DNA Structure Flashcards
What is the central dogma of biology?
- it deals with the detailed residue-by-residue transfer of sequential information
- it states that such information cannot be transferred back from protein to either protein or nucleic acid
Draw out the DNA to RNA to protein flow chart?
DNA - DNA - replication
DNA - RNA - transcription
RNA - DNA - reverse transcription
RNA - RNA - replication
RNA - protein - translation
What are the three components of nucleic acids/DNA?
- base pairs
- phosphodiester / Phosphate Group
- (deoxy)ribose / Sugar
What is DNA?
DNA is a polymer composed of two polynucleotide chains that coil around each other
What are the two forms of nucleobases?
- pyrimidine
- purine
What are the five base pairs?
Which ones are based from pyrimidines and which ones are based from purines?
pyrimidine:
- cytosine
- uracil
- thymine
purine:
- adenine
- guanine
Which base pairs pair up?
How many hydrogen bonds between each?
AT - adenine and thymine
- 2 hydrogen bonds DA/AD
CG - cytosine and guanine
- 3 hydrogen bonds ADD/DAA
What is ribose?
- a sugar and has standard structure of sugar
- it goes between planar and cyclic structure - there is an equilibrium which exists between the two
- it is metabolically produced from glucose (reduction of glucose)
How is deoxyribose produced?
- it is generated from ribose 5-phosphate by enzymes called ribonucleotide reductases which catalyse the deoxygenation process
- nucleobase replaces the OH on the RHS
What is the main link between two nucleotides?
- phosphodiester links 5’ to 3’
- this asymmetric linkage gives DNA strands direction (gives it curved structure)
Define nucleobases, nucleoside and nucleotide?
- nucleobase = base pairs
- nucleoside = base pair + sugar
- nucleotide = base pair + sugar + phosphate
What are the five nucleosides called and therefore what are the five nucleotides?
- adenosine
- cytidine
- guanosine
- thymidine
- uridine
- adenosine 5’-phosphate
- cytidine 5’-phosphate
- guanosine 5’-phosphate
- thymidine 5’-phosphate
- uridine 5’-phosphate
What is the antiparallel duplex?
- one side of the DNA strand going from 5’-3’ down and the other side 5’-3’ up
What is the primary structure of DNA?
- sequence of nucleotides
How is DNA duplex formed?
- with strand of complementary sequence (complementary bases in opposite order)
What can be said about link between stability and G-C contetnt?
- longer duplex with higher G-C content = more stable
- more hydrogen bonds so more stable
How do you find complementary sequence?
- split strand into three base pairs
- write down complementary bases
- reverse the order to give strand in 5’ to 3’ format?
What are main features of DNA double helix? (handed, turn, width, nucleotides per turn, grooves, base stacking distance)
- right handed
- 1 turn = 33A
- width = 20A
- 10.5 nucleotides per turn
- major and minor groove
- base stacking distance = 3.3A
Why is DNA in a double helix?
- negatively charged phosphate groups repel each other so when they are separated there is a reduced electrostatic repulsion
- stacking of nucleobases through hydrophobic/van der Waals interactions compact duplex vertically - removal of water (as water would disrupt hydrogen bonding if bases closely packed) causing hydrophobic collapse and pi stacking
- base pairs hydrogen bond
What are three forms of double helix forms?
When do these usually occur
- A-DNA - right handed - occurs under dehydrated conditions or in hybrid DNA-RNA
- B-DNA (most common) - right-handed - found in cells under physiological conditions
- Z-DNA - left-handed - after DNA has undergone methylation - common in some diseases (Alzheimer’s)
What is triplex DNA?
- where 3rd strand binds in major groove
What is quadruplex DNA?
- 4 strands of DNA around a metal ion
- G-Quadruplex found in telomeres (end of chromosomes)
- protects DNA ends and stop DNA repair systems from treating them as damaged
- allows copying of ends which wouldn’t be possible with 3’ end
What are some examples of tertiary structures of DNA?
- hairpin (small loop)
- stem-loop (large loop)
- Holliday junction
What are some differences between DNA and RNA structures? (sugar, base paid, single or double stranded, use, location)
- DNA contains 2-deoxyribose
- RNA contains ribose
- DNA uses thymine
- RNA uses uracil
- DNA is usually double stranded
- RNA is usually single stranded
- DNA - stores genetic information
- RNA - protein synthesis and gene regulation
- DNA located in nucleus
- RNA located in cytoplasm
Why is ribose more easily hydrolysed than 2-deoxyribose
- further possible hydrogen bonds patterns from extra OH so phosphodiester more easily hydrolysed
What are some RNA structures?
- hairpin
- bulge
- stem-loop
- bubble/interior loop
What is a nucleosome?
- DNA coiled around proteins called histones to produce nucleosomes
- 8 protein units required for each nucleosome
What is a chromosome?
- DNA coiled around proteins called histones to produce nucleosomes which are further packed to produce chromosomes
How is nanotechnology used with DNA?
- predictable sequence-specific hybridisation can be used to create 3D nanostructures for a wide variety of nanotechnological applications
What are the functions of DNA?
- DNA directs machinery of a cell to make specific proteins
- stores the hereditary information of an individual
- has the ability to mutate - allows for new characteristics (evolution)
