Exam 2: Ch 6 Flashcards
noncoding DNA constitutes ___% of human chromosomal DNA
98.5%
DNA fingerprint
variations between repetitious stretches of DNA can be used to identify a person
transposable (mobile) DNA elements
within cellular genomes these mobile elements can copy themselves and move throughout the genome
45% of human genome
gene
the entire nucleic acid sequence that codes for synthesis of a protein or functional RNA
intron and exons
intron: noncoding regions of DNA found between genes and within genes
exon: relatively similar sequences in coding region selected for by evolution
2 types of short noncoding RNAs and basic functions
siRNA and miRNA
miRNA: regulate translation and mRNA stability
siRNA: breaks down mRNA after transcription so no translation
introns can process some RNA…
siRNA
miRNA
long noncoding RNA (regulate transcription by influencing chromatin structure)
where did mitochondria and chloroplasts evolve from?
intracellular eubacteria that developed symbiotic relationships with ancient eukaryotic cells
their DNA is an evolutionary remnant
chromatin
complex of DNA and the proteins that organize it
can be visualized as chromosomes during mitosis
genomics
computer based methods for analyzing and interpreting vast amounts of sequence DNA
nucleosomes
fundamental building blocks of chromatin
complex of DNA and histones
coding region
the nts that code an amino acid sequence or functional RNA
what does a gene contain
the coding region
all the DNA sequences required to synthesize a particular RNA transcript (these sequences can be located anywhere… not just in coding region)
enhancer
transcription control region
can be >50kb away from the coding region
cistron
a genetic unit encoding a single pp
most eukaryotic mRNAs are ____cistronic
mono
each mRNA encodes a single pp
in a bacterial polycistronic mRNA where is the ribosome located?
near the start site for each of the cistrons
translation initiation can begin at any of these sites
produces multiple proteins
in eukaryotic monocistronic mRNA where is the ribosome located?
5’-cap structure where ribosome binds
translation begins at closest AUG start codon
are introns usually longer than exons?
yes
longest in tintin gene…17,106bp
mutations in ____, _____, and _________ ______ ______ may all influence expression of the protein encoded by a simple transcription unit
exons, introns, transcription control regions
approximately ___% of human transcription units are ____
90%, complex
alternative splicing in fibronectin
multiple copies of 5 types of exons separated by introns
determines whether or not the secreted protein contains domains that adhere to cell surfaces
in fibroblasts and hepatocytes…ECM component
a mutation in the control region or in an exon shared by alternatively spliced mRNAs will affect…
all the alternative proteins
a mutation in an exon present in only one alternative mRNA will affect…
only the protein encoded by that mRNA
isoform
various proteins encoded by alternatively spliced mRNAs expressed from a single gene
solitary gene
25-50% of protein-coding genes are represented only once in the haploid genome
lysozyme
an enzyme that cleaves polysaccharides in bacterial cell walls
found in egg white protein and human tears
duplicated gene
genes with close but nonidentical sequences often located within 5-50kb of one another
gene family
a set of duplicated genes that encodes proteins with similar but nonidentical aa sequences
ex. genes encoding beta-like globins
protein family
the encoded, closely related, homologous proteins produced by a gene family
ex. kinases, vertebrate immunoglobulins, olfactory receptors
all hemoglobins formed from the different beta-like globin gene family carry oxygen in the blood, but….
exhibit different properties that are suited to their specific functions in human physiology
ex. A(y) and G(y) pp are expressed only during fetal life and have a higher affinity for oxygen
pseudogene
nonfunctional sequences even though they have exon-intron structure
mark location of gene duplication that occurred in our ancestors
not deleterious
segmental duplication
duplication of segments of a chromosome
occurred fairly often during evolution of multicellular plants and animals
members of gene families that arose relatively recently in evolution are often found…
near each other on the same chromosome
could also be found on different chromosomes
major cytoskeletal proteins
actins
tubulins
intermediate filaments (keratin)
heavily used gene products are encoded by…
multiple copies of genes
tandemly repeated arrays
genes encode identical or nearly identical proteins or functional RNAs
for genes encoding rRNA and nonprotein-coding RNAs like those involved in RNA splicing
why are tandemly repeated RNA genes needed?
to meet the great cellular demand for their transcripts
ex. during early embryonic development cells have a doubling time of 24 hrs and need enough rRNA to manage this
smRNA
small nuclear
function in RNA splicing
snoRNA
small nucleolar RNA
function in rRNA processing and base modification in the nucleus
miRNA
micro RNA
regulates the translation and stability of specific mRNAs
non-protein coding genes can encode…
functional RNAs
globin proteins comprise > __% of the total protein in developing red blood cells
50%
globin genes expressed at maximum rate
2 types of repetitious DNA
interspersed repeats (more common)
simple-sequence/satellite (less common)
satellite DNA (simple sequence DNA)
perfect or nearly perfect repeats of short sequences
6% of genome
1-500 bp
interspersed repeats
more common type of repetitious DNA
longer sequences of repeated DNA consisting of several types of transposable elements
microsatellite DNA
1-13 bp (most common is 1-4)
causes Huntington disease and myotonic dystrophy type 1
2 functions of satellite DNA
formation of centromeric heterochromatin that is necessary for proper segregation of chromosomes to daughter cells in mitosis
telomeres
minisatellites
larger than microsatellites
slight differences in lengths in individuals can be directed with Southern blotting
used for DNA fingerprinting
unclassified ____ DNA occupies a significant portion of the genome
spacer
25%, occurs between transcription units and is not repeated elsewhere in the genome
enhancers found here sometimes
what are transposable/mobile DNA elements
interspersed repeats, moderately repeated DNA, intermediate repeat DNA
sequences are copied and inserted into new sites in the genome by transposition
“selfish DNA” exist only to maintain themselves
during transposition of a mobile element, adjacent DNA…
is sometimes also mobilized
2nd mechanism for causing chromosomal DNA rearrangements
2 categories of mobile elements
those that transpose directly as DNA
those that transpose via an RNA intermediate that is transcribed from the mobile element by an RNA polymerase then converted back into dsDNA by reverse transcriptase
DNA transposons (transposons)
mobile elements that transpose directly as DNA
retrotransposons
mobile elements that transpose using an RNA intermediate
move but also remain at original location
analogous to infection by a retrovirus
insertion sequence
IS element
inserted stretches of DNA into the middle of a gene
inverted repeat
region that encodes transposase (enzyme required for transposition of IS element to new site)
3 functions of transposase in transposons
excise IS element in donor DNA
makes staggered cuts in a short sequence in target DNA
ligates 3’ termini of IS element to 5’ ends of cut donor DNA
2 types of retrotransposons
those containing long terminal repeats
those lacking long terminal repeats (most common)
long terminal repeats
250-600bp that are found on either end of the coding region in LTR retrotransposons
can function as a promoter and directs RNA processing
most common LTR retrotransposons in humans are
ERVs: endogenous retroviruses
nonviral retrotransposons
lack LTRs and are most common in mammals
moderately repeated DNA sequences
form 2 classes
2 classes of nonviral retrotransposons
long interspersed elements (LINEs)
short interspersed elements (SINEs)
key step in retroviral life cycle
forming retroviral genomic RNA from integrated retroviral DNA
LINEs are found in… and in humans…?
found in protozoans, insects, plants, and mammals
in humans… 3 families similar in mechanism of transposition but different in sequence (only L1) functional
LINE structure
flanked by short direct repeats
2 long ORFs
ORF1: encodes an RNA binding protein
ORF2: encodes a reverse transcriptase protein w/ DNA endonuclease activity
SINEs
2nd most abundant class of mobile elements in human genome
do not encode protein
transcribed by same nuclear polymerase used for tRNA
processed pseudogene
nonfunctional genomic copies of mRNA
flanked by short direct repeats
mobile element human diseases
hemophilia, Duchenne muscular dystrophy
exon shuffling
recombination between mobile DNA elements in introns of 2 separate genes
generates new genes made from new combinations of preexisting exons
3 ways mobile DNA elements are not parasitic selfish molecules, and have contributed to evolution
promote generation of gene families
creation of new genes via exon shuffling
forming complex regulatory regions that provide multifaceted control of gene expression
multiple genetic systems of eukaryotes
primary nuclear system
secondary systems with their own DNA: ribosomes, tRNAs in mitochondria and chloroplasts
mtDNA
mitochondrial DNA
some cells contain more than others
mitochondria contain multiple mtDNA molecules
inherited maternally and cytoplasmically
products of mitochondrial genes are not _____
exported
heteroplasmy
when mutations in mtDNA are found, cells contain a mix of mutant and wild-type mtDNAs
chloroplast transformation has led to the engineering of plants that are resistant to…
bacterial and fungal infections, drought, and herbicides
bioinformatics
use of computers to analyze sequence data (genomes)
by comparing aa sequences of a protein encoded by a newly cloned gene with he sequences of proteins of known function an investigator can look for…
sequence similarities that provide clues to the function of the encoded protein
related proteins exhibit more sequence similarity than the genes encoding them
BLAST computer program
BLAST
basic local alignment search tool
divides new protein sequence into shorter fragments and searches database for matches–assigns P values
low vs high p values
low p value: higher sequence similarity
high p value: less sequence similarity
structural motifs
short sequences recurring in many different proteins
similar functions
homologous (BLAST)
sufficiently similar in sequence to suggest a common ancestral sequence
ex. tubulin family of genes
paralogous (BLAST)
sequences that diverged as a result of gene duplication
orthologous (BLAST)
sequences that arose due to speciation (different species)
ORF
open reading frame where protein-coding sequences are found
stretch of DNA >100 codons beginning with start codon and ending with a stop codon
expressed sequence tag (EST)
aligned to a partial cDNA sequence
phenomena that generate more complexity in expressed proteins of higher eukaryotes
alternative splicing yielding multiple functioning mRNAs
variations in post-translational modification of proteins
increased numbers of cells built of the same kinds of proteins
