MMT: organization of the genome

Question 1

Differentiate between DNA, chromatin, chromosomes, genes and the genome.

Answer 1

Chromatin: DNA + histone and non-histone proteins; histone is about half the mass of chromatin!
Chromosomes: made up of chromatin
Genes: made up of chromosomes
Genome: all of the genes in a person

Question 2

Define the 2 types of chromatin proteins.

Answer 2

Non-histone: Any proteins binding that are not histones; involved in DNA replication, transcription, DNA repair and chromatin remodeling

Question 3

Describe the components of a nucleosome core particle

Answer 3

A nucleosome core particle consists of 2 molecules of H2A, H2B, H3, and H4 histone types (histone octamer) with DNA wrapped around it. The histones in the octamer have positively charged amino acids in their N-terminal tails that help bind the DNA wrapping around them. H1 is closely associated but not in the core particle.

Question 4

what amino acids are typically found in the T-terminal tails of histones

Answer 4

lysine, arginine, and serine residues that are covalently modified by specific enzymes

Question 5

define linker DNA

Answer 5

connects nucleosome core particles together

Question 6

what are the three main types of covalent modifications in the amino terminal tails of histones

Answer 6

acetylation, phosphorylation, and methylation

Question 7

describe acetylation in terms of covalent modifications of histones

Answer 7

Acetylation: the positively charged R group gets acetylated. By neutralizing its positive charge, we can loosen up the DNA. This is because the removal of the positive charge reduces affinity of the amino terminal talks for DNA. The acetylated regions also serve as binding sites for non-histone proteins that can regulate transcription or remodel chromatin.

Question 8

describe phosphorylation in terms of covalent modification of histones

Answer 8

the OH in serine can be phosphorylated

Question 9

describe methylation of histones

Answer 9

lysine, arginine, or histidine can be methylated. This can recruit effector proteins involved in chromatin remodeling and transcription regulation.

Question 10

what are the two main components of genomic structural organization

Answer 10

chromatin and nucleosomes

Question 11

what are the higher order chromatin structures?

Answer 11

chromatin fibers (solenoids), extended and condensed loops, and metaphase chromosomes

Question 12

describe solenoids

Answer 12

nucleosomes packed together into fibers of about 30 nm

Question 13

describe extended and condensed loops (generally)

Answer 13

DNA solenoids during interphase are arranged in loops anchored to the chromosome scaffold or nuclear matrix.

Question 14

what is included in the DNA scaffold? what is it?

Answer 14

include lamins, topoisomerases, and components of centromeres/telomeres. they anchor extended and condensed loops.

Question 15

describe metaphase chromosomes

Answer 15

Tightly coiled loops & chromosome scaffold, each
metaphase chromosome consists of sister chromatids
connected at centromere - approx. 1400 nm

Question 16

Explain the structural and functional differences between euchromatin and heterochromatin

Answer 16

Euchromin is associated with extended/diffuse loops of solenoids, and are typically more transcriptionally active as they are more open.
heterochromatin is associated with condensed/highly compact loops of solenoid. It is highly compacted and generally transcriptionally inactive.

Question 17

describe the main classes of repetitive sequences in the human genome

Answer 17

• Simple sequence repeats (Microsatellites and minisatellites)
• Retrotransposons: short interspersed element, long interspersed elements (1/5th of the genome!), long terminal repeat elements. Not currently active in our genome.
• DNA transposons: not currently active in our genome
• Segmental duplications

Question 18

describe the main classes of non-repetitive sequences in the genome

Answer 18

Exons: Coding sequences constitute approximately 1.5% of human genome
Introns: Transcribed sequences removed by mRNA processing- 35-40% of genome

Regulatory Elements: Promoter, Enhancer, Silencer elements of genes

Pseudogenes: Non-functional genes; estimate of 20,000 in human genome. Had a use at one point, but now have been “turned off”

Question 19

define a gene

Answer 19

DNA sequence that codes for a functional RNA or protein product

Question 20

describe regulatory elements

Answer 20

Intergenic sequences that regulate transcription of a gene such as the promoter region, enhancers and silencers

Question 21

describe a protein coding sequence

Answer 21

Translated mRNA sequence between start and stop codons

Question 22

describe the 5 ́-UTR and 3 ́-UTR ends of DNA

Answer 22

• 5 ́-UTR: Noncoding sequence between the 5 ́cap (m 7 Gppp) and AUG start codon of mRNA
• 3 ́-UTR: Noncoding sequence between the stop codon and polyA tail (An ) of mRNA

Question 23

Explain the functional differences between an intron and an exon

Answer 23

Exon contains an actual coding sequence. Includes/ starts and ends with 5 ́-UTR and 3 ́-UTR of mRNA

Introns: get spliced out of the final copy and do not code for anything in the final gene

Question 24

Differentiate between gene families, tandemly repeated genes and pseudogenes

Answer 24

Pseudogene: A nonfunctional copy of a gene; it can’t be transcribed.
Gene Families: A group of related genes derived from a common ancestor. These genes
may be expressed at different stages of development or in different tissues and cell types
Tandemly Repeated Genes: Multiple copies of the same gene. A large quantity of the gene product is essential for normal cell function

Question 25

Describe the role of DNase I

Answer 25

Endonuclease that digests regions of DNA strands NOT protected by protein

Question 26

13. Define the histone code

Answer 26

Covalent modifications to N-terminal tails of histones occur in innumerable
possible combinations.

Question 27

What is the approximate size of the human genome

Answer 27

3 x 109 (3 billion) bp