DNA structure and replication

Which bases are purines?

A & G

Which bases are pyramidines?

C, T, U

what is a purine structure

nitrogen 9- joins to another molecue  - pic

what is a pyrimidine structure

• nitrogen 1 - the region that connects to other parts 

• pic

What is a nucleoside?

Base + sugar

What is a nucleotide made of ?

1. nitrogenous base 

2. pentoose sugar 

3. 1/2/3 phosphates 

. What is a monophosphate nucleotide

Base + sugar + phosphate

what are 2 types of sugar in nuceloutides

• ribose ( RNA)

• deoxyribose (DNA)

what is the structure of ribose and deoxyribose

what is the structure of phosphate

pink

what are the bonds ( where known) and between what that makes the nucleotides

• base + carbon 1 of sugar - join with glycosidic bond 

• phosphate + carbon 5 of sugar - phosphorylated with kinase 

• 2 more phosphate join

Which group forms the 5' end of a nucleotide and which group forms a 3' end?

5' - phosphate group
3' - hydroxyl group

how does Nucleic acid strands have polarity

• its polarity in direction 

• 5' is when carbon 5 of the last sugar on one side is bound to phosphate 

• 3' is when carbon 3 of the last sugar on the other side is bound ot a hydroxyl group 

Which bases bind to which via hydrogen bonding

A-T
C-G

How many H-bonds are there between A-T and C-G? 

A-T: 2
C-G: 3

what direction is the hydrogen bond betwee the bases in comparision to the helix

perpindicular

What does anti-parallel binding of DNA mean

The 3' end of one strand is bound to the 5' end of the other. 

What are the two grooves in the DNA double helix called

• Major and minor groove

explain the structure of DNA overall

1. its made of repeating nucleotides 

2. the nucleotides are joined with 5'3' phosphodiester bonds 

3. hydrogen bonds between the bases makes a double strand 

4. they make an antiparallel spin 5' and 3' are paired 

5. the 2 chains coil making a double helix

is DNA a right or left helix

right - twist clockwise 

how many nucleotides per turn on DNA

10

how long is one turn and whats the helix diameter

length: 3.4nm 
diameter: 2nm

describe linear DNA and where is it found

• double stranded 

• long

• bound to protein to make chromatin 

• found in eukaryotes chromosomes 

• in nucleas

describe circular DNA and where is it found

• single strand 

• super coiled ( the helix coils again)

• in prokaryotes, makes nucleotied can have plasmids 

• found in plant chloroplast 

• eukaryotes mitchondria 

what are chromosomes

chromotin- DNA and protein (histone)  is packed into nuclosome then condensed into chormosomes, done by supercoiling 

how and when was DNA discovered

• between 1944 and 1952 

• expirements with bacteria and virus showign DNA was genetic material 

what 2 sets of data where used to find out the structure of DNA

1. xray diffraction 

2. base composition analysis of hydrolysed DNA samples

what is X ray diffraction

firing x rays on purified crystalised DNA showing its a helix structre

what is chargaffs rule

• studying the base compotision in DNA 

• A - T and C- G had similar compositions in all organisms 

What is the genome?

The entire set of genes in the chromosomes of an organism. 

what are the 2 ways genetic info can be transfered

1. inheritence - passing gentic info from 1 cell to another through DNA replication DNA-DNA

2. expression - expressing the gentic info through protein synthesis DNA- RNA

highly conserved meaning

sequences for gene has few mutations between species as major change is harmful

What is the name of the temperature at which one half of the helical structure is lost?

Melting temperature (Tm)

Where does DNA replication take place?

Specialised regions of the nucleus with a cluster of proteins

overview of DNA replication

1. hydrogen bonds break the Double Strand unwinds 

2. 2 templates made

3. free nucleotides do complpementary base pairing 

4. it twist to a helix

5. semi conservitive as it has one parental and one daughter strand

Why is the DNA double helix only unzipped a little bit at a time during DNA replication?

To prevent mutations

what is a replication fork

the point on the double helix where the new strands are being formed, there are 2 sides to the strand

Which direction does DNA synthesis occur?

5' to 3' end

What does helicase do?

Unwinds DNA into 2 strands by breaking hydrogen bonds between the bases

rWhat does topoisomerase do?

Releases supercoils in DNA - when the DNA double helix spins on itself 

What are single strand binding proteins? (SSBs)

Tetramers ( protein made of 4 subunits)  that bind to single stranded DNA so it cannot bind to another strand and remakign the helix during DNA replication

What is primase?

An RNA polymerase that makes short RNA primers. 

What is a primer?

A short nucleic acid sequence that provides a starting point for DNA synthesis. 

can DNA polymerease start its own strand

no, it needs primers

What does DNA polymerase do

Synthesises DNA by adding nucleotides to sugar-phosphate backbone. It has proof-reading ability. 

What does the sliding clamp do?

It helps DNA polymerase hold onto the strand its copying. 

What does RNaseH do?

Removes RNA primers after the DNA polymerisation is finished extending the fragment

What does DNA ligase do?

Forms phosphodiester bonds between nucleotides to form a long strand. 

Which strand in the replication fork is replicated continuously?

Leading strand

Which strand in the replication fork is replicated discontinuously

Lagging strand

What are the names of the short fragments produced in the lagging strand during DNA replication

Okazaki fragments 

how are the 2 chains on the replication fork replicate simultanously

• dna polymerease works from 5'-3' but one strand is 3' to 5' direction

• so there is discountious replication in the lagging strand with fragmented nucleotides 

pic

what happens to the gaps between the okazaki fragemnts

• each okazaki fragemnt has primers which are removed

• free nucleotides join 

• DNA ligase makes phosphodiester bonds joining them

how mnay mistakes does DNA polymerease III make

1 mistake for every million nucleotides

how is a new daughter strand made after the template strand is exposed

1. Single Strand Binding proteins (SSB) bind to the single stranded DNA to stop the two strands from annealing 

2. the enzyme primase, synthesis RNA primers that bind to the strand

3. DNA polymerease adds complementary nucleoties (dNTPS) startign from 5'-3' makign the lagging and leading strands

4. 1 pyrophosphate ( 2 phosphates) is released per dNTPS that joined 

5. DNA polymerease uses exonuclease activity to proof reading frm 3' to 5' to make sure its correct nucleotides

6. after DNA synthesis the RNA is removed

what are telomeres

• Telomeres: tandem repeats (GGGTTA in humans) at chromosome ends

• Functions:

  • Prevent chromosome fusion

  • Solve DNA replication end problem → telomerase adds repeats so important DNA isn’t lost during division

What is random assortment of maternal and paternal chromosomes?

• During metaphase there is random assortment if their chromosomes which help with genetic variation

simple explination of the stages of the cell cycle

1. G0- when the cell isnt dividing 

2. G1- growth, cell gets ready to synthesise DNA

3. S- DNA replication, its synthesised 

4. G2- contunued growth, proteins made for mitosis

5. M - mitosis 

summary

all definitions

• 
  primase: RNA polymerase that makes short RNA primers.

•  melting temperature: temp when hald of the helican structure is lost

• SSB: stop the 2 strands from annealing 

• RNA primers: bind to start of dna so that dna polymerease can work 

• DNA polymerase: add the nuclotides, uses exonucleas activity to proof read

• dNTPS: nucleotides

• okazaki fragment: short pieces of nucleotides on the lagging strand

• DNA ligase: make phsophodiester bonds between nucleotides 

• helicase: unzips the 2 strands 

• RNaseH: remove RNA primers 

• slding clamp: helos dna polymerease hold onot the strand its copying

• topisomerase: make a supercoil 

• nucleotide: sugar phsophate base

• nucleoside: sugar base