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Cytophysiology > Chapter 6 - The Eukaryotic Genome (DONE) > Flashcards

Chapter 6 - The Eukaryotic Genome (DONE) Flashcards

1
Q

Data storage analogy:

A

Nucleotide -> Motifs -> Genes -> Chromosomes -> Nucleus -> Cell

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2
Q

Within which distinct compartments are the human genome contained within?

A
  • the nucleus

- the mitochondria

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3
Q

Around how many genes are contained within the nucleus?

A

20,000 - 25,000 genes

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4
Q

How many genes are contained within the mitochondria?

A

37 genes

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5
Q

Whatare the genes inthe mitochondria essential for?

A

They are essential for normal mitochondrial function and is exclusively of maternal origin.

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6
Q

DNA + protein = ?

A

Chromatin

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7
Q

What contains the structural blueprint for all genetic instructions?

A

DNA contains the structural blueprint for all genetic instructions.

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8
Q

What are the bases of the DNA?

A
  • Two of the bases are heterocyclic compounds or purines (adenine (A) and guanine (G))
  • Two are six-member rings known as pyrimidines (cytosine (C) and thymidine (T))
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9
Q

Where does the double-helix structure of DNA derive from?

A

The famous double-helix structure of DNA derives from its phosphate-deoxyribose backbone.

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10
Q

What does the backbone of the DNA comprise from?

A
  • It comprises five-carbon sugar (pentose) molecules bound to a nucleoside (A, G, C, or T).
  • The pentose molecules are also asymmetrically joined to phosphate groups by phosphodiester bonds.
  • Hydrogen bonds between complementary (G:C or A:T) nucleotides (a nucleoside linked to a sugar and one or more phosphate groups) interact to stabilize and form the doublehelix structure.
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11
Q

What are histones:

A

Histones are a heterogeneous group of closely related arginine- and lysine-rich basic proteins

  • make up 1/4 of amino acid residues.
  • These positively charged amino acids help histones to bind tightly to the negatively charged sugar phosphate backbone of DNA.
  • They provide for the compaction of chromatin.
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12
Q

What is the length of the nucleus of a human in diameter?

A

The nucleus of a human cell is typically 6μm in diameter but contains DNA which at its maximum stages of condensation is only about 1/50,000th of its linear length.

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13
Q

How many levels of packaging of DNA take place in order that DNA in individual chromosomes fits into the 1.4 μm chromosome seen at metaphase?

A

At least four levels of packaging of DNA take place in order that DNA in individual chromosomes fits into the 1.4 μm chromosome seen at metaphase.

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14
Q

What does the nucleosome core consist of?

A
  • complex of eight histone proteins (two molecules each of histone H2A, H2B, H3, and H4)
  • double-stranded DNA wound.
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15
Q

How many basepairs (bo) if DNA are associated with the nucleosome particle?

A

146 base pairs (bp) of DNA are associated with the nucleosome particle
-50 to 70bp span of linker DNA bound by a linker histone H1 separates each nucleosome.

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16
Q

Function of nucleosome?

A
  • packaging of DNA
  • regulate gene expression or activity, by determening whether the DNA sequences can be accessed by transcription factors, allowing the factors to regulate expression of a nearby gene
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17
Q

Genome

A

A set of genetic information collectively called genome

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18
Q

Each core histone has _________

A

a structured domain and an unstructured amino-terminal “tail” of 25 to 40 amino acid residues.

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19
Q

Give examples of enzymatic modification of the amino-terminal tails that modifies the histones’ net electric charge and shape:

A
  • acetylation
  • methylation
  • phosphorylation

These modifications are reversible and are thought to prepare the chromatin for DNA replication and transcription.

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20
Q

Acetylation and deacetylation of lysine residues:

A

These processes are important in making DNA more or less accessible to transcription factors (proteins that regulate gene expression by direct binding to DNA).

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21
Q

What defines the transcriptional activity of a given chromatin region?

A

The interplay of acetylase and deacetylase activities defines the transcriptional activity of a given chromatin region.

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22
Q

What does lysine residue acetylation do?

A
  • They weakens the DNA-histone interactions and makes the DNA more accessible to factors needed for transcription.
  • Therefore, histone acetylation is generally associated with transcriptional activation.
23
Q

What is histone deacetylation is associated with?

A

It is associated with gene silencing.

24
Q

What catalyzes histone acetylation?

A

It is catalyzed by histone acetyl transferases or HATs

25
Q

Heterochromatin

A
  • Densely packed or compacted regions of chromatin
  • Are genetically inactive.
  • Transcription is inhibited because the DNA is packaged so tightly that it is inaccessible to the proteins responsible for RNA transcription.
26
Q

Euchromatin:

A
  • Less densely compacted chromatin regions in a transcriptionally active nucleus.
  • Are commonly undergoing, or preparing for, or have just completed transcription.
  • It represents uncoiled chromatin structures that allow RNA polymerases’ and regulatory proteins’ access to DNA.
27
Q

What are chromosomes composed of?

A

noncovalent complex of one very long linear duplex DNA and associated histone proteins.

28
Q

How is the chromosome structure?

A

Chromosome structure varies with the cell cycle, from the -loose threadlike appearance in G1 phase
-tightly compacted state observed during M phase. Chromosomes require three sequence elements for their propagation and maintenance as individual units.

29
Q

What are telomeres?

A

Telomeres are hexameric DNA repeats [(TTAGGG)n] found at the ends of chromosomes that serve to protect the chromosome from degradation.

30
Q

What serve as “handles”?

A

Sequence elements known as centromeres serve as “handles,” which allow mitotic spindles to attach to the chromosome during cell division.

31
Q

What happens as the cell progresses through the mitotic or M phase of the cell cycle?

A

The nuclear envelope breaks down, and chromosomes segregate into the opposite poles of the cells (to form daughter cells), while a kinetochore forms consisting of the centromere and mitotic spindles. The centromere also serves as a boundary that separates the two arms of the chromosome (placement varies for different chromosome types).

32
Q

What have to happen in order for DNA in chromosomes to replicate?

A
  • In order for DNA in chromosomes to replicate, a specific nucleotide sequence acts as a DNA replication origin.
  • Each chromosome contains multiple origins of replication, dispersed throughout its length.
33
Q

Where can we find a series of direct repeat DNA sequences?

A

At the origin of replication, there is an association of sequencespecific, double-stranded DNA binding proteins with a series of direct repeat DNA sequences.

34
Q

What does ploidy refers to?

A

Ploidy refers to the number of chromosome copies within a cell.

35
Q

What does diploid mean?

A
  • Most of the somatic cells within the body are diploid, meaning that each nucleus has two copies of each chromosome, one deriving from the mother and other from the father.
  • Germ cells are the exception to this rule, which contain a single copy of each chromosome and are known as haploid.
36
Q

How many bp is in the haploid genome?

A

The haploid genome of each human cell consists of 3.0 × 109 bp of DNA, divided into 23 (22 somatic and 1 sex) chromosomes.

37
Q

How many pairs of genes does the the entire haploid genome code for?

A

The entire haploid genome contains sufficient DNA to code for nearly 1.5 million pairs of genes.

38
Q

Telomeres?

A
  • hexameric DNA repeats (TTAGGG)n found at the ends of chromsomes that serve to protect chromosomes from degradation.
39
Q

centromeres

A
  • sequence elements which allow mitotic spindles to attach to ch during cell division
  • they also serve s boundaries to seperate short arm “p” of ch from long arm “q”
40
Q

ploidy?

A

number of chromosome copies within a cell.

41
Q

how many genes are present in human genome?

A

20,000 - 25,000

42
Q

what are micro-RNAs?

A
  • class of genes involved in many human diseases

- regulates 30% of all proteins within a human proteome

43
Q

how much genome do repeating DNA sequences comprise?

A

50%

44
Q

two classes of repeat DNA sequences?

A
  • satellite DNA

- LINES and SINES

45
Q

satellite DNA?

A

-highly repetitive sequences
-clustered
-not transribed
-present in 1- 10 illion copies per haploid genome
-associated with telomeres and centromeres
- categorized into
=> alpha satellite (171 bp) several million base pairs
=> mini satellite (20-70bp) few thousand base pairs
=> micro satellite (2,3 or 4 bp) length of a few hundred basepairs

46
Q

short tandem repeats (STR’s)

A

microsatellites of 2 to 6 bp important in forensic lab because they can readily be amplified with polymerse chain reaction

47
Q

trinucleotide repeats?

A
  • microsatellites sequences
  • can undergo expansion
  • if expand abnormally may result in an unstable and defective gene
48
Q

LINES and SINES

A
  • unclustered sequences
  • present at less than 10x6 copies per haploid genome
  • transcribed to RNA accroding to size
  • LINES (long interspersed elements) 7,000bp (20 - 50,000 copies)
  • SINES (short interpsresed elements) 90 to 500bp (100,000 copies)
49
Q

Gene

A

complete sequence region necessary for generating a functional unit

50
Q

Examples of epigenetic mechanisms

A
  • methylation of cytosines
  • tissue-specific chromatin alterations

note: epigenetic mechanis do not alter the DNA sequence of the genome.

51
Q

what percentage of genome encodes instructions for synthesis of protiens?

A

2%

52
Q

methylation of cytosines

A
  • involved in DNA methylation
  • major site is a cytosine base in DNA
  • specially the 5’ cytosine adjacent to a guanosine base (5’-CG-3’)
53
Q

tissue-specific chromatin alterations?

A
  • differences in chromatin structure within tissues (euchromatin and heterochromatin)
  • stably inherited changes
  • ## specific for given tissue

Cytophysiology (13 decks)

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