Unit 5
biotechnology
gel electrophoresis
gel made of a polymer as a sieve to separate a mixture of nucleic acid fragments by length
micropipette nucleic acids into gel
nucleic acids are drawn towards positive end of the gel
used to separate and visualize DNA fragments
shorter molecules move faster than longer ones
restriction enzymes
enzymes that cut DNA molecules at a limited number of specific locations
also called resitriciotn endonucleases
protect bacterial cell by cutting up foreign DNA from other organisms or phages
used to close foreign DNA into bacterial plasmids
most restriction sites are symmetrical
short DNA sequence
each restriction enzyme recognizes a very specific restriction site
cuts both DNA strands at precise points within restriction site
sticky ends
created from restriction enzymes cleaving sugar phosphate backbones in the 2 DNA strands in a staggered manner
can form hydrogen bonded base pads (hybridize) with complimentary sticky ends on any other DNA molecules cut with the same enzyme
temporary pairing, can be made permanent by DNA ligase
recombinant DNA
Process of cloning pieces of DNA using bacteria
first step is to obtain a plasmid (originally isolated from a bacterial cell and genetically engineered for efficient cloning)
then insert DNA from another source (foreign DNA) into it
resulting plasmid is recombinant dna
definition
a molecule containing DNA from 2 different sources, often different species
after process is complete, the plasmid can be turned back into a bacterial cell, called a recombinant bacterium
reverse transcriptase
turns sample sets of mRNAs into double stranded DNAs with corresponding sequences
resulting double stranded DNA called complimentary DNA (cDNA)
chapter 15
feedback inhibition
allows a cell to adapt to short term fluctuations in the supply of a substance it needs
when the product of a reaction shuts down the reaction, product is the inhibitor
cells can adjust the production of certain enzymes, can relate the expression of genes encoding the enzymes
parts of a gene
operon
segment containing operator, promotor, and genes they control
operator
"on-off switch"
segment of DNA
positioned within promotor or between promoter and enzyme coding genes
repressor
binds to operator and blocks attachment if RNA polymerase to the promoter
preventing transcription of the genes
specific for the operator of a particular operon
corepressor
small molecule that cooperates with a repressor portion to switch an operon off
inducer
inactivates the repressor
specific small molecule
activator
protein that binds to DNA and stimulates transcription of a gene
cAMP is an activator
trp operon
one of many operons in E.Coli genome
trp operon turned on in default state
can be switched on and off by trp repressor
means that RNA polymerase can bind to the promoter and transcribe regions of the gene
trp repressor protein
expressed continuously at a low rate
when tryptophan binds to trp repressor at an allosteric site the repressor protein changes to the active form to sttscth to the operator, turn the operon off
binding of repressors to operators is reversible
lac operon
inducible operon because it is usually off but can be stimulated into transcription
repressible operon because its transcription is usually on but can be inhibited
gene for β-galactose (lacZ) is part of lac operon which includes 2 other genes for coding enzymes that function in the use of lactose
entire transcription unit is under the command of one main opener and promoter
regulatory gene: lacI
located outside operon
codes for allosteric repressor protein that can switch off the lac operon by binding to the operator
is the protein product of a regulatory gene
inactive by itself, needs tryptophan as corepressor in order to bund to operator
lac repressor
active by itself
binds to operator and switches lac operon off
inducer inactivates it
CRP
cAMP receptor protein
activator
binds to DNA and stimulates transcription
when cAMP binds to it, CRP assumes active shape and can attach to a specific site at the upstream end of the lac operon
eukaryotic gene expression
chromatin modification
DNA packed into elaborate complexes called chromatin
chromatin helps regulate gene expression
DNA attaches to protein scaffolding at promoter
chemical modifications to histone can influence protein structure and gene expression
modifications catalyzed by enzymes
transcription of control elements and enhancers
enhancer
chromatin modifications do not change DNA sequence, but they can still be passed down to daughter cells
group of distal elements control elements
transcription
general transcription factors
act @ promoter of all genes
essential for all protein coding genes
a few bind to TATA box, many bind to proteins
interaction of general factors & RNA Pol 3 w/ a promoter usually leads to low rate of initiation and production of a few RNA transcripts
RNA trancripts come from non-expressed genes
specific transcription factors
bind to control elements
high levels of transcription in specific proteins depend on specific factors
proximal and distal control elements
each enhancer associated with one gene
activator proteins -> DNA binding domain & activation domains
facilitates series of protein-protein interactions, results in enhanced transcription
RNA processing
alternative RNA splicing
different mRNA molecules produced from same primary transcript, depends on introns and exons
regulatory proteins specific to a cell type control intron-exon choices by binding to RNA sequences w/ in primary transcript
can significantly expand the repertoire of a eukaryotic genome
mRNA degradation
gene expression also regulated in translation
many proteins undergo chemical modifications to make them functional
selective degradation
strictly regulates how long each protein is functional
miRNAs and siRNAs
miRNA
small single stranded RNAmolecules
capable of binding to complementary to complementary sequences in mRNA molecules
longer precursor is processed by cellular enzymes into an miRNA
single stranded RNA about 22 nucleotides long hat forms a complex with one or more proteins
siRNA
distinction based on subtle differences in the structure of precursers
blockage of gene expression by siRNA is called RNA interference (RNAi)
associate with same protiens, produce similar results
chapter 9
key features
genome
a cells endowment of DNA, genetic information
chromosomes
structures of packaged DNA, make replication and distribution manageable
chromatin
complex of DNA & proteins that is the biulding blocks for chromosomes
haploid cells
cell or organism that has only a single set of chromosomes, gamete sex cells, 23 in humans, meiosis
diploid cells
cell or organism that has paired chromosomes, 46 in humans, somatic body cells, created by mitosis
sister chromatids
joined copies of original chromosomes
centromere
region of chromosomal DNA where chromatid is attached most closely to the sister chromatin
interphase
G1
first gap
S
synthesis
G2
second gap
miotic stages
prophase
chromatin fibers become more tightly coiled, condensing into discrete chromosomes
nucleoli disappear
sister chromatids disappear
miotic spindle begins to form
centrosomes move away from eacother
metaphase
centrosomes @ opposite ends of cell
all chromosomes @ metaphase plate
kinetochores of each sister chromatid attached to kinetochore microtubules
anaphase
cohesion proteins are cleaved
each chromatid becomes full chromosome
2 daughter chromosomes move to opposite ends of cell
cell elongates
non-kinetochore microtubliles lengthen
telophase
2 daughter nuclei formed in cell
nucleoli reappear
remaining spindle microtubules are depolymerized
cytokinesis
2 daughter cells appear
involves formation of cleavage furrow in animal cells
miotic spindle
begins formation in cytoplasm during prophase, made of fibers, microtubules, & associated proteins
centrosomes
subcellualr region containing material that functions throughout cell cycle to organize the cells microtubules
plant cells
no cleavage furrow, cell plate instead
cell plate enlarges until surrounding membrane fuses with perimeter of plasma membrane
animal cells
actin filaments interact w/ myosin molecules
ring contracts
cleavage furrow deepens
binary fision
"division in half"
asexual reproduction
prokaryotic cellular division
cell cycle control system
cyclically operating set of molecules in the cell that both triggers and coordinated key events int he system
density dependent inhibition
when cells get too crowded, they stop dividing
anchorage dependence
where cells need something to cling onto in order to divide
cancer
tumors
malignant
metastasis
spread of cancer cells from their original location
benign
able to spread to other parts of the body, can/will kill you
abnormal cells in one spot, not spreading/can't move to other parts of the body, won't kill you
chapter 16
oncogenes and proto oncogenes
oncogenes
cancer causing genes
porto-oncogenes
code for proteins that stimulate normal cell growth & division
tumor suppressor genes
p53 gene
guardian angel gene
codes for specific transcription factor that codes for specific synthesis of proteins to inhibit cycle
multistep model (of colon cancer)
causes of cancer
UV light
radiation
cigarette smoke
viruses that disrupt photo-oncogenes
hereditary mutations in photo-oncogenes
prometaphase
nuclear envelop fragmanets
chromosomes continue condensing
each of 2 chromatids each has a kinetochore
checkpoint: no go ahead signal causes cell to exit cycle and enter G0
G0
non-dividing stage
click to edit
DNA is only replicated during synthesis
codes for release of other inhibitors to the cell cycle