Understand the central dogma
DNA -> transcription -> RNA -> translation -> protein
Be able to discuss how genomes are organized in bacteria and eukaryotes
Bacteria: chromosome is a single, double stranded circular DNA molecule (inside of nucleoid). Many also contain one or more smaller circular DNA molecules that are free in the cytosol called plasmids.
Eukaryotes: genes are portioned into chromosomes, the diploid number depending on the species. A human somatic cell ie is 46. Each chromosome contains a single, very large duplex DNA molecule, which vary in length over a 25-fold range. Each chromosome is eukaryotes carries a characteristic set of genes. They also have introns which are non-translated segments of DNA (coding are called exons). Centromeres link the chromosome to the mitotic spindle during cell division while telomeres stabilize the chromosome.
Describe the ways DNA can be effectively packaged in various systems such as virsus, bacteria, and eukaryotes. You should be able to describe differences and similarities across these systems.
Virus: single RNA or DNA molecule in a protein coat, genomes vary in size, circular at some point in their life
Bacteria: stored in plasmids and nucleoid
Eukaryotes: packaged into chromosomes in nucleus, containing 1 large duplex DNA with set of genes. Diploid. Compact
Know what supercoiling is and how/why it occurs
All cells maintain their DNA in a state that is underwound- having fewer right-handed helical turns per given length of DNA than B form, causing structural strain on the DNA that causes it to twist upon itself. Underwinding: thermodynamic strain on the strand, causing supercoiling effect, facilitates the seperation of strands for replication and transcription. It reduces the amount of space DNA takes up so it can be effectively packaged into small spaces.
What is the linking number? What is positive or negative supercoiling?
Linking number is the number of times the twisting strand penetrates a surface. When a molecule is relaxed, the linking number is simply the number of base pairs per turn, which is close to 10.5, so the LK for a 2100bp molecule is 200. If there is a break it is UNdefined.
The degree of underwinding in cellular DNA generally falls in the range of 5-7% or -.05 -0.07.
Supercoiling induced by underwinding is therefore defined as negative supercoiling, whereas DNA that is overwound results in positive supercoiling.
How is supercoiling resolved?
The enzymes that increase or decreases the extent of DNA underwinding are topoisomerases which change the linking number (they play an important role in the processes such as replication and DNA packaging)
Type 1: break one of the 2 DNA strands, passing the unbroken strand through the break, and rejoining the ends changing the Lk by factor of 1.
Type 2: breaks both strands and changes Lk in increments of 2.