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Biochemistry > Genomic Structure and Organization > Flashcards

Genomic Structure and Organization Flashcards

1
Q

A _____ is a chromosomal segment that encodes for a single polypeptide chain or RNA molecule or plays a regulatory function

A
  • gene
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2
Q

A _______ is the total genetic information contained in a cell, an organism, or a virus

A
  • genome
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3
Q

A ______ is a compact strand of DNA that is encoded with genes; composed of chromatin; formed during nuclear division

A
  • chromosome
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4
Q

_______ is DNA complexed with histones and other proteins; typically dispersed throughout the nucleus during interphase

A
  • chromatin
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5
Q

In bacteria, chromosomal compaction largely occurs by __________

A
  • negative supercoiling
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6
Q

In eukaryotes DNA is confined to the ______ and wrapped around proteins called ______

A
  • nucleus

- histones

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7
Q

The compact structure of DNA in bacterial cells is called a _____

A
  • nucleoid
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8
Q

The nucleoid exists in the ______, with a few attachments to the membrane

A
  • cytosol
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9
Q

Eukaryotic genomes vs prokaryotic genomes

A
  • eukaryotic genomes are much larger
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10
Q

Prokaryotic cells have ____ chromosome per cell, whereas eukaryotic cells have ____ chromosome per cell

A
  • one

- two copies of each

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11
Q

After separating repeat DNA bands appear as ______ and are sometimes called _______

A
  • satellites

- satellite DNA

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12
Q

Repetitive sequences making genomes in eukaryotic cells larger includes:

A
  1. AT repeats on satellite bands
  2. duplication of functional genes such as ribosomal or tRNA
  3. Alu sequences
  4. Intron sequences
  5. Pseudogenes
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13
Q

The nuclear envelope contains ____ to allow the free diffusion of small molecules between the nucleus and cytoplasm

A
  • pores
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14
Q

Eukaryotic chromosomal DNA are within the _____ as ______ held in place by the nuclear envelope

A
  • nucleus

- chromatin

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15
Q

______ and ______ assist with the selective transport of RNA and protein

A
  • exportins

- importins

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16
Q

Transcription and translation can never be coupled because protein synthesis occurs in the ______ and mRNA synthesis occurs in the _____

A
  • cytoplasm

- nucleus

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17
Q

The nuclear pore complex contains nucleoporins that allows selective transport of _____ and _____ molecules into and out of the _____

A
  • RNA
  • protein
  • nucleus
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18
Q

Chromatin is wound around ______ and ______ proteins

A
  • histone

- non histone

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19
Q

The portions of DNA that cannot be digested are called _______

A
  • nucleosomes
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20
Q

______ are the fundamental building blocks of chromatin structure

A
  • histones
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21
Q

The basic repeating structure in chromatin is the _______, in which two superhelical turns of DNA are wrapped around about an _____ of histones

A
  • nucleosome

- octamer

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22
Q

Chromatin during interphase can exist in two major forms

A
  1. euchromatin

2. heterochromatin

23
Q

______ is transcriptionally active

A
  • euchromatin
24
Q

_____ is thick and transcriptionally inactive

A
  • heterochromatin
25
Q

________ is a technique used to identify chromosome neighborhoods, or regions that are in close contact in 3 dimensional space but are apart linearly

A
  • chromosome conformation capture
26
Q

The discovery and use of restriction enzymes specifically to _____ DNA is crucial to genome mapping and sequencing

A
  • cleave
27
Q

Importance of host induced restriction and modification

A
  • can isolate homogenous DNA fragments of precisely defined length by treating DNA with a restriction nuclease in vitro and then resolving the fragments in the digest on an electrophoretic gel
28
Q

The three major types of restriction- modification systems

A
  1. type 1
  2. type 2
  3. type 3
29
Q

Each restriction/modification system consists of 2 enzymes

A
  1. DNA methylase

2. endonuclease that catalyzes a double stranded DNA break

30
Q

Most widely used in the sequence-specific endonucleases are ______ enzymes

A
  • type 2 enzymes
31
Q

Restriction enzymes are named according to the _____ and the _____. For example EcoRI is the type I restriction enzyme from E. coli strain

A
  • species

- strain

32
Q

Among the three types of restriction systems, _____ nucleases are the only one that cleave within the target site

A
  • Type 2
33
Q

Restriction enzymes are specific for DNA sequences (most with _______) and ______ states

A
  • twofold rotational symmetry

- methylation states

34
Q

These nucleases may generate _____, or 5’ or 3’ _____

A
  • blunt ends

- overhangs

35
Q

Structure of a type 2 DNA methylase

A
  • the structure shows that DNA bases undergoing methylation rotate completely out of the DNA duplex
  • is a ternary complex containing Hha methylase, DNA and S-adenosylhmocysteine
36
Q

Once a restriction map of a genome is determined, the genome can be fragmented using ________

A
  • restriction endonucleases
37
Q

Genome fragments can be cloned into vectors forming a _____ for sequence analysis

A
  • library
38
Q

Each clone in the library possesses a sequence, and these sequences can be arranged using information from the _______

A
  • restriction map
39
Q

________ uses a process to generate random fragments; regions of overlapping sequences are used to arrange the sequences in the correct order

A
  • shotgun sequencing
40
Q

The _________ yielded a final sequence of genomes

A
  • human genome project
41
Q

Large genomes can be mapped using ________

A
  • fluorescent in situ hybridization (FISH)
42
Q

The location of a gene on a chromosome can be identified by tagging an amplified DNA sequence with a _______

A
  • fluorescent dye
43
Q

FISH as a DNA probe is _____ and _____ in the presence of a chromosome

A
  • denatured

- annealed

44
Q

The location of the fluorescent dye is visualized using ______ and identifies the regions of DNA complementary to the ____

A
  • microscopy

- probe

45
Q

_____ are variable sequences within the same region that can be used for mapping

A
  • polymorphisms
46
Q

MboI recognizes the restriction site ____

A
  • GTAC
47
Q

If an individual has ___________ a region of DNA sequence is not cut by MboI, it will not cleave at this site

A
  • restriction fragment length polymorphism (RFLP)
48
Q

______ is a technique for detecting the presence of a specific DNA sequence in a genome with the use of a nitrocellulose filter

A
  • southern blotting, or southern transfer
49
Q

Restriction length polymorphisms can be used to locate genes on human genome that, when mutated, contribute to specific _________

A
  • disease states
50
Q

________ allows for the detection of minute amounts of specific DNA sequences in a pool of unspecific DNA

A
  • southern blotting
51
Q

Southern blotting technique uses ________, no two individuals have the same pattern of them

A
  • restriction fragment length polymorphisms (RFLPs)
52
Q

The _______ revolutionized molecular biology can amplify small amounts of DNA in vitro

A
  • polymerase chain reaction (PCR)
53
Q

_______ is a technique used to make multiple copies of a segment of DNA of interest, generating a large amount of copies from a small initial sample

A
  • polymerase chain reaction (PCR)

Biochemistry (15 decks)

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