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BIOL366 (Biochem II)
Chapter 6
66
Biology
Undergraduate 4
10/14/2009

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Term
Genome consists of ______ and ______
Definition
Unique Sequences (single-copy genes), Repeat Sequences (Multiple Copies per genome.)
Term
____% of the genome consists of protein encoding genes. These portein encoding genes consist of ______.
Definition
30, introns and exons
Term
Exons make up less than ___% of the genome.
Definition
2
Term
Repeated sequences include ______ and ______ which makes up approximately _____ and ____% of the genome.
Definition
Transposable elements, and highly repitious DNA, 45%,3%
Term
(T/F) A single DNA molecule is found in each chromosome?
Definition
True
Term
________ and _______ contain their own different genomes.Which are very small consisting of only of ______ to _____ kb.
Definition
Mitochondia, Chloroplasts,20,150
Term
Monocistronic genes
Definition
mRNA encodes for a single protien (most eukaryotic mRNA's)
Term
Polycistronic Genes
Definition
operon mRNA's in prokaryotes in which a single mRNA can encode for multiple proteins.
Term
Describe the typical human genome
Definition
50 kbp long with ≥ 95% of the sequence consisting of intons and 5' - 3' UTRs
Term
intron and exon length
Definition

introns = 90 bp - 17.1 kbp

exons = 50 - 100 bp

Term
Lower eukaryotes usually lack _____
Definition
introns
Term
Solitary genes
Definition
One copy per haploid genome, make up 25 - 50% of protein coding genes in multicellular organisms
Term
Gene Families
Definition
protein encoding genes that have similar sequences whcih evolved through gene duplication
Term
Gene Families clusters
Definition
2 - 30 members involved in gene encoding protein families (ie. α and β globins). A few contain several hundred members (ie kinases, immunoglobins, olfactory receptors.)
Term
[image]
Definition

Beta globin genes are a good example of a gene cluster family

 

psuedogenes- "dead" genes that have the same cluster intron/exon organization found in active genes. They are no longer expressed because they lack control elements.

active members- expressed at different times (e.g., ε in the embryo, β in the adult)

Alu emelent- 300 bp repeat sequence in the non transcribed spacer DNA b/t genes.

Term
Tandemely Repeated Genes
Definition
occur in tandem arrays of identical or nearly identical repeated copies one after the other in a head to tail arrangement. Used for genes that code for rRNAs, tRNAs, histones, U2 snRNAs.
Term
How do tandem array genes differ from gene family clusters?
Definition
where individual members show sequence variations and are separated by non-identical spacer DNA
Term
Tandem arrays are present in what gene transcripts?
Definition
tRNA, rRNA, U2 snRNA, histones
Term
miRNAs
Definition
Regulate gene expression and are derived from non-protein coding RNAs
Term
Organismal DNA differences are mainly due to ____.
Definition
Non-coding DNA. DNA transcribed into nonprotein-coding RNA (introns, repetitious DNA,
spacer DNA)
Term
What is Satelite DNA?
Definition
Simple sequence DNA with tandem repeats of perfect or nearly perfect repeats of relatively short
sequences, 14-500 bp long
Term
Satelite DNA tandem arrays ... How long, where are they located, and why are they required?
Definition

1.) DNA with tandem repeat arrays of 20 - 100 kbp

2.) Located in centromeres and telomeres

3.) for proper segergation of chromosomes (mitotic spindle attachement sites) and maintainance of chromosome ends (telomeres)

Term
Microsatelite DNA ... what they are, where they are located, what they do.
Definition

1.) Simple Sequence DNA with Tandem Repeats of 1-13 bp

2.) occasionally occur within transcription units where mutations that lead to expansion of the repeats is associated with a number of human diseases (e.g., myotonic dystrophy, spinocerebellar ataxia)

Term
Minisatelite DNA
Definition

Simple Sequence DNA that is composed of 14 - 100 bp repeats in arrays of 1-5 kb long (20-50 repeats)

 

 

Term
DNA fingerprinting
Definition

Micro Satelite sequence of repeat units is highly conserved among individuals but the number of repeats is highly variable

 

DNA fingerprinting makes use of PCR reactions with a mixture of primers flanking a number of different minisatellites resulting in a pattern of varying size bands the pattern uniquely identifies any individual with mathematical certainty

[image]

Term
Transposable Elements
Definition
composed of a very large number of copies of repeats from a small number of families. These interspersed repeats have the unique ability to move from one site to another. Have no specific function other than an evolutionary role of genes
Term
Transposition
Definition
the relitively infrequent movment of mobile DNA from transposons. May also occur in somatic cells.
Term
2 major classes of mobile DNA elements, and how do they differ
Definition

 

[image]

1.) DNA transposons -are found in both bacteria and eukaryotes

2.) Retrotransposons- require an RNA intermediate, they are found only in eukaryotes and move by a process analogous to retrovirus genome insertion, and are evolutionarily related

Term
Bacterial DNA Transposons
Definition

[image]

First descovered as spotaneous mutations duet to insertion of a DNA sequence into a coding region of a gene and called IS elements. These IS elements are 1-2 kbp and transpose at low frequencey most transpose anywhere at random into a host chromosome.

Term
Mechansim of Bacterial DNA Transposition
Definition

[image]

Transposase makes blunt-end cuts next to the inverted repeat sequences in IS element. Transposase makes staggered cuts in target DNA and ligates unpaired stretch to IS element. DNA pol w/ ligation fills in cellular gap to generate short direct repeat target-site sequences. Size of short targe site repeats depend on on the particular IS element (5,9, 11 bp)

Term
What are the 2 classes of retrotransposons, and how do they differ
Definition

LTR (Long Terminal Repeat sequences) - 6 -11 kbp long that contain LTR and genes similar to those found in retroviruses targets 5-10 bp of direct repeats

Non-LTR retrotransposons- the largest element is 6 kbp (they are smaller) and they all lack LTR's and are distanly related to retroviruses, target A/T rich regions

Term
What enzymes are encoded by retrotransposons?
Definition
Transposase functions as a reversed transcrptase and intergrase.
Term
What is the life cycle of a retrovirus (5 steps)
Definition

1.) Retrovirus containing genomic ssRNA and Reverse Transcriptase enters the cell via fusion causing the loss of the protein coat which froms a viral nucleocapsid.

2.) The viral DNA is copied through reverse transcription

3.) The DNA is transported into the nucleus and integrated into the host chromosome creating a Provirus

4.) Transcription occurs creating retrovirus protiens

5.) Complete retroviruses emerge from the cell in a process called budding

Term
LTR retrotransposons are similar to retrovirus genomes because of they encode for what? How are they both similar?
Definition

[image]

Transposase Enzyme = reverse transcriptase/integrase

and virus capsid proteins that lack the envelope proteins (defective)

 

Both contain Transcription control elements that are flanked by short direct repeats. Both are transcriped by RNA pol II. Both have LTR regions

Term
What are the 2 classes of non-LTR retrotransposons?How large are they, and what are their target sites for transposition?
Definition

LINES - long interspersed elements (900 bp)

SINES - short interspersed elements (100 -400 bp)

 

Both target A/T rich regions

Term
21% of the genome consists of 3 families of LINES, what are they? The vast majority of LINES don't have intact ____, instead they are ________ and contain many _________.
Definition

L1,L2,L3

ORFs, truncated, mutations

Term
What are the second most abundant class of mobile elements in the human genome? 
Definition
SINES - (100-400bp)
Term
SINES contain what specific elements in what numbers, what does it's name mean, and where are they located?
Definition
1.1 milliion Alu elements (300 bp) from the presence of a single Alu restriction site in the element. Scattered throughout the genome b/t genes and within intorns (like the beta-globin cluster)
Term
How do LINES and SINES differ? How are they the same?
Definition
Both are non-LTR retrotransponsons both have and A/T rich region. However, SINES do not encode proteins. 
Term
Can LINE and SINE insertions be detrimental?
Definition
Yes, L1 and SINE insertions in genes are resposible for 1 in 600 mutations that cause significant disease in humans.
Term
What are processed psuedogenes?
Definition
DNA copies of mRNAs that are integrated into the genome. They lack introns and generally contain multiple mutations.
Term
What is the difference in origin between processed pseudogenes and pseudogenes?
Definition

Pseudogenes originate from gene duplication and unequal crossing over events.

Processed pseudogenes are derived from mRNA copied into DNA and then integrated.

Term
Mobile DNA and genome evolution occurs by what means?
Definition

Exon shuffling between different genes by recombination (ie. b/t Alu elements in introns).

They have contributed to generation of gene families and formation of complex regulatory regions to control gene expression.

Term
what does BLAST sequence comparison mean?
Definition

BLAST - basic local alignment search tool

BLAST is an effective computer program that evalutates wheter any 2 or more sequences are related (protein or DNA), and then generates a stat score of significance for alignment that indicate whether or no the alignment could be due to chance.

Term
What BLAST p-value indicate that the alignment could be due to chance?
Definition
>10^-3
Term
What words (3) describe relationships between gene families and their evolutionary history? What do they mean?
Definition

Homologous - sufficiently similar to suggest common ancestry

Paralogous- genes reulted from gene duplication

Orthologous- result from speciation

Term
T/F the no of protein-coding genes is not directly related to biological complexity
Definition
True
Term
What % of known genes have an unknown function?
Definition
50%
Term
How are all Eukaryotes related?
Definition
proportion of genes devoted to particular functions is roughly similar in all eukaryotes with some notable exceptions (defense and immunity)
Term
Total length of cellular DNA
Definition
100,000x a cells length, 2.8 10^8 bp almost 10 cm in length.
Term
Interphase DNA, DNA extracted from isotonic buffers (physiological salt concentration), Extracted from Low ionic strength buffer.
Definition
Chromatin fibers, 30 nm fibers, 10 nm fibers (beads on a string)
Term
Nucleosome structure
Definition
Beads on a string on the 10nm fiber. Protein core of nucleosomes is an octamer of histones 2 copies of each H2A, H2B, H3, H4. THe core is wrapped by 147 bp of DNA in all eukaryotes (less than 2 turns) 15 - 90 bp of free DNA links nucleosomes
Term
Structure of 30 nm Chromatin Fiber
Definition
10-nm strand folds to form a zig-zag ribbon. 2 nucleosomes strands wind to form a two-start left hand helix. Contains an additional histone protein H1. H1 is bound to DNA as it enters and exits nucleosome cores (one/nucleosome)
Term
Histone Tail Modifications
Definition
Histones have flexible tails (N or C terminal) extending from the nucleosome structure that play a role in condesation. Can be modified by phosphorylation, Methylation, Acetylation, and Ubiquination.
Term
Heterochromatin regions
Definition
Regions of chromosomes that don't fully condense following mtiosis (centromeres, telomeres, and other discrete regions). Actively transcribed genes are often found in these regions. 
Term
Histone tail modifications in euchromatin
Definition
governs condensation and decondensation. Acetylation in particular is much more extensive in euchromatin.
Term
Chromosome Scaffold
Definition
histones removed from metaphase chromosomes. Long loops of 30 nm DNA attach to a protein scaffold. These loops range from 1-4 million bp in size. Far apart genes are joined closer together via SARs (scaffold associated regions)and MARs (matrix-attachment regions).
Term
Scaffold loops are how long?
Definition
1-4 million bp
Term
What are SARs and MARs
Definition
Scaffold associated regions of looped fibers in chromosome scaffold. Matrix attachment regions
Term
Chromonema fiber
Definition
condensened 30 nm fiber in metaphase chromosomes. 100 - 130 nm. this further condesences to middle prophase chromatid 200-250 nm fiber all the way to metaphase chromatid 500 - 750 nm
Term
How long are LTR regions in retrotransposons, and what do they contain, what are they flanked by
Definition
250 - 600 bp, contain transcription control elements, short direct repeats
Term
bacterial DNA transposon structure
Definition

1.) IS element (1-2 kb) with a protein coding region for transposase enzyme

2.) protein region is flanked by 50 bp inverted repeats (part of the IS element

3.) IS element is flanked by target-site direct repeats of (5-11 bp)

Term
LTR retrotransposon structure
Definition

[image]

LTR retrotransposon ( 6-11 kb) contains a protein coding region flanked by LTR reagions (250 - 600 bp) LTR regions are flanked by target-site direct repeats (5-10 bp)

Term
Non-LTR retrotransposon structure
Definition

LINES and SINES

[image]

SINES do not encode proteins but contain Alu elements

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