Exam II review starting w/Lecture 18 Flashcards
Several key differences b/w gene regulation in eukaryotes and bacteria
In eukaryotes:
-Each gene has its own promotor and is transcribed separate
DNA must unwind from histones before transcription
Transcription/Translation are separated in time and space
What caused hemophilia in the family of Tsar Nicholas
Defect in splice site caused inactivation of hemophilia gene
Collinearity
Concept that a continuous sequence of nucleotides in DNA encodes a continuous sequence of AAs in proteins
-The number of nucleotides in gene is proportional to number of AAs in protein
Do eukaryotic genes display collinearity, and how was this decision made
It does not appear so. After hybridizing DNA to mRNA, researchers realized that there are non-coding regions of DNA b/w some coding regions
Which sequences at beginning and end of RNA are not translated
Promotor, RNA coding sequence, Terminator
Function of 5’ cap
Facilitates binding of ribosome to 5’ end of mRNA
Function of 3’ tail
Increases stability, facilitates binding of ribosome
RNA editing does what
Alters nucleotide sequence of mRNA
RNA splicing function
Removes noncoding introns
Facilitates export of mRNA to cytoplasm
Splicing of pre-mRNA requres
Consensus sequences at the 5’ and 3’ splice sites and a weak one at the branch point
RNA splicing takes place within a
Spliceosome
If a splice site were mutated and splicing did not take place, what would happen to the protein encoded
It would be shorter than normal
RNA editing is carried out by
Guide RNAs
Steps in RNA posttranscriptional processing
- 5’ cap is added
- 3’ poly a tail added
- RNA splicing
siRNA origin, target
Origin- mRNA, transposon or virus
Target- Genes from which they were transcribed
miRNA origin, target
Origin- RNA transcribed from distinct gene
Target- Genes other than those from which they were transcribed
snoRNA
Primarily guide chemical modifications of other RNA
Formation of rRNA
Produced from precursor RNA transcripts that are methylated, cleaved and proceed to mature rRNA
Somatic mutations
Arise in tissues other than those that produce gametes
Not passed on
Germ-line mutations
Arise in tissues that produce gametes
Passed to offspring
De novo mutation
Alteration in gene that is present for the first time in one family member
Can be germ line or somatic
Transition mutation
Substitution of a purine for a purine or pyrimidine for pyrimidine
Transversion mutation
Purine for pyrimidine or visa versa
Loss of function mutation
Complete or partial absence of normal function
Usually recessive
Neutral mutation
Missense mutation that alters the amino acid sequence but does not change function
Silent mutation
Mutation changes codon sequence but not the amino acid
Missense mutation
Base substitution that results in a different amino acid
Nonsense mutation
Mutation that changes a sense codon into a termination codon
Tautomeric shifts
Proton position shifts, allowing mispairing of a base
What causes insertions and deletions
Unequal crossing over
Intercalating agents
Insert themselves between adjacent bases in DNA, distorting the helix
Ames test
Bacteria that cannot synthesize histidine due to a mutation are placed in a histidine-free media and exposed to a mutagen
-Any chemical that increases the number of colonies (due to reverse mutation) is mutagenic and likely carcinogenic
Base excision repair
Removes and replaces single mismatches
Nucleotide excision repair
Removes bulky DNA lesions like pyrimidine dimers
Xeroderma pigmentosum is caused by
Defect in NER
Direct repair
Example- methyltransferase removes extra methyl group that had caused pyrimidine alkylation (Guanine->O6 methylguanine)- restores back to guanine
Transposable elements make up what % of DNA
45
Short flanking direct repeats
Short flanking repeats are present on both sides of the TE
- Do not travel with the TE
- Regenerated at the point of insertion after staggered cuts are made
Terminal inverted repeats
Sequences are inverted and complementary on the same strand
Recognized by enzyme that catalyze transposition
Required for transposition
Replicative transposition
Copy and paste- new copy is introduced at new site while old copy remains at original site
Enzymes involved in replicative transposition
Transposase- binds to end of transposon and catalyzes the movement
Resolvase- Separates the two transposons contained in a cointegrate
Non replicative transposition
Cut and paste- removed from one area of DNA and added to another
- Cleavage requires transposase produced by transposable element
- Original site repaired using homologous template
Retrotransposons
RNA transcribed from DNA transposable element
RNA is copied back to another DNA site using reverse transcriptase
-Have long terminal direct repeats
-These are more common that DNA transposons in eukaryotes
SINE and LINES constitute what % of DNA respectively
SINEs- 11%
LINES- 21%
Transposable element oriented in same direction leads to
Deletion
Transposable elements oriented in opposite direction leads to
Inversion
Transposons in genome evolution
Some say it has no positive effect and is only harmful
Some say it creates genetic diversity and is useful
Effect of mutated p53 on transposable elements/cancer
P53 may be a repressor of transposable elements. If it is not functioning, excessive transposable elements may destabilize the genome
Human genome project social consequences
First large scientific undertaking to dedicate a portion of its budget for research into social, legal and ethical implications of the increasing knowledge of human genetic makeup
Genomics is
The branch of molecular biology concerned with structure, function, evolution and mapping of genomes
Whole genome mutagenesis
Can identify genes associated with specific traits
Synthetic genomics
Uses aspects of genetic modification of pre-existing life forms, or artificial gene synthesis, to create new DNA/chromosomes or entire lifeforms
Metagenomics
The study of genetic material recovered directly from environmental samples
-evaluating human microbes
Comparative genomics
Comparing genomic features among organisms
Look at evolutionary changes
Paleogenomics
The study of the evolutionary history through the examination of preserved genetic material from the remains of ancient organisms (this is also comparative genomics)
HLI
Human longevity inc.
Combines genomic and phenotypic information to accelerate the understanding of human health
SDS PAGE
Method for the separation of charged molecules by their molecular masses
-Denatured proteins
Isoelectric focusing
Separates native proteins by differences in their isoelectric point
2D PAGE
Proteins are separated by charge in one dimension and by mass in the other dimension
Mass spectrometry
Ionizes chemical species and sorts them based on their mass to charge ratio
-Can determine the identity of a protein in question as long as it has been identified previously and is in system
Protein microarray
Tracks the interactions b/w proteins and can determine the function of proteins on a large scale
Yeast 2 hybrid
Takes advantage of fact that binding domain and activating domains can still work when separated but placed close together
-Identifies protein-protein interaction or protein-DNA interaction on small scale
Interactome
The whole set of molecular interactions in a particular cell
Mechanism of prion disease
a-helix converted to b-sheet structure causes prion
Triggers chain reaction that forms amyloid fibers and plaques
Cruetzfeldt-Jacob disease
BSE mad cow disease
SIFT
Predicts whether an amino acid substitution affects protein function
Ab neutralisation
Neutralizing Abs block parts of the surface of bacterial cell to render its attack ineffective
Ab agglutination
Abs glue together foreign cells into clumps that are attractive for phagocytosis
Ab precipitation
Abs glue together serum-soluble antigens, forcing them to precipitate out of solution in clumps that are attractive for phagocytosis
The most important genes deciding the fate of a transplanted cell/organ belong to the ___ family
MHC
MHC gene is located on chromosome
6
Genes in what family are linked to Type 1 Diabetes
HLA family account for approximately 40-50% of familial T1D
The hygiene hypothesis
A farming environment protects against development of asthma, hay fever and atopic sensitization in children
Determination
Cell becomes restricted to given developmental pathway
Differentiation
Cell becomes dedicated to perform a specific function
Embryonic stem cells are (potency), they are found where and can become
Pleuripotent- found in ICM of blastocyst, can form any cell in body besides placenta
Where are totipotent cells found
In the morula
Hematopoietic stem cells are (potency)
Multipotent
Somatic cell nuclear transfer
Used to clone sheep/monkeys
Nucleus taken out of egg cell, replaced with nucleus from donor cell and develops normally
Egg polarity gene function
Establishment of main body axes (anterior-posterior/dorsal-ventral)
Segmentation gene function
Determination of number and polarity of body segments
Homeotic gene function
Establishment of identity of each segment
Egg polarity genes are from mom/dad
Maternal origin- determination of axes of embryo are initiated by maternal mRNA
Morphogen
A protein that affects the developmental fate of surround region through a concentration gradient
Determination of the dorsal ventral axis is by
Dorsal gen
Determination of the anterior posterior axis is by
Bicoid, nanos, hunchback genes
Bicoid is concentrated anteriorly
Nanos is concentrated posteriorly
Gap gene mutations
Delete groups of adjacent segments
Pair-rule gene mutation
Delete same part of pattern in every other segment
Segment polarity gene mutation
Affect polarity of segment; part of segment replaced by mirror image of part of another segment
Homeotic genes
Determine the identity of individual segments
Hox genes
Products are TFs
They contain DNA sequence Homeobox- encodes a protein domain (the homeodomain) which when expressed can bind DNA
-Order of hox genes is physically the same as order of expression on anterior-posterior axis of developing animal
Tbox genes
Plays role in inducing mesodermal germ layer and coordinating outgrowth of arm/leg
Helix loop helix genes
Important in myogenesis
Code for helix loop helix TFs
Involved in homodimerization and heterodimerization
Forkhead (Fox) genes
Type of helix loop helix family
Expressed in many developing organs throughout the body
Homeobox containing genes play major role in
Cranio-caudal segmentation, not only along main body axis but within development of many organs
Homeobox containing genes are activated 5-3 or 3-5 fashion
3-5 fashion, opposite of transcription direction
Genes on 3’ end are expressed earlier and more anteriorly than on 5’ end
Loss of function mutations in homeobox results in
Posterior to anterior transformations
Gain of function mutations in homeobox results in
Anterior to posterior transformations
Homeobox is ____ nucleotide sequence coding for ___ amino acid homeodomain
180 nucleotide sequence coding for the 60 amino acid homeodomain
Hox genes in mammals
4 clusters of Hox genes containing 9-11 genes each
Order of homeobox genes activated
Egg polarity genes Gap genes Pair rule genes Segment polarity genes Homeotic genes
Heterotaxy
Lack of differentiation of right sided and left sided organs during fetal development
(may have two right lungs)
Population genetics
The study of the distribution and change in frequency of alleles within populations
Evolution
A change in the gene frequency over time in a population
Population
A group of interbreeding, sexually reproducing individuals sharing a common set of genes
Hardy Weinberg law
Allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences
Hardy Weinberg assumptions
Population is large Random mating No mutations No migration No natural selection
Alleles identical by descent
Alleles descended from the same copy in a common ancestor
Alleles identical by state
Alleles that are the same in structure and function but are descended from two different copies in ancestors
Inbreeding depression
Increased appearance of lethal and deleterious traits with inbreeding
Inbreeding increases the percentage of homozygous individuals in the population
Outcrossing
The avoidance of mating between related individuals
Natural selection
The differential survival and reproduction of individuals due to difference in phenotype
Migration
Movement of populations, groups or individuals. Migration enables gene flow - movement of genes from one population to another
Genetic drift
The change in frequency of a gene allele in a population due to random sampling of organisms
