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)

IMG_1569

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