Session 4 ILO's - DNA Flashcards
Appreciate the vast amount of DNA information available in a cell nucleus
- DNA has to be tightly packed in the nucleus because:
- On average, each cell contains 2 Metres of DNA, which fits into a 6 micrometre cell
- Each cell contains 1 copy of all the genes in the body, although they are not all activated within each cell
How many chromosomes does a human have?
- Each cell normally contains 23 pairs of chromosomes, for a total of 46 chromosomes.
- 22 of these pairs are called autosomes (look the same in both males and females).
- 23rd pair (the sex chromosomes) differ between males and females (males = XY, females = XX)
Describe how eukaryotic DNA is packaged into chromosomes/Describe how DNA is packaged into a cell
DNA wraps around histones to form nucleosomes, which are the beads of ‘beads on a string of DNA’. Nucleosomes can tightly pack together to form 30 nm fibres. These fibres and beads on a string are the ‘decondensed forms’ of a chromosome. Chromosomes can condense much further looping the 30 nm fibres
In the highly condensed form chromosomes display their classical ‘chromosome shape’. This X-shape is a chromosome in replicated form; it consists of two identical chromatids; each chromatid has one double-stranded DNA molecule
Outline the relationship between the DNA double helix, chromatin, chromosomes, genes, genomes and the GATC letters in a DNA sequence
- Each chromosome is one extremely long molecule of DNA, which can contain hundreds and thousands of different genes
- Chromosomes can exist in 2 states - a replicated and unreplicated state
Describe and recognise the structural components of nucleic acids
- Nucleic acids are either DNA or RNA and are polynucleotides
- Nucleotides are made up of 3 components:
1. Pentose sugar
2. Base (A, G, C, T, U (Uracil is only found in RNA))
3. Phosphate group
Describe and outline the primary, secondary, tertiary (and quaternary structure of DNA)
Primary structure:
Long chain of nucleotide monomers, joined by phosphodiester bonds
Secondary structure:
Hydrogen bonds (either 2 or 3 bonds) between complimentary base pairs - DNA strands formed are anti-parallel and complimentary
Tertiary structure:
Right handed double helix with anti-parallel strands (with major and minor grooves) - helix held together by the stacking of the base pairs with Van de Waals forces plus the hydrogen bonding between pairs
Outline the quaternary structure of eukaryotic DNA
The large shapes and structures that can be made by nucleic acids e.g. the core histones forming the histone octomer then forming the NDA and forming the ‘beads on a string’ nucleosome array
Compare and contract DNA and RNA
DNA = Deoxyribonucleic acid (bases: A, C, G, T)
RNA = Ribonucleic acid (bases: A, C, G, U)
DNA is double stranded, RNA is single stranded
DNA has an H group on the 2nd carbon, RNA has an OH group on the 2nd carbon
Describe the relationship between DNA sequences, DNA molecules, chromatin and chromosomes
COME BACK TO
DNA sequence forms an alpha helix, which then forms ‘beads on a string’ formation with histones, which can then be further condensed to chromatin, which is then further condensed to chromosomes (only in the process of division i.e. mitosis/meiosis)
Outline and explain the processes occurring at a DNA replication fork
Describe the structure of the DNA double helix
In the genetic code GATC, which bases are purines and which are pyrimidines?
Purines: G & A (Guanine and Adenine)
Pyrimidines: C, T & U (Cytosine, Thymine and Uracil)
Combinations:
G = C
A = T
A = U
Which bonds hold the DNA molecule together?
Phosphodiester Bonds?
Describe DNA replication in eukaryotes in broad detail (steps, which
general enzymes are involved, copying of leading strand and lagging strand; Okazaki fragments)
3 Steps:
Initiation
Elongation
Termination
Describe the initiation step of DNA replication in prokaryotes
- The origin of replication is first recognised
- This looks like a small bubble
- You have 2 replication forks which are going to move in opposite directions
- Initiation requires recruitment of DNA polymerase and other specific proteins
- In order for the process to start, it needs to be kick started by another Enzyme called Primase (are DNA polymerase can only extend a 3 prime end)
- The primase generates a small RNA primer - a small RNA template, which the DNA polymerase can bind to, and it will then move along the DNA template strand, and copy it
Describe the elongation step of DNA replication in prokaryotes
Elongation:
- Replication forks move in opposite directions, copying the DNA
- DNA helicase unwinds the DNA double helix
- DNA polymerase extends 3’ ends only, leading to a leading strand (a continuous copy of the template, which will then be translated into a protein). In parallel, a second lagging strand is also copied, and this is a discontinuous process, and Okazaki fragments are formed (later in lecture describes what these are)
- DNA ligase joins the fragments
Describe the termination stage of DNA replication in prokaryotes
Termination:
- When 2 replication forks meet, an enzyme called DNA ligase joins the final fragments together
- At this point, we have an exact copy of the original circular chromosome, so
Occurs when each of the Okazaki fragments have fused together i.e. one chromosome = one DNA molecule
Describe the main functions of the enzymes involved in the process of DNA replication
- DNA primase
- ‘kick start’ DNA replication, specifically initiation
- Makes short RNA primer, which permits DNA polymerase to bind, and start copying the chromosome.
(makes very short sequences of RNA to allow DNA polymerase to work)
- DNA polymerase - slides along the single strand template of DNA reading its nucleotide bases as it goes along and inserting new complementary nucleotides
- DNA Helicase - unwinds/unzips DNA ready for DNA polymerase
- DNA ligase - joins together Okazaki fragments of the lagging strand by forming a bond between the phosphate group of one strand and the deoxyribose group on another
Describe what is meant by semiconservative replication
Means that half of the DNA is kept from the original template i.e. is conserved!
Describe DNA replication in prokaryotes in broad detail
- Prokaryotes have a single, circular chromosome
- DNA replication starts at the ‘origin of replication’ or origin, which is a point on this circular chromosome
- 3 steps - initiation, elongation, termination
- Studying DNA rep in prokaryotes helps you understand that of eukaryotes
What is DNA?
A double helix with a sugar phosphate back bone
What is the genetic code made up of?
4 Base pairs - Adenine, Thymine, Guanine and Cytosine
How is DNA packaged in a cell?
By wrapping around histone proteins and further coiling
What does DNA replication in prokaryotes involve?
A single origin of replication
Compare DNA replication in eukaryotes to DNA replication in prokaryotes
DNA replication in eukaryotes is more complex
Very very briefly summarise what DNA replication in eukaryotes consist of
- Multiple replication bubbles
- Leading strand and lagging strand
- Okazi fragments
Compare DNA replication in eukaryotes compared with prokaryotes
- In eukaryotes, DNA is linear and much larger
- In prokaryotes, DNA is circular and much smaller
- Because chromosomes are linear and larger in eukaryotes, they are copied in parallel, so …
- …Multiple origins of replication are formed at the same time, making replication bubbles - see image
- The replication forks (the ends of these bubbles) move towards each other, so that the chromosome can be copied in parallel
Describe the first step of Eukaryotic DNA replication
Initiation:
- In order for the process to start, it needs to be kick started by Primase (as DNA polymerase can only extend a 3 prime end)
- The primase generates a small RNA primer ( a small RNA template, which the DNA polymerase can bind to), which permits DNA polymerase to bind to the template strand
- DNA polymerase will bind at the 3’ end of a strand within the origin
What are the 2 sides of the unwound DNA helix called? Explain each one
- The leading strand - the coding strand of DNA, which is used to produce the amino acid sequence coding for a protein
- The lagging strand - the opposite complementary strand, bound in the antiparallel orientation
Describe the second step of Eukaryotic DNA replication
Elongation:
- DNA polymerase moves along the leading strand, from 3’, towards the 5’ end, copying it, making a new copy of DNA
- In parallel, a second DNA polymerase binds to the 3’ end of the lagging strand, which is much shorter
- The lagging strand is copied in a series of short fragments, called Okazaki fragments.
- This occurs because the DNA is still being unwound as the lagging strand is copied
- DNA ligase stitches the Okazaki fragments together so that you have a complete copy of the lagging strand
- The newly formed DNA is wound up into a helix, leading to perfect copies of the original DNA, as nice, would up helix
Describe the third step of Eukaryotic DNA replication
Termination:
- Eventually, the two or more replication bubbles meet
- The replication forks move along the molecule, unwinding them
- As they meet, the whole molecule will separate into 2 fragments, and ligase will stick together the different pieces of DNA
- Two stands of DNA have been produced
