Lecture 3 Flashcards
describe dna structure
DNA is composed of an alternating sugar/phosphate backbone Bases are linked to the sugar There are four bases: A = Adenine C = Cytosine G = Guanine T = Thymine Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate deoxyribose backbone of the double helix with the bases pointing inwards
what are purines and pyrimidines and how do they pair in DNA
Purines
- adenine (A)
- guanine (G)
Pyrimidines
- thyamine (T)
- cytosine (C)
Pairing - A : T = 2 bonds - C : G = 3 bonds Base pairing in DNA 
describe DNA replication
Replication of DNA occurs during Interphase. Exact copies of all the DNA on all chromosomes is made.
Base pairing allows each strand to serve as a template for a new strand.
New strand is 1⁄2 original and 1⁄2 new DNA.
describe strands of DNA
Genetic information is carried on only one of the two strands of the DNA. This is the coding strand.
DNA strands have directionality, and the different ends of a single strand are called the “5’ (five prime) end” and “3’ (three-prime) end”
The strands of the helix are anti-parallel with one being 5’ to 3’ the opposite strand 3’ to 5’.
describe the first step in DNA replication
The first step of DNA replication is the breaking of the hydrogen bonds between the bases of the antiparallel strands.
The splitting happens in places of the chains which are A-T rich.
describe DNA replication bubbles
Replication starts by numerous bubbles forming in the DNA as the strands split apart.
The formation of bubbles allows replication to proceed at numerous sites in the DNA molecule, making the process faster.
At each end of the bubble a “replication fork” is formed.The DNA strand that runs from 3’ to 5’ – the 5’ being closest to the replication fork is called the leading strand and the DNA strand that runs 5’ to 3’ is the lagging strand.

unwinding of parental strands
The formation of the fork is under the control of two enzymes topoisomerase and helicase.
Helicase uses energy from the ATP to break the hydrogen bonds holding the base pairs together.
This allows the two parental strands of DNA to begin unwinding and form the replication fork.
Topoisomerase takes up the stress of the unwinding by breaking and then re-joining the phosphodiester bonds.
At each nucleic acid of an unpaired base “single strand binding proteins” are formed to prevent the strand being split up or degraded.
describe replication of a leading strand
Initiation is accomplished using a strand of RNA called a RNA primer, attached to the parental strand at the initiation site.
Two enzymes are involved – primase and α-DNA polymerase.
Primase attaches the primer, and α- DNA polymerase then begins the process of attaching nucleic acids.
α-DNA polymerase is not nearly as processive as δ-DNA polymerase, so once the initiation has been made δ- DNA polymerase takes over and simply adds nucleic acids to the exposed 3’ hydroxyl group of the chain.
δ-DNA polymerase can only build on to the 3’ end of an existing DNA strand, it cannot initiate replication.
The leading parental strand, that which goes from 3’ to 5’, can be transcribed continuously from the initiation point until it meets the next ‘bubble’ along the chain
describe replication of lagging strand
• In the synthesis of the lagging strand, the uncoiling of the helix occurs in the opposite direction to which δ- DNA polymerase works. The process therefore has to be done in pieces, called Okazaki fragments.
• Initiation is accomplished again using a RNA primer, attached to the parental strand at the initiation site.
• Primase adds RNA primers onto the lagging strand, which allows synthesis of Okazaki fragments from 5’ to 3’.
• α-DNA polymerase then begins the process of attaching nucleic acids.
• δ-DNA polymerase takes over until the next RNA primer is reached.
• Each Okazaki fragment requires priming.
• Okazaki fragments are approximately 150 nucleotides long in eukaryotes. They are separated by ~10-nucleotide RNA primers.
• The RNA primers need to be removed.
• This process is dependent on the actions of nucleases. Over the last two decades, several nucleases, including RNase H, flap endonuclease 1 (FEN1) and Dna2, have been implicated as being involved in processing of Okazaki fragments.
• The gap is then filled and proofread by δ-DNA polymerase.
• Flap Endonuclease creates ligatable nicks at the border of Okazaki fragments.
• DNA ligase I connects the Okazaki fragments, following replacement of the RNA primers.
RNA primers are removed, followed by enzyme ligase connecting (ligating) the two Okazaki fragments into one continuous newly synthesized complementary strand.
• Completion of lagging strand DNA synthesis requires processing of up to 50 million Okazaki fragments per cell cycle in mammalian cells.
• Mutations that affect the efficiency of RNA primer removal may result in accumulation of unligated nicks and DNA double-strand breaks. These DNA strand breaks can cause varying forms of chromosome aberrations, contributing to development of cancer that associates with aneuploidy and gross chromosomal rearrangement
1000 bases/second = lots of typos. what does DNA polymerase δ do
- proofreads and corrects typos
- repairs mismatched bases
- removes abnormal bases
- repairs damage throughout life - reduces error rate from 1 in 10,000 to 1 in 100 million base
describe Hereditary nonpolyposis colorectal cancer (HNPCC)
- Associated with mutations in genes involved in the DNA mismatch repair (MMP) pathway.
- MMR eliminates single base mismatches and insertions/deletions that may arise during replication.
- Tumours in Lynch Syndrome are caused by mutations in MLH 1, MSH 2 and MSH 6 genes which are involved in the repair of mistakes.
describe termination of the lagging strand
- Eventually, the last RNA primer attaches.
- But, in order to change RNA to DNA, there must be another DNA strand in front of the RNA primer.
- The RNA primer degrades.
- Because eukaryotes have linear chromosomes, DNA replication is unable to reach the very end of the chromosomes.
- This means that each newly-synthesized DNA strand is shorter at than the equivalent strand in the parental DNA.
- This could be a big problem!
what are tellers
The cell solves this problem by having telomeres at the ends of chromosomes, where they prevent the loss of valuable genetic information by acting as a disposable buffer.
• Thus each of the daughter chromosomes will have a shortened telomere, but not coding information.
• It is estimated that human telomeres lose about 100 base pairs from their telomeric DNA at each mitosis.
• After ~60 mitotic divisions, the telomeres are completely gone (Hayflick limit).
• This is a normal process in somatic cells.
Telomeric ends

explain telomerase becoming mistakingly active
- Telomerase can become mistakenly active in somatic cells, sometimes leading to cancer formation. Increased telomerase activity is one of the Hallmarks of cancer
- Within the germ cell line, which passes DNA to the next generation, telomerase extends the repetitive sequences of the telomere region to prevent degradation.
- Werner syndrome, also known as “adult progeria”, is a rare, autosomal recessive progeroid syndrome (PS), which is characterized by the appearance of premature aging. 1:100,000 births. Accelerated telomere shortening
describe DNA transcription
The synthesis of an RNA molecule from DNA is called Transcription
All eukaryotic cells have five major classes of RNA. 1. Messenger RNA (mRNA)
2. Ribosomal RNA (rRNA)
3. Transfer RNA (tRNA)
4. Small nuclear RNA (snRNA) 5. MicroRNA (miRNA)
The first three are involved in protein synthesis, while the small RNAs are involved in mRNA splicing and regulation of gene expression.
what is RNA and explain coding strands
an important type of nucleic acid that plays several roles in the production of a protein. RNA is necessary to carry the instructions of the DNA out of the nucleus and to the ribosomes
With the exception of T for U changes, the coding strand corresponds exactly to the sequence of the RNA primary transcript, which encodes the protein product of the gene.
