BIO202 Exam 4 Flashcards
What is the trp operon?
A gene that codes for the amino acid tryptophan. It’s turned off when tryptophan levels are high and turned off when they are low.
What regulates the trp operon?
Tryptophan levels and the trp repressor. When the trp repressor is bound to tryptophan, operon expression is blocked
What regulates tryptophan biosynthesis?
The trp operon and attenuation
Silent mutation
When a change in a nucleotide pair transforms one codon into another that is translated into the same amino acid. Results in no observable change on the phenotype.
missense mutation
Substitutions that change one amino acid into another.
nonsense mutation
When a point mutation changes a codon for an amino acid into a stop codon
mutagens
physical and chemical agents that interact with DNA and cause mutations
reciprocal translocation
parts of two non-homologous chromosomes are switched
TATA box
A sequence of nucleotides found at the promoter of eukaryotes. It plays an important role in forming the transcription initiation complex by binding a general transcription factor. The binding of the general transcription factor to the TATA box allows for RNA pol II to bind correctly for transcription.
Point mutation
The substitution of one nucleotide base in DNA for another
Nucleosome
DNA wound around a core of histones
Activators
Specific proteins which enhance transcription in eukaryotes. They bind control elements in enhancers, mediator proteins, and general transcription factors.
Splicing
Takes place after transcription and is one way the pre-mRNA is processed to prepare the mRNA for translation. Spliceosomes proteins remove introns.
Enhancers
Regulate transcription by enhancing the activity of RNA-polymerase at a single promoter site.
gene regulation
determining which genes are expressed
Operons
Exist in bacteria but not in eukaryotes. They are a cluster of genes coding for proteins that function together
Properties of operons
Genes are adjacent and have a single promoter. 1 mRNA is made that codes for several proteins.
Transcription
RNA polymerase binds to a promoter and moves down the gene to make RNA
polycistronic mRNA
codes for more than one protein (bacteria)
monocistronic mRNA
codes for 1 protein (eukaryotes)
Operator
DNA region between the promoter and the first gene of the operon (only in bacteria)
Where are operons located?
Only in bacteria
Repressor proteins
Can inhibit transcription by binding operator and blocking RNA polymerase. They are examples of regulator proteins.
Regulator proteins
Bind DNA and affect transcription
Who is tryptophan made?
In E. coli it is made by a biochemical pathway. A precursor compound is converted to trp by a series of steps - each catalyzed by an enzyme.
Where do the enzymes needed for trp synthesis come from?
A different gene codes for each one
When is the Trp operon expressed?
Only if Trp is not available in the environment
Trp repressor
It is specific for the Trp operon and it will always bind Trp if it is available. Binding changes the repressor’s conformation.
When does Trp repressor bind to the operator?
Only when it is bound to Trp
Mutation
uncorrected error in DNA sequence
Insertion or deletion
One or more bases is added or left out
Effect of missense mutation
When a point mutation changes that amino acid sequence, it can have a large/small effect on protein function or no effect at all.
Sickle cell disease
Caused by a missense mutation on the beta-globin gene
Frameshift mutations
Change a reading frame and they drastically change the amino acid sequence and are very serious.
Reading frame
Division of bases on a strand into codons
Insertions or deletions
Extra or missing nucleotides. Unless they occur in multiples of 3, they are frameshift mutations
Alterations in chromosome structure
Result from abnormal chromosomes breakage; not crossing over in meiosis
Deletion
Part of the chromosome is lost
Duplication
Part of the chromosome is duplicated
Inversion
Part of the chromosome is turned backwards
Translocations can lead to
cancer
Transcription initiation complex
RNA pol. and transcription factors
Control elements
Specific transcription factors that bind to DNA at sequences and help the initiation complex bind the promoter
Proximal control elements
Close to the promoter
Distal control elements
They’re far from the promoter. Groups of these are called enhancers
Enhancers
Groups of distal control elements
Activators and repressors in eukaryotic cells
Specific transcription factors that bind enhancers to control gene expression
DNA-bending proteins
bring activators close to the promoter. Activators can bind general transcription factors and mediator proteins.
Tissue specific transcription factors
Are only present in some cells. Genes they regulate are only expressed in those cells. Unless needed, activators for certain genes are not present.
Combinatorial control of gene activation
Several control elements regulate each gene. Different activators bind each one. Independent adjusting the levels of each activator can fine-tune the gene expressions
Coordinately-controlled genes
Each is associated with a separate copy of the same control element that binds the same activator.
SRE
Sterol response elements are associated with genes for cholesterol synthesis in human cells. Each has its own promoter and they’re on different chromosomes. Each gene s expressed only when cholesterol levels are low.
How is cholesterol produced in human cells?
When cholesterol levels are low genes for synthesis are expressed. An activator, SREBP binds to each SRE to stimulate transcription of that gene.
Coordinate expression
When genes are expressed together that produce the enzymes that work together
Histone tail acetylation
loosens chromatin and enhances transcription
Protein domains
Can fold independently and can contain different secondary structure elements. They can also have independent functions.
Proteins are mix and match combinations of different
domains
Exon shuffling
Can rearrange domains in new combinations making new genes
SH2 domain
binds phospho-tyrosine to another protein
Helix-turn-helix
HTH domain that binds DNA
All cancers
Have unregulated cell division and result from mutations
PDGFR
PDGF reception is a receptor tyrosine kinase on the plasma membrane that binds PDGF (growth factor) in the bloodstream
Constitutively-active mutants
Always have the active conformation; even without getting a signal. This can lead to unregulated cell division
Oncoprotein
Constitutively active protein that can cause cancer
Oncogene
mutated gene for protein
Proto-oncogene
normal gene that becomes an oncogene when mutated
Mutagens
agents causing mutations
Carcinogens
can cause cancer
p53
A transcription factor that stimulates production of proteins that slow the cell cycle (allow time for DNA to repair), repair DNA, and/or kill cell by apoptosis if damage is too bad.
Genome projects
Sequencing the entire genome of a species
Transposable elements
Can replicate and insert new copies in genome. (Rare) Have no known function and are probably parasites in our genomes.
Transposons
Move in a genome by a DNA intermediate
Retrotransposons
Move in a genome using a RNA intermediate. Most transposable elements in eukaryotic genomes are retrotransposons. Always remain in original site as well as inserting a copy in a new site.
Transposon mobility
Sometimes called cut and paste (transposon is cut out of old site and moves into a new site in genome).
Sometimes called copy and paste (Transposon stays in the original site, but a copy is made and inserted in a new site)
Reverse transcriptase
Retrotransposon is transcribed into RNA that codes for a protein: reverse transcriptase. It is translated and makes a complementary DNA copy of the RNA so it can be inserted into another site (Copy and paste).
Retroviruses
Most likely derived from retrotransposons. DNA made enters the nucleus and inserts permanently into a chromosome. Then transcribed to make more viral RNA
Multigene families
Groups of similar genes whose protein products perform related functions.
Pseudogenes
Genes in the cluster that are never expressed. May have non-functional promoters.
Unequal crossing-over
Chromosomes break and rejoin in different places. As a result, 1 chromosomes gets 2 copies of a gene and the other gets 0.
Viruses
Infectious particles that contain ONLY a nucleic acid genome, a protein coat(capsid), and a few other proteins. They sometimes have a membrane envelope.
They can’t live independently. They must infect a host to reproduce.
How do viruses function?
They take over host cell machinery for almost all steps in making new viruses. Host cell becomes a factory for virus production.
RNA-dependent RNA polymerase
A special viral enzyme used to make complementary copies of viral RNA.
Capsid proteins
viral proteins made on free ribosomes using host cell
Glycoproteins
viral membrane proteins made on bound ribosomes. They’re transported to the plasma membrane in vesicles
3 ways bacteria can acquire new DNA
Transformation, transduction, and conjugation.
Transformation
Uptake of free DNA (bacteria)
Transduction
bacteriophages carry DNA between cells
Conjugation
“bacterial sex”; transfer of chromosomal DNA between bacteria from F+ cell OR Hfr cell to a F- cell.
The temporary joining of 2 bacteria by sex pili extending from 1 cell. Sex pilus usually breaks part way through the transfer and only part of the chromosome is transferred.
Sex pilus
Hollow tube. DNA moves through it between cells.
F (fertility) factor
Piece of DNA that codes for sex pilus proteins. ONLY bacteria with F factor make sex pili.
Where do F factors exist?
They’re either integrated into the chromosomes or free as plasmids
Plasmid
Small, circular self-replicating DNA that’s separate from the chromosome
F+ cell
Has F factor as plasmid
Hfr
Jas F factor in chromosome
F- cell
Has NO F factor
Nucleic acid probe
Short, synthetic, single-stranded DNA fragment complementary to the gene of interest
PCR
Polymerase chain reaction can find the correct cDNA in a complex mixture and make many copies of it. (Used in insulin treatments for diabetes)
What is the 3-step cycle that PCRs undergo?
- Heat: to denature (separate strands)
- Cool: primers bind template strands
3: Extend: DNA polymerase makes a new strand, starting with the primer
What is the 3-step cycle that PCRs undergo?
- Heat: to denature (separate strands)
- Cool: primers bind template strands
3: Extend: DNA polymerase makes a new strand, starting with the primer
Restriction enzymes
endonucleases that cleave DNA at specific sequences
Plasmids
Replicate in bacteria and can accept foreign DNA fragments.
They can contain genes for antibiotic resistance that allow bacterial growth even with antibiotics.
Separation using agarose gels
DNA fragments can be separated from each other based on length
How are DNA fragments separated by length?
Using agarose gel and an electric field this can be done. All DNA fragments are negatively charged and move toward the anode. Short fragments can move through the gel faster than the long ones.
Detecting DNA fragments in agarose gel
The gel is soaked in a fluorescent dye that binds the DNA
Tube gels
Are used to separate fluorescently-labeled DNA fragments. The strands move down the tube with the longest labeled strands near the top and the shortest at the bottom
How to detect DNA fragments in tube gels
A laser is passed through fluorescently-labeled DNA fragments and detects them as peaks.
ddNTPs
dideoxy-NTPs can be added to a strand in order to determine a nucleotide sequence (by labeling them with a fluorescent dye). They lack the 3’OH but otherwise, it’s the same as a dNTP. They end the strand.
Goal of genetically modified (transgenic) plants and animals
- Disease resistance
- Better nutritional properties
- Faster growth
Spermatogenesis
The formation of sperm. It occurs in the seminiferous tubules tightly packed in the testes.
Seminiferous tubules
Immature sperm cells are at the outside of the tubule wall. They move inward as they mature, meiosis also occurs. Mature sperm are then release into the lumen of the tubules.
Ovary
Where eggs form via oogenesis.
Follicles
Layers of cells surrounding each egg in the ovary
Ovulation
Each month 1 egg bursts from the follicle and is released into the oviduct
Fertilization
fusion of two haploid gametes to give diploid zygote
Where does fertilization occur?
In the oviduct. Then the zygote moves to the uterus for implantation
Acrosome
vesicle in the head of sperm
Acrosome reaction
Fusion of acrosome with plasma membrane of sperm (secretion of contents)
Cortical reaction
blocks polyspermy which is lethal
Cortical granules
Vesicles stored in the egg just under the plasma membrane. Release contents of the cortical granules cause material surrounding egg to lift egg surface and harden into fertilization envelope; blocks sperm
blastomeres
new cells formed during cleavage of zygote
morula
Solid ball of cells formed during cleavage
blastula
Formed after cleavage when the cells move and embryo changes shape to a hollow ball of cells with lumen called a blastocoel
blastocoel
lumen of blastula
Gastrulation
When cells moves to change the shape of an embryo and form the gastrula. One side of blastula pushes in at blastopore. Continues to push in to form the archenteron
What part of the body will the blastopore become?
The anus
What part of the body will the archenteron become?
The digestive tract
Meroblastic cleavage
off-center blastocoel
Holoblastic cleavage
blastocoel in the center
Where does cleavage occur in mammals?
In the oviduct
Blastocyst
Human’s version of a blastula. It’s a hollow ball of cells with an inner mass inside and a trophoblast outside.
Inner cell mass
The part of the blastocyst that undergoes gastrulation and becomes the whole embryo.
Trophoblase
The part of the blastocyst that becomes part of the placenta
Placenta
A combination of blood vessels from mother and embryo. Allows exchange of nutrients, wastes, and gases.
Pattern formation
setting up basic body plan so tissues and organs develop in the right place
Mutation of bicoid
destroys function and gives an embryo with two back ends (no front end)
Embryonic lethal
A mutation that gives defective protein. As a result, organism dies early in development.
Bicoid protein
A transcription factor that stimulates expression of certain genes that control segment formation.
Segments
Basic units of pattern formation in flies (both embryo and adult) Adult structures develop from segments in the larva.
Homeotic genes
Control development of each segment into an adult structure.
They form a gene family and code for transcription factors that share a short conserved sequence; homeobox that encodes a homeodomain
Homeotic mutation
Yields a defective homeotic gene. If this happens, another homeotic gene takes over. As a result, one body part is substituted for another.
Stem cells
Undifferentiated cells that can differentiate into other cell types
Embryonic stem cells
Cells from blastocyst that can differentiate into all tissues
Totipotent cells
can give rise to all cells of an adult
Pluripotent stem cells
Are present even in adults. They can differentiate into some but not all cells types.
Master regulatory genes
protein products commit a cell to a particular fate
