Lecture 1: DNA Chromosomes and Genomes 1 Flashcards
What are genes?
The information-containing elements that determine the characteristics of a species.
Look over S strain and R strain experiment that was used to discover that DNA carried the hereditary information.
Keep Working Hard
What type of linkage are nucleotides joined together by?
phosphodiester linkage between 5’ and 3’ carbon atoms to form nucleic acids
Polynucleotides have a polarity, what are they?
- 5’ phosphoryl end
- 3’ hydroxyl end
** remember: read strand 5’ to 3’ **
What is a nucleotide?
A 5-carbon sugar and nitrogenous base covalently linked via a glycosidic bond.
- sugar in DNA is deoxyribose
- adenine, cytosine, guanine, and thymine are bases
How many base-pairs make up 1 turn of the double helix strand?
1 turn every 10 base-pairs
What does antiparallel mean?
antiparallel -> each strand’s sequence is complementary to its partner.
Which 2 nitrogenous bases are purines?
- adenine
- guanine
Which 2 nitrogenous bases are pyrimidines?
- cytosine
- thymine
How many hydrogen bonds are between guanine and cytosine pairs? How about adenine and thymine pairs?
- Adenine pairs with Thymine = 2 H-Bonds
- Guanine pairs with Cytosine = 3 H-bonds
What does genome reger to?
Genome -> a complete set of information in an organism’s DNA.
True or False:
At replication, the entire genome must be duplicated and passed to the daughter cell.
True
What two things did the discovery of the structure of DNA provide a mechanism for?
- complimentary strands allow the genome to be replicated
- each strand serves as the template
True or False:
Each chromosome is a single long linear DNA molecule associated with proteins that fold and pack it into compact structure.
True
* similar to packing 24 miles of thread into a tennis ball *
What does chromatin consist of?
DNA + Protein = Chromatin
Which two cell types does not contain two copies of each chromosome (maternal and paternal homologs)?
- Germ Cells
- RBCs
How many nucleotides and chromosomes is the human genome composed of?
The human genome is 3.2 x 10^9 nucleotides distributed over 24 different chromosomes.
What type of chromosomes make up the 46 total chromosomes in a normal phenotypic person?
- 22 pairs of autosomes and 2 sx chromosomes
- 46 total chromosomes
Which type of stain is used in cytogenetics laboratories for karyotype analysis of chromosomes?
Giemsa Stain
What is giemsa stain used for in cytogenetics laboratories?
- the banding pattern can be seen with Giemsa stain under light microscopy
- allowed chromosomes to be identified and numberd
Other than using Giemsa stain, what other cytogenetic technique can be applied to distinguish chromosomes apart?
Whole Chromosome Painting
What is whole chromosome painting useful for?
Useful for looking at translocations (an abnormal recombination event).
What type of chromosome and disease does the translocation of chromosomes 9 and 22 result in?
- Philadelphia Chromosome
- Commonly found in chronic myelogenous leukemia
- BCR-ABL fusion gene
What information is found on chromosomes?
- Genes
- encoding proteins
- encoding RNA molecules
- Interspersed DNA that does not contain genes
- regulatory information
- “Junk” DNA
About how many genes code for proteins in the human genome?
21,000
What is the largest number of exons per gene in the human genome?
178
What is the smallest number of exons per gene in the human genome?
1
About what percetage of a gene comprises a coding region? Also, what percentage of that is transcribed, but not translated?
5%
- 1.5% is percentage of DNA sequence in exons (protein-coding sequence)
- 3.5% percentage of DNA in other highly conserved sequences
- transcribed, but not translated
What happens to chromosomes during interphase?
Chromosomes are replicated; they are decondensed and can’t be easily distinguished.
What happens to chromosomes during mitosis?
They become highly condensed and separated into two daughter nuclei.
What are the three requirements in order to be a chromosome?
- A copy must be passed on to each daughter cell at division: requires replication, separation of copies, and partitioning to daughter cells.
- DNA replication origin: where duplication of the DNA begins.
-
Centromere: allows one copy of each duplicated and condensed chromosomes ot be pulled into each daughter cell when the cell divides.
- The kinetochore protein complex attaches to the centromere.
- Telomeres: at the ends of a chromosome, contain repetitive sequences that enable the ends to be efficiently replicated.
How much more condensed are mitotic chromosomes than interphase DNA?
500 times
What type of DNA binding proteins are involved in forming chromosomes?
Histones and non-histone chromosomal proteins.
What is a nucleosome?
The most basic unit of chromosome packing is the nucleosome.
- chromatin isolated directly from interphase nucleus forms 30 nm thick thread
- if partially unfolded it forms “beads on a string” (string = DNA; beads = DNA wound around histones)
How does digestion of DNA by nucleases work?
Digestion with nucleases break down DNA by cutting between nucleosomes and degrading the exposed DNA between nucleosome core particles (linker DNA).
How many histone proteins does each individual nucleosome core particle consist of?
8 Histone Proteins (histone octamer) and 2X stranded DNA that is 147 nucleotide pairs long.
What sub-units compose a histone octamer?
2 molecules each of H2A, H2B, H3, and H4
About how many nucleotide pairs long do nucleosomes repeat?
Repeat every 200 nucleotide pairs or so.
What are histones?
Histones are small proteins with common structural motif called histone fold.
True or False:
A high resolution structure of nucleosome core particle is disc-shaped with DNA wrapped 2.0 turns.
False - high resolution structure of nucleosome core particle is disc-shaped with DNA wrapped 1.7 turns.
What regulation is controlled by covalent modifications on the N-terminal amino acid tail that extends out from the nucleosome core particle?
Important for chromatin regulation.
How many hydrogen bonds are formed between DNA and the histone core in each nucleosome?
142
What type of interactions are there between DNA and histones?
- hydrogen bonding
- hydrophobic interactoins
- salt linkages
True or False:
Histones are highly conserved, and thus, most canges would be lethal.
True
** there are only 2 differences between pea and cow H4**
What do histone tails function to do?
Histone tails help to condense chromatin.
- histone tails are largely unstructured, suggesting that they are highly flexible.
- tails can form interactions with adjacent nucleosomes
What does the histone subunit H1 do?
changes the path of the DNA as it exits the nucleosome
What are the characteristics of histone H1?
- linker histone
- larger than other histone proteins
- also less well conserved
- contacts both DNA and protein
- changes the path of the DNA as it exits the nucleosome
True of False:
Nucleosomes are in a constant state of flux.
True
*DNA is unwrapped in the nucleosome 4 times per second, and remains unwrapped for 10-50 milliseconds before tightening up again*
What do chromatin remodeling complexes allow for?
Further loosening of DNA/histone contact.
What changes the structure of the nucleosome temporarily, making DNA less tightly bound?
The ATP-dependent chromatin remodeling complex.
Look over the chromatin remodeling mechanism to understand how the DNA is made available to other proteins in the cell.
What does the proposed zig-zag model explain?
Nucleosome Packing
- stacking may be facilitated by histone tails (esp H4)
- histone H1 “linker histone” is present in 1:1 ratio with nucleosome cores
** forms a dense fibrous structure with a diameter of 30 nm **
