions or hybrid DNA-RNA
3. Z-DNA - left handed = seen in diseases when DNA has undergone methylation

Question 19

what is the secondary structure of DNA

Answer 19

the double helix formed by two complimentary strands coming together

could be B, A or Z DNA
or triplex or quadruplex

Question 20

what are triplex and quadruplex DNA

Answer 20

triplex = the addition of a third strand of DNA strand binding into the major groove

quadruplex = 4 DNA strands held round a metal ion, found in telomeres, protects DNA ends and allows ends to be copied

Question 21

what is the tertiary structure of DNA

Answer 21

the 3D folded shape of the polymer

Question 22

give three ways in which DNA and RNA differ structurally

Answer 22

DNA has T, RNA has U

DNA is normally double stranded and RNA single stranded

DNA has deoxyribose sugar and RNA has ribose (so RNA has more hydrogen bonding sites so the phosphodiesters are more easily hydrolysed)

Question 23

What type of structures does RNA exist in

give 4 examples of what the structure of RNA might be

Answer 23

complex structures

such as:
hairpin
stem loop
bulge
bubble

Question 24

how is DNA packaged into the nucleus

Answer 24

in structures called nucleosomes

DNA is wound round histone proteins = nucleosomes and these are packed in chromosomes

8 histones are needed to make 1 nucleosome

Question 25

how can RNA be beneficial in Nanotechnology

Answer 25

can use RNA to create structures for desired uses

e.g cages or tubes

especially useful for getting things into the body as our body is less likely to reject it and can target certain areas