Lecture 1: DNA, Chromosomes, and Genomes Flashcards
A DNA molecule consists of…
Two complementary chains of nucleotides.
What makes up a nucleotide?
Each nucleotide contains a 5 carbon sugar (deoxyribose), a phosphate, and a base.
Describe how nucleotides are linked together to form DNA.
The nucleotides are covalently linked into a polynucleotide chain (a DNA strand) through the sugars and phosphates, forming a “backbone.” A DNA strand has its chemical polarity (5’ and 3’). A DNA molecule is composed to two DNA strands held together antiparallel by hydrogen bonds between the paired bases. This results in the double helix structure of DNA.
Which base is this?
adenine
Which base is this?
cytosine
Name some physical properties of Nucleosides and Nucleotides.
- Very soluble in water
- Nucleobases and nucleosides are uncharged at biologically relevent pH’s
- Nucleotides carry negative charge at physiological pH
- Nucleosides and nucleotides are relatively stable over a wide range of pH’s
- Purine and pyrimidine bases absorb uv strongly at 260 nm
Explain the structural properties of Nucleosides and Nucleotides
- The five membered ring in pentose sugards is very flexible
- The rings are not co planar and two of the atoms twist outside of the plane
- Due to the substitution patterns in nucleosides, two conformations are preffered
- This “sugar puckering” is defined by the 2’ and 3’ carbons above the plane and are known as C2’-endo and C3’-endo conformations
- These two conformations are in rapid flux in solution
Draw the C-2 Endo Formation. What kind of molecule is it preffered in?
Draw the C-3 endo formation. Where is this preferred?
Define the term genome
The complete set of information in an organism’s DNA
Is anti or syn conformations preferred in purines and pyramidines?
Anti is preferred in both. SYN doesn’t even exist for pyramidines. It does exist in purines, but syn is preferred. It is due to steric hindrance in both cases.
What does semi-conservative replication mean?
It means that one template strand from the parent will be encorporated into each daughter cell
What does “c value” mean?
C value is the genomic content. Plants have very large c values
Define the term “karyotype”.
Karyotypes describe the number of chromosomes and how they look under a microscope. Attention is paued to their length, position of centromeres, banding pattern, difference between sex chromosomes and physical characteristics.
For humans, roughly how many nucleotides do we have? And how many chromosomes?
Humans: 3.2 x 10^9 nucleotides
46 chromosomes total (22 pairs and then X + Y in males or two X’s in Females)
During which phase of a cell during a eukaryotic cell cycle is there a lot of gene expression? When does DNA replicate itself?
Interphase is where there is a lot of gene expression. Interphase is also where DNA gets replicated.
Each DNA molecule that forms a linear chromosome must contain which elements? In other words, what are the DNA sequences reaquired to produce a chromosome that can be replicated and then segregated?
Two telomeres, a centromere, and a few origins of replication
Explains nucleosomes as the classic “beads on a string”. What does a nucleosome include? How do you break down the linker DNA? If you break down it even further what are the components? (HINT: think of the flowchard from lecture)
Explain how nucleosomes can be very dynamic.
Nucleosome is dynamic when it opens, allowing for DNA binding proteins.
Through ATP hydrolysis, nucleosomes can be slid downstream by ATP-dependent chromatin remodeling complexes.
Explain how the following picture relates to position effect.
In chromosome breakage and rejoining events, the zone of silencing (where euchromatin is converted to heterochromatin) spreads for dirrerent distances in early embryos. These distances are then passed down (once heterochromatic condition is established on chromatin it is inhereited by all progeny. The white gene in flies creates red pigment. White+ aka normal flies have all red eyes. In flies where a normal white gene has been moved near a region of heterochromatin, the eyes are mottled. The presence of red/white patches reveals that the state of transcriptional activity, as determined by the packaging of the gene into chromatin can be passed down/inherited.
We can regulate chromatin structure and gene expression by modifying which parts of histones?
What are the four covalent modification examples?
Modification of the core histone tails regulates chromatin structure and gene expression.
Four examples of covalent modification: Acetylation, Methylation, Phosphorylation, Ubiquination
Remember: Acetylation generally means activation/opening up for transcription
Methylation generally causes in activation
What two kinds of complexes can spread chromatin changes along a chromosome?
Reader-Writer Complexes and ATP-dependent chromatin remodeling proteins
What do barrier DNA sequences do? Also, what are their three main courses of action?
Barrier DNA sequences block the spread of reader-writer complexes.
Mechanism of Barrier Action:
A. Tethering a region of chromatin to nuclear pore complex
B. Tight binding of barrier proteins to nucleotides
C. Recruiting group of highly active histone modifying enzymes to erase histone markers
Which base is this?
thymine
Which base is this?
Guanine
