Lecture #2 Flashcards
Nucleotides are the Building Blocks of DNA
DNA: deoxyribonucleic acid
Each nucleotide contains:
- Phosphate group
- sugar
- nitrogenous base
sugars
-DNA
- RNA (one has a hydroxyl group, one doesn't)The Nitrogenous Bases
2 types of bases
- pyrimidines
- purines
Pyrimidine
- Cytosine, Thymine, Uracil
Purine
- Adenine and GuanineCreating a DNA strand
Nucleotides covalently bind to each other through the phosphate group.
- sugar interacts w/ phosphate group at the 3’ and 5’ position.
- strands of DNA exhibit “chemical polarity”
5’ to 3’
Hydrogen bonds create the second strand
Double Stranded DNA
Nucleotides pair with thei rpartner through hydrogen bonds.
-A-T
-C-G (has to do with hydrogen bond pairing)
Creates a complementary strand
- 3’ to 5’
-Cytosine and guanine is more stable b/c of the more hydrogen bonds
Hydrogen bonding creates a planar region
DNA double Helix
DNA molecular twists upon itself to form a helix.
- Right handed helix
- 10 bp/ turn
This conformation is the most energetically stable
- Bases are on the inside
- Sugar/Phosphate backbone
Various proteins interact using the grooves
~2m of DNA per cell
- Nucleus is 5-8 um
DNA is packed into chromosomes
DNA is coiled around proteins and packed into higher ordered structures.
- Humans: 3.2x10^9 nucleotides w/ 24 pairs of chromosomes.
- 22 pairs of autosomal chromosomes; 2 sex chromosomes.
Each cell contains two copies of each chromosome
- maternal and paternal
- homologous chromosomes
chromosome
Chromosome Characteristics
Gene vs non- gene encoding regions Gene recording regions contain the instructions for making a particular protein Non- gene encoding regions -"Junk DNA" - regulatory regions - RNA
Major Regions
Heterochromatin: Highly compacted (gene poor)
Euchromatin: More relaxed (gene rich. more proteins can get in)
Centromere: Constricted region on the chromosome used to attach sister chromatids.
Telomere: sequences of repeating nucleotides located on both ends of the chromosome. (Protect DNA)
Chromosomes can exist in multiple states
Chromosomes change as the cell passes through the cell cycle
Interphase: G1 to G2
-Chromosomes are more relaxed and extended.
Mitosis: Chromosomes are more condensed.
(S)–> chromosomes get replicated
Interphase chromosomes are “relaxed”: Why?
Chromosomes are replicated during the “S” stage of the cell cycle
- Synthesis
Chromosomes replication occurs at replication origins.
-Multiple points
- Why?
Our chromosomes are much longer.
Must replicate quickly
Mitotic vs. Interphase chromosomes
Chromosomes entering mitosis are highly condensed
- All chromosomes closer together, and easily divided at this point.
Sister chromatids held together by centromeres.
Easily separated into different cells.
Technique to visualize chromosomes
Karyotyping: Display of the 46 human chromosomes
Staining
- Giemsa: works (reacts) better w/ A and T’s b/c they are not as strong.
- Dark and light banding
- The banding for each chromosome is unique.
Painting
- Make probes for specific chromosomes regions.
- Label probes w/ flouresent dyes
- View the chromosomes through a flourescence microscope.
Technique to visualize chromosomes part 2
Painting can be done when cell is in interphase or Mitosis
Interphase chromosomes occupy discrete regions within the nucleus
- Attached to the nuclear envelope.
How are chromosomes compacted?
Nucleosomes are basic unit of chromatin compaction.
- Less compacted form of chromosome
- DnA + proteins
147bp of DNA wrapped around an 8 proteins called histones.
- 2 copies of H2A, H2B, H3 and H4
- H1 histones link nucleosomes together
Histones: building blocks of the nucleosome
H2A, H2B, H3 and H4
- 2 copies of H3 and H4 form a tetramer
- one copy of H2A and H2B form a dimer
Highly basic (positively charged)
pH lysings and argenins
pH 7--> (+) charged neutral
Interact with DNA (negatively charged)
sugars--> nutral
Nitragenous base--> neg.Why does the packaging need to be dynamic?
Changes in the nucleosome structure allows access to DNA.
Chromatin Remodeling Complexes
- ATP dependent; needs multiple cycles of ATP hydrolysis.
- Acts to reposition and partially de-condense the chromatin
- Some are deactivated during mitosis; Why is this a good idea?
So the job can get done.
Why does the packaging need to be dynamic part 2
Protein Modifications (Post-translational Modifications) - Small chemical groups or proteins attached to a protein after translation has occured.
Modifications
- Acetylation
- Methylation
- Phosphorylation
- Ubiquitination
Small protein
76 amino acids
found in most Eukaryotic cell
Protein modifications affect nucleosome stability
Protein modifications can alter histone function, nucleosome stability and histone-protein interactions.
Histones are modified on their N (closest to amino group) and C termini (closest to carboxyl group)
Different patterns of modifications yield different outcomes.
Modifications affect higher order packing more significantly than individual nucleosome stability
- small disturbances vs. large alterations - chemical groups vs. small proteins
Protein modifications affect nucleosome stability Part 2
Modifications can either de-stabilize (relax) or stabilize (condense) nucleosomes
- Methylation of histones generally leads to gene silencing.
- Ubiquitination of H2B generally leads to gene activation
- Ubquitination of H2A generally leads to gene silencing.
Chromosomes contain relaxed and condensed regions
-Regions of euchromatin are usually gene rich and expressed.
- Regions of heterochromatin are usually silenced.
- 10% of interphase chromosome
- Take up Giemsa stain more readily (easily stained)
- Some regions are permanently silenced.
X- inactivation
Why does it matter?
Gene expression
Changes in chromatin structure can be inherited
Epigenetic Inheritance
- “Epi” in greek means “on”
- superimposed on genetic inheritance based on DNA.
During mitosis each daughter cell receives 1/2 its DNA from the parent cell
- Inherits the nucleosome condensed chromosome
The daughter cell has a copy of the modification made in the parent cell
- DNA and histone
Upon replication the daughter cell “remembers” the modifications.
