DNA and Chromosomes Flashcards by Chris Idone

What are the relative amounts of T/A and G/C in the genome?

50/50

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How can you distinguish DNA from RNA (dNTPs from NTPs)?

DNA:
• Sugar is deoxyribose
• Double-stranded
• Oxygen removed from 2’ carbon (H bound to 2’)

RNA:
• Sugar is ribose
• Single-stranded
• Hydroxyl group (OH)

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How can you distinguish pyrimidines from purines?

• Pyrimidines: one ring (thymine, cytosine)

• Purines: two ring (adenine, guanine)

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(1) How do histone interact with DNA to form chromatin? (2) Is this interaction sequence specific?

(1)
• Histones - positive charge
• DNA - negative charge
• Opposites attract
• Nucleosome - complex of DNA and protein
• Nucleosome —> solenoid —>

(2) No. Protein can interact with DNA in general (i.e., general interaction)

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What is the difference between heterochromatin and euchromatin?

Heterochromatin:
• highly condensed
• Compact form of chromatin
• Concentrated in centromeres and telomeres
• Prevents gene expression (silenced genes)

Euchromatin:
• Less condensed
• Active genes

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What are the differences between bacterial and eukaryotic chromosomes?

Bacteria:
• Circular structure (no centromeres or telomeres)
• Relatively small genomes
• No chromatin
• Not contained in a membrane compartment
• Replicated chromosomes segregated through binary fission

Eukaryotes:
• Multiple linear chromosomes (have centromeres and telomeres)
• Relatively large genomes
• Contains highly organized and regulated chromatin structure
• Contained in an enveloped membrane compartment (nucleus)
• Replicated chromosomes segregate via a microtubule-based spindle

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Describe Griffith’s experiment. What did it demonstrate?

• Two strains of Streptococcus pneumoniae: S strain (pathogenic strain) and R strain (harmless strain)

• Found that

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What are the functions of replication origins?

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What are the functions of centromeres?

Allow duplicated chromosomes to be separates during M phase

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What are the functions of telomeres?

• Contain repeated nucleotide sequences required for replication and protection of chromosomal ends

• Serve as a protective cap

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How do these chromosomal regions compare between prokaryotes and eukaryotes: replication origins, centromeres, and telomeres

Prokaryotes:
• Only 1 replication origin
• No centromeres or telomeres

Eukaryotes:
• Multiple replication origins
• Has one centromere and two telomeres

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What is chromatin remodeling? Why is it important?

Chromatin-remodeling complexes:
• Catalyzes nucleosome sliding (pulls on DNA of its bound nucleosome and loosens its attachment to histone octamer)

• Use ATP hydrolysis to pull on nucleosomal DNA, loosening its grip around histone

• change position of DNA wrapped around histones

• allows (or prevents) different proteins access specific regions of DNA

Important for:
• Gene expression
• DNA replication
• DNA repair

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How can histones be modified to activate gene expression? Inhibit gene expression? In general, where do these modifications occur on the histone subunits?

Activate - acetylation (e.g., acetylation at K4)
• Acetylation opens chromatin (promotes gene expression)
• Acetyl groups neutralize + charge on histone tails

Inhibition - Methylation (e.g., methylation at K9)
• Silenced
• Lushes into heterochromatic state

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How is the genetic code expressed?

4-letter nucleotide alphabet of DNA is converted to 20-letter amino acid alphabet of proteins

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What are karyotypes useful for?

• Identifying individual chromosomes
• Keeping track of chromosome number
• Identifying large deletions and translocations

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How chromosomes arranged in a karyotype?

Arranged from large to small:

Chromosome 1 (largest) —> chromosome 22 (smallest)

Karyotypes are generated from mitotic chromosomes. Why?

Chromosomes would not be visible if they were interphase chromosomes

What is a genome?

Complete set of chromosomes present in a cell or organism

T or F: a genome always reads 5’ to 3’

True

Genes can be located on either strand of DNA (coding) strand. What is the other strand called?

Template strand

How do genes differ in different organisms?

• Genes are closely packed in yeast genome

• Genes are more spaced apart in higher organisms (e.g., humans)

Compare interphase and mitotic chromosomes.

Interphase:
• Not randomly distributed
• Occupy distinct location within nucleus (anchored in nuclear membrane or lamina)
• Prevents chromosomes from getting entangled
• Interact with nuclear envelope
• Chromosomes inhabit certain locations in nucleus

Mitotic:
• Highly condense/compact
• Not anchored (need to be segregated during mitosis)

What is the nuclear lamina and what is it composed of?

• Cytoskeleton of nucleus
• Intermediate filaments

Nucleolus

• Electron-dense
• Where ribosomal RNA is made/synthesized
• Where ribosomal genes are
• “Factory for making ribosomes”

Nucleosome

DNA + histone protein (basic unit of chromatin structure)

Why would salt make histone dissociate from correspond DNA? (How so you get histones to dissociate from DNA?)

Histones tend to have positive charge (allows snug interaction with DNA (negative charge)) High salt competes with positive and negative charges

Is histone-DNA interaction sequence specific?

• No, protein can interact with DNA in general • General interaction • Not specific sequence

Where would you see a histone-DNA specific interaction (sequence specificity)?

Transcription

Explains the levels of compaction.

1. Naked DNA - Simplest level of compaction (no compaction) 2. 10 nm fiber (first level of compaction); “beads on a string” 3. 30 nm fiber (solenoid) 4. 250 nm 5. 700 nm 6. Mitotic chromosomes - most compact form (1400 nm)

What is H1 and is its function?

• Linker histone • Changes path of DNA as it exists from nucleosome (Helps compact nucleosomal DNA)

T or F: chromatin-remodeling complexes are inactivated during mitosis

True

What are examples of histone modifying enzymes?

Kinases, methylases, and acetylases

T or F: Interphase chromatin is not compact.

F: interphase chromatin is compact, but is about 20X less condensed than mitotic chromosomes

What are histone-modifying enzymes?

Enzymes that catalyze chemical modification of histones

Histone tails are subject to the following covalent modifications:

1. Addition/removal of acetyl group 2. Addition/removal of phosphate group 3. Addition/removal of methyl group

T or F: interphase chromosomes ONLY contain euchromatin.

F: Interphase chromosomes contain BOTH heterochromatin and euchromatin

Heterochromatin make up about _____% of interphase chromatin.

Describe the experiment done by Avery, MacLeod, and McCarty

• Aimed to identify molecule responsible for bacterial transformation in Griffith’s experiment • Used molecules such as RNA, protein, DNA, lipid, and carbohydrates • Demonstrated that DNA was the transforming principle that transformed R strain to S train

Explain the Hershey and Chase Experiment

• Studied T2 (virus that infects and destroys E. coli; made entirely of protein and DNA) • Radioactive phosphorus (32P) • Radioactive sulfur (35S) • Found that much of 32P-labeled DNA had entered bacterial cells, while majority of 35S-labeled proteins remained in empty virus heads • Demonstrated that viral DNA enters bacterial host cells, whereas viral protein does not (genetic material had to be made of DNA)