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Genetics Chapter 12 Flashcards

1
Q

Origin of replication for Eukaryotes

A

linear DNA, multiple origins of replication

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2
Q

Origin of replication for Prokaryotes

A

circular DNA with 1 origin of replication

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3
Q

Transcription location for both eukaryotic and prokaryotic

A

Prokaryotes: cytosol
Eukaryotes: nucleus

Both eukaryotic and prokaryotic DNA polymerases build off RNA primers made by primase

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4
Q

Chromosomes

A

contain genetic material

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5
Q

Genome

A

genetic material

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6
Q

Chromatin

A

packaging of DNA and histones (DNA protein complex)

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7
Q

Bacterial Chromosomes Structure

A
  • Circular molecule in cytosol
  • 1 Origin of replication
  • DNA segments between genes: intergenic regions
  • Bacterial genes are often found in operons
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8
Q

Operons

A

group of genes that function as SINGLE UNIT controlled by ONE promotor

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9
Q

Bacterial Genome Compaction

A

Nucleoid-associated proteins (NAPs) form the micro and macrodomains
Bend DNA or act as bridges between DNA regions

Histone-like nucleoid structures (H-NS)

Structural maintenance of chromosomes (SMC)

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10
Q

Eukaryotic Chromosomes Structure

A

Linear chromosome in nucleus

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11
Q

Eukaryotic Genes

A
  • Genes in between the centromeric and telomeric
  • Yeast: small genes + few introns
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12
Q

DNA Supercoiling

A
  • Both underwinding and overwinding of the DNA double helix can induce supercoiling
  • DNA structures that differ in supercoiling are called topoisomers of each other
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13
Q

DNA Supercoiling Affects Chromosome Function

A

In E. coli, there is one negative supercoil per 40 turns of the double helix

Helps in the compaction of the chromosome

Creates tension that may be made by DNA strand separation

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14
Q

Control of Supercoiling

A

DNA gyrase (a.k.a. topoisomerase II)

DNA topoisomerase I

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15
Q

DNA gyrase (a.k.a. topoisomerase II)

A

Creates negative supercoils using energy from ATP

Can also relax positive supercoils when they occur

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16
Q

DNA topoisomerase I

A

Relaxes negative supercoils

Breaks one strand and rotates the DNA

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17
Q

Supercoiling Enzymes as Drug Targets

Two main classes of drugs inhibit bacterial topoisomerases, but do not inhibit eukaryotic ones

A

Quinolones
- ciprofloxacin (“Cipro”)
- quinine

Coumarins

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18
Q

Negative supercoiling

A

supercoils from LEFT (underwinds)

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19
Q

Positive supercoiling

A

right hand turn (overwinding)

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20
Q

When helicase unwinds the DNA, it creates tension at the replication fork (where the strands separate). This tension is known as

A

supercoiling- relieved by Topoisomerase

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21
Q

Discuss the various roles of supercoiling and why cells need to be able to do it.

A

Genetic diversity
Replication
DNA strand separation

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22
Q

Telomeres

A

contains many copies of DNA sequences at the end of the chromosomes

This will protect the genome from degradation

Preserves information

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23
Q

Genome complexity

A

Genome complexity is not correlated with organismal complexity
Variation is not necessarily related to complexity

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24
Q

Sequence Complexity

A

Refers to the number of times a particular DNA sequence appears in the genome

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25
Unique or non-repetitive sequences
structural genes + introns and other noncoding DNA
26
Moderately repetitive
Includes rRNA and transposable elements
27
Highly repetitive
Some are transposable elements (Alu elements) Others are clustered together in tandem arrays
28
telomerase in normal cells
Telomeres shorten every cell division as we age Normal telomeres allow for cell division and tissue generation
29
telomerase in cancer cells
Cancer cells maintain their telomeres despite undergoing repeated cell divisions Cancer cells activates telomerase→adding genetic units onto the telomeres to PREVENT them from shortening
30
Describe the location, composition, and function of telomeres and centromeres
Centromeres binds two sister chromatids Telomeres are repetitive sequences of nucleotides at the end of chromosomes Centromeres are made up of repeated DNA
31
Nucleosomes
Nucleosomes are octamers of histone proteins + DNA Nucleosomes join to Form a 30-nm Fiber which shortens the total length of DNA 7-fold
32
Histone N-terminal tails
Histone N-terminal tails modulates the structure and function H2A,H2B,H3 and H4 are the core histones (2 of each) H1 is the linker histone
33
Histone Proteins
DNA is wrapped around histones
34
Chromosome compaction
increases during cell division
35
Histone tails are modified
Modifications are correlated with heterochromatin or euchromatin
36
Acetylation: adding acetyl groups
histones remove positive charges→relaxing DNA-histone attraction→ allowing for MORE TRANSCRIPTION→EUCHROMATIN
37
Methylation: adds methyl groups
either increasing or decreasing transcription DNA methylation suppress gene transcription—>heterochromatin
38
Euchromatin
- Less condensed, transcriptionally active Chromatin is LOOSELY bound to nucleosomes Present when DNA is ACTIVELY TRANSCRIBE LIGHTER “You actively LIGHTER/loose”
39
Heterochromatin
Tightly and transcriptionally inactive TIGHTLY PACKED NUCLEOSOMES DNA is inactive DARKER Found: telomeres & centromeres
40
Nuclear matrix: .... composed of two parts
creates higher order structure and compacts DNA into radial loop domains Nuclear lamina — fibers lining the inner membrane Internal nuclear matrix — connects to lamina, fills nucleus interior
41
Radial Loop Domains
Matrix-attachment regions (MARs) also known as Scaffold-attachment regions (SARs) are DNA sequences interspersed in the genome They anchor to the nuclear matrix, forming radial loops
42
Transposition
integration of transposable elements (TEs) of DNA into the chromosome “jumping genes”
43
Simple Transposition
“cut and paste” mechanism aka transposons increases TE number during DNA replication
44
Insertion Elements (IS element)
The simplest type of TE Both ends have inverted repeats (IRs) Contains the transposase gene
45
What is required for transposition?
Transposase (enzyme) and Indirect repeats
46
Transposase
removes and reinserts
47
Autonomous TEs
Autonomous TEs contain all the information necessary for transposition to occur
48
Nonautonomous TEs
Nonautonomous TEs lack a gene that is necessary for transposition to occur
49
Retrotransposition
TE is transcribed into RNA, then reverse transcriptase makes DNA copy that is inserted in the genome retrotransposons or retroelements
50
The steps of transposition and retrotransposition
Step 1: transposase is made from the transposable elements Step 2: transposase monomers bind IRs Step 3: transposase dimerizes bringing IRs together Step 4: DNA is cleaved between Drs and IRs, releasing the TE comes from the chromosome Step 5: TE is reinserted in a new location
51
All TEs are
All TEs are flanked by direct repeats (DRs), also called target-site duplications These direct repeat sequences go in the same direction on both sides
52
Where do TEs insert in the genome?
When TEs excise from the genome, they leave behind a DR “scar” Target sequences depend on the TE family TEs prefer AT-rich sequences TEs make up a significant portion of the genome
53
LTR(long terminal repeats) Retrotransposons
Related to retroviruses, but cannot make viral particles Contain long terminal repeats (LTRs) at both ends Encode reverse transcriptase and integrase
54
Non-LTR Retrotransposons
Less like retroviruses May encode reverse transcriptase /endonuclease Some derived from normal eukaryotic genes Ex: Alu in humans
55
The significance of direct repeats flanking transposable elements and how they are made.
Flanking of direct repeats play an important role in the insertions of transposable elements (TE) After TE are removed, these repeats are left behind as footprints Footprints can alter gene expression
56
P elements in Drosophila can cause
sterility P elements are a TE that was found in natural populations of Drosophila but not in the laboratory strains
57
Biological Significance of TEs?
Selfish DNA hypothesis TEs exist because they can Like parasites, can proliferate in host as long as they do not overly harm the host TEs offer an advantage In bacterial, may carry antibiotic-resistance genes May cause insertion of exons into the coding region of other genes, providing new functions – exon shuffling
58
Negative Effects of TEs
Insertions can cause mutations Excisions can cause chromosome breaks and rearrangements When transposon activity is not regulated and kept under control, they can cause chromosomal abnormalities and sterility
59
In a bacterium, the region of the cytoplasm where the compacted chromosome is located is called the
nucleoid
60
What is a nucleoid?
A region in a bacterial cell where the compacted chromosome is located.

Genetics (5 decks)

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