Genomic Structure and Organization Flashcards
A _____ is a chromosomal segment that encodes for a single polypeptide chain or RNA molecule or plays a regulatory function
- gene
A _______ is the total genetic information contained in a cell, an organism, or a virus
- genome
A ______ is a compact strand of DNA that is encoded with genes; composed of chromatin; formed during nuclear division
- chromosome
_______ is DNA complexed with histones and other proteins; typically dispersed throughout the nucleus during interphase
- chromatin
In bacteria, chromosomal compaction largely occurs by __________
- negative supercoiling
In eukaryotes DNA is confined to the ______ and wrapped around proteins called ______
- nucleus
- histones
The compact structure of DNA in bacterial cells is called a _____
- nucleoid
The nucleoid exists in the ______, with a few attachments to the membrane
- cytosol
Eukaryotic genomes vs prokaryotic genomes
- eukaryotic genomes are much larger
Prokaryotic cells have ____ chromosome per cell, whereas eukaryotic cells have ____ chromosome per cell
- one
- two copies of each
After separating repeat DNA bands appear as ______ and are sometimes called _______
- satellites
- satellite DNA
Repetitive sequences making genomes in eukaryotic cells larger includes:
- AT repeats on satellite bands
- duplication of functional genes such as ribosomal or tRNA
- Alu sequences
- Intron sequences
- Pseudogenes
The nuclear envelope contains ____ to allow the free diffusion of small molecules between the nucleus and cytoplasm
- pores
Eukaryotic chromosomal DNA are within the _____ as ______ held in place by the nuclear envelope
- nucleus
- chromatin
______ and ______ assist with the selective transport of RNA and protein
- exportins
- importins
Transcription and translation can never be coupled because protein synthesis occurs in the ______ and mRNA synthesis occurs in the _____
- cytoplasm
- nucleus
The nuclear pore complex contains nucleoporins that allows selective transport of _____ and _____ molecules into and out of the _____
- RNA
- protein
- nucleus
Chromatin is wound around ______ and ______ proteins
- histone
- non histone
The portions of DNA that cannot be digested are called _______
- nucleosomes
______ are the fundamental building blocks of chromatin structure
- histones
The basic repeating structure in chromatin is the _______, in which two superhelical turns of DNA are wrapped around about an _____ of histones
- nucleosome
- octamer
Chromatin during interphase can exist in two major forms
- euchromatin
2. heterochromatin
______ is transcriptionally active
- euchromatin
_____ is thick and transcriptionally inactive
- heterochromatin
________ is a technique used to identify chromosome neighborhoods, or regions that are in close contact in 3 dimensional space but are apart linearly
- chromosome conformation capture
The discovery and use of restriction enzymes specifically to _____ DNA is crucial to genome mapping and sequencing
- cleave
Importance of host induced restriction and modification
- 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
The three major types of restriction- modification systems
- type 1
- type 2
- type 3
Each restriction/modification system consists of 2 enzymes
- DNA methylase
2. endonuclease that catalyzes a double stranded DNA break
Most widely used in the sequence-specific endonucleases are ______ enzymes
- type 2 enzymes
Restriction enzymes are named according to the _____ and the _____. For example EcoRI is the type I restriction enzyme from E. coli strain
- species
- strain
Among the three types of restriction systems, _____ nucleases are the only one that cleave within the target site
- Type 2
Restriction enzymes are specific for DNA sequences (most with _______) and ______ states
- twofold rotational symmetry
- methylation states
These nucleases may generate _____, or 5’ or 3’ _____
- blunt ends
- overhangs
Structure of a type 2 DNA methylase
- 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
Once a restriction map of a genome is determined, the genome can be fragmented using ________
- restriction endonucleases
Genome fragments can be cloned into vectors forming a _____ for sequence analysis
- library
Each clone in the library possesses a sequence, and these sequences can be arranged using information from the _______
- restriction map
________ uses a process to generate random fragments; regions of overlapping sequences are used to arrange the sequences in the correct order
- shotgun sequencing
The _________ yielded a final sequence of genomes
- human genome project
Large genomes can be mapped using ________
- fluorescent in situ hybridization (FISH)
The location of a gene on a chromosome can be identified by tagging an amplified DNA sequence with a _______
- fluorescent dye
FISH as a DNA probe is _____ and _____ in the presence of a chromosome
- denatured
- annealed
The location of the fluorescent dye is visualized using ______ and identifies the regions of DNA complementary to the ____
- microscopy
- probe
_____ are variable sequences within the same region that can be used for mapping
- polymorphisms
MboI recognizes the restriction site ____
- GTAC
If an individual has ___________ a region of DNA sequence is not cut by MboI, it will not cleave at this site
- restriction fragment length polymorphism (RFLP)
______ is a technique for detecting the presence of a specific DNA sequence in a genome with the use of a nitrocellulose filter
- southern blotting, or southern transfer
Restriction length polymorphisms can be used to locate genes on human genome that, when mutated, contribute to specific _________
- disease states
________ allows for the detection of minute amounts of specific DNA sequences in a pool of unspecific DNA
- southern blotting
Southern blotting technique uses ________, no two individuals have the same pattern of them
- restriction fragment length polymorphisms (RFLPs)
The _______ revolutionized molecular biology can amplify small amounts of DNA in vitro
- polymerase chain reaction (PCR)
_______ 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
- polymerase chain reaction (PCR)
