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Chapter 10: Molecular Biology of the Gene, Chapter 12- DNA Technology and…
Chapter 10: Molecular Biology of the Gene
The Structure of Genetic Material
Experiments found DNA to be genetic material
Griffith's Experiments
Found bacteria became pathogenic when mixed with dead infected bacteria
Bacteriophages "phages"
: viruses that exclusively infect bacteria
Hershey and Chase tested with a T2 phage
Found that a virus attaches to hose, injects DNA (not protein), produces new phage proteins and DNA, lyse to release
DNA and RNA
long chains of
nucleotides
: monomers of nucleic acids, considred
polynucleotides
(nucleotide polymer chain)
Bonds are formed by
sugar-phosphate backbone
Nucleotide bases: thymine/
uracil
& cytosine (pyrimidines), adenine & guanine (purines)
DNA = deoxyribonucleic acid
Watson & Crick used experiments and Rosalind Franklin's picture to find that DNA is a
double helix
with complementary nucleotide bonds (
thymine
&
adenine
and
cytosine
&
guanine
)
DNA Replication
When DNA replicates, each daughter contains one parent strand =
semiconservative model
Proceeds in two directions and multiple sites
Starts at origins of replication, creating bubbles that elongate then fuse together
DNA polymerase
enzymes link the DNA nucleotides to growing daughter strands
Daughter strand grows from 5' to 3'
When growing 3' to 5', can only do so in Okazaki fragments which are pieced together by
DNA ligase
The Flow of Genetic Information from DNA to RNA to Protein
Proteins link genotypes and phenotypes
DNA goes through
transcription
to create RNA, which goes through
translation
to create a protein
Transcription: the synthesis of RNA from DNA
Initiation
:
RNA polymerase
(enzyme that forms a new RNA strand by following base-pairing rules during transcription) attaches to
promoter
( acts as the binding site for RNA polymerase and determines where transcription starts) and begins to open double helix and synthesize RNA using complementary nucleotide bases
Elongation
: new RNA strand grows and begins to peel away from DNA, synthesis of RNA continues to follow base-pairing rules
Termination
: when RNA polymerase reaches
terminator
DNA, will detach from new RNA and gene
Translation: the synthesis of a protein from RNA
Codon (three-letter word) to amino acid (protein word). The interpreter is tRNA
Transfer RNA
transfers amino acids from the cytoplasm to the polypeptide in the ribosome, picking up appropriate amino acids and recognizing appropriate codons from the mRNA
tRNA has an
anticodon
: a specific codon triplet that compliments an mRNA codon
Takes place in the
ribosome
: coordinates functioning of mRNA, tRNA, and catalyzes polypeptide synthesis
Has sites where mRNA and tRNA bind. Made of subunits that have proteins and
ribosomal RNA
(rRNA)
tRNA attaches to A site (for arriving tRNA in ribosome), polypeptide chain bonds with new amino acid, then tRNA translocates to P site which leaves room for new tRNA
gene
: a region of DNA that can be expressed to produce a functional product that is either a polypeptide or an RNA molecule
Codons
(sets of three bases) translate into amino acids
Triplet code: the genetic instructions for amino acid sequence that comes in threes (codons)
Genetic code
(amino translations of each of the nucleotide triplets) dictates codons
Start codon
marks whee translation begins on mRNA while
stop codon
signals the stop of translation and does not code for an amino acid
messenger RNA is processed before leaving the nucleus
mRNA
: the kind of RNA that encodes amino acid sequences
Introns
(non-coding stretches of nucleotides) are removed, and
extrons
(parts of the gene that are expressed) are joined together
Cutting and pasting process is called
RNA splicing
Mutations can affect genes
mutation
: any change to genetic information of a cell or
virus
(an infectious particle consisting of little more than “genes in a box”; a bit of nucleic acid wrapped in protein coat called a
capsid
)
Silent point mutation
: a substitution that causes no change in the amino acid sequence
Mutagen
: any chemical or physical agents that can cause mutations
Missense point mutation
: when a substitution changes which amino acid a codon codes for
Nonsense point mutation
: when a substitution turns an amino acid codon into a stop codon
Frameshift mutation
: when an addition or subtraction of a codon changes the groupings of codons
The Genetics of Viruses and Bacteria
viral DNA can become part of the host chromosome
Lytic Cycle
results in the lysis of the hose cell to release the new virus
becomes a virus factory until the lytic lyses and releases
Lysogenic cycle
is when viral DNA replicates without destroying hose cell
inserted into bacterial chromosome to create a
prophage
, viral DNA is then transfered to daughter cells
Phage DNA enters bacterium and forms a loop
Plants and animals become diseased when RNA viruses synthesize
enters cytoplasm, protein coat is digested, RNA synthesis is conducted by the viral enzyme, the protein is created or new viral genomes are created, they assemble, and exit cytoplasm to infect other areas
Emerging viruses
: ones that seem to burst on to the scene, becoming apparent to medical community suddenly
Ex.
AIDS
: acquired immunodeficiency syndrome
Ex.
HIV
: human immunodeficiency virus that causes AIDS
Example of a
retrovirus
: RNA virus that reproduces by means of a DNA molecule
Carries reverse transcriptase: catalyzes reverse transcription,; the synthesis of DNA on an RNA template
viruses differ from
prions
: a misfolded form of a normal brain protein
Bacteria transferring DNA
transformation
: uptake foreign DNA from the surrounding environment
Transduction
: the transfer of bacterial genes by a phage
Conjugation
: DNA transfer between mate bacteria cells swap DNA
F factor
: carries genes for making sex pili and other requirements for conjugation, contains origin of replication
Plasmid
: a small, circular DNA molecule separate from the bacterial chromosome
R plasmid: plasmids that carry genes that can affect the survival of the cell
Chapter 12- DNA Technology and Genomics
Gene Cloning and Editing
Genes can be cloned
biotechnology
: the manipulation of organisms or their components to make useful products
DNA technology
: modern laboratory techniques for studying and manipulating genetic material
Genetic engineering
: the direct manipulation of genes for practical purposes
CRISPR-Cas9 system
Recombinant DNA
: formed when scientists combine pieces of DNA from two different sources
plasmids
: small, circular DNA molecules that replicate separately from the much larger bacterial chromosome
key tools for
DNA cloning
: the production of many identical copies of a target segment of DNA
bacterial plasmid serves as the
vector
, DNA from another organism is isolated containing gene of interest, the plasmid and DNA are cut with the same enzyme to isolate the gene of interest. The targeted fragment and plasmid DNA are then combined and have
DNA ligase
added to join the molecules. The recombinant plasmid is then taken up by a bacterium through transformation to reproduce.
clones
are then made
Process is called
gene cloning
reverse transcriptase
(a viral enzyme that can synthesize DNA from an RNA template) can help just get isolated gene by getting
complementary DNA
(DNA that results from reverse transcriptase, represents only the subset of genes that had been transcribed into mRNA)
Enzymes are used to "cut and paste" DNA
restriction enzyme
: the cutting, bacterial enzyme tools to cut and paste DNA, has own specific sequence it looks for and cuts with a zig-zag cut creating sticky ends
restriction site
: a particular short DNA sequence targeted by a restriction enzyme
restriction fragments
: the cut pieces of DNA that is yielded by the restriction enzyme
Nucleic acid probes
can help label
the labeled, complementary molecule used to find a specific gene or other nucleotide sequence within a mass of DNA
highlights gene of interest for better targets for researchers
Genetically Modified Organisms
recombinant cells and organisms can mass-produce gene products
easiest to do with bacteria
sometimes use eukaryotic cells because they produce glycoproteins
We can manipulate a whole animal to provide human proteins
Impacts on the pharmaceutical industry and medicine
Treating diseases
human insulin- bacteria synthesizes and secretes the human form of insulin
human growth hormone- provided to children with dwarfism when they don't produce enough
Diagnosing diseases- technology pins microorganisms that can cause disease
Preventing diseases
vaccines
: harmless variant or derivative of a pathogen—usually a bacterium or virus—that is used to stimulate the immune system to mount a lasting defense against that pathogen, thereby preventing disease
GMOs are changing agriculture
genetically modified organism
: organisms that have acquired one or more genes by artificial means
transgenic organism
: the recombinant organism resulting from a gene that is transplanted from one organism into another, typically of another species
Desired trait is modified, then plasmid is put into the plant cell to combine with chromosome, then the plant grows and passes traits down
Concerns about GMOs
Are they safe for humans? Tested in pigs and found no significant differences. Also tested in kids and found the GMO food increased production of vitamin A
Environmental safety. GMOs can transfer modified genes to surrounding wildlife
Companies are not required to label GMOs in America
Gene therapy can treat diseases
gene therapy
: alteration of a diseased individual’s genes for therapeutic purposes
gene from a healthy person is cloned, converted to RNA, then inserted into the RNA genome of a harmless virus. Bone marrow is taken from patient and they are infected with the recombinant virus, which then inserts DNA into the patient's DNA. The engineered cells are put back into patient, which then produces desired protein
DNA profiling
analysis of genes can produce a DNA profile
helped with
forensics
: the scientific analysis of evidence for crime scene investigations and other legal proceedings
provided evidence in forensic investigations
DNA profiling
: the analysis of DNA samples to determine whether they came from the same individual
DNA samples are isolated, selected markers are amplified, and then amplified markers are compared
PCR method amplifies DNA sequences
polymerase chain reaction
(PCR): a technique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the laboratory. Uses primers
Primers
: short, chemically synthesized single-stranded DNA molecules with sequences that are complementary to sequences at each end of the target sequence. Will help direct DNA polymerase enzymes
Reaction mixture is heated to separate DNA double helices. Then, strands are cooled and primer molecules hydrogen-bond target sequences. Then, heat-stable DNA polymerase builds new DNA strands by extending the primers
Sorting DNA by size
gel electrophoresis
: a method that separates macromolecules on the basis of size, electrical charge, or other physical properties
DNA fragments are put into wells, which then flow down gel toward positively charged side of power source. Longer molecules stay near the top and shorter molecules are near the bottom
Short tandem analysis is used
repetitive DNA
: consists of nucleotide sequences that are present in multiple copies of the genome
short tandem repeat
(STR): repetitive DNA that is short sequences repeated many times in a row
STR analysis
: a method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome
Genomics and Bioinformatics
small segments of DNA can be sequenced directly
uses new technology ex. nanopore sequencer
Genomics
the study of complete sets of genes (genomes)
started with studying just bacteria, then moved to complete organisms
can compare genomes to find gene functions
Human Genome Project
massive, publicly funded scientific endeavor to determine the nucleotide sequence of all DNA in the human genome and identify the location and sequence of every gene
Found that only 1.5% of human genome codes for proteins
Most of genome is repetitive DNA that includes transposable elements and related sequences
New technology
whole-genome shotgun method
: the cloning and sequencing of DNA fragments using restriction enzymes to reassemble the full sequence
can provide wealth of data quickly
Chops up chromosome with restriction enzymes into DNA fragments, sequences the fragments, aligns them, and reassembles the full sequence
Bioinformatics
: the application of computational methods to the storage and analysis of biological data
Similar study of
proteomics
: systematic studies of the full protein sets (proteomes) encoded by genomes
Chapter 11- How Genes are Controlled
Control of Gene Expression
Prokaryotic Cells
Operon
: A cluster of genes with related functions, along with the control sequences
Regulatory gene
: codes for the repressor
Repressor
: binds to the operator and physically blocks the attachment of RNA polymerase
Operator
: between the promoter and the enzyme genes, acting as the switch
Promoter
: a site where the transcription enzyme, RNA polymerase, attaches and initiates transcription
Activator
: proteins that turn operon on by binding to DNA and stimulating gene transcription
Can be inducible (molecule must be present to inactivate repressor) or repressible (molecule must be present to activate repressor)
Repressors can regulate the production of proteins
Gene regulation
: the turning on and off of genes
Overall process by which genetic information flows from genes to proteins is called
gene expression
Chromosome structure can affect gene regulation
Differentiation
: cells must become specialized in structure and function, with each type of cell fulfilling a distinct role
DNA packing
DNA double helix wraps around
histones
(small proteins that DNA wraps around)
DNA and histone beads create
nucleosomes
Nucleosomes can wrap tighter into a tight helical fiber, and even further into a looped domain
Looped domain compacts into duplicated metaphase chromosome
homeotic gene
: the master control gene that regulates groups of other genes that determine anatomy
Chemical modifications
Can add methyl to turn a gene off, becomes part of gene and is inherited
epigenetic inheritance
: inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
X chromosome inactivation
: makes sure that one X chromosome in the female somatic cells is tightly coiled into a
Barr body
so that it barely functions so X chromosomes don’t produce double the proteins it needs. X that is inactivated is random.
X chosen is random
Causes expression of random traits. Ex. tortoiseshell cat
Eukaryotic Cells
Transcription factors
: (proteins that are essential for the transcription of all or specific protein-coding genes) are needed for RNA polymerase to function and transcribe
Need activator proteins to bind to
enhancers
(DNA control sequences that are located far away on the chromosome from the gene they help regulate)
Alternative RNA splicing
(an RNA transcript can be spliced multiple ways into multiple different proteins for different jobs. 90% of protein coding genes because of this in humans) also controls different gene expression
Later stages are also subject to regulation
Breakdown of mRNA in the cytoplasm
Initiation of translation can be delayed
Protein processing duration and breakdown
Noncoding RNAs control gene expression
microRNA
(miRNA): bind to complementary sequences on mRNA molecules to degrade the mRNA (match directly) or block translation (mostly binds)
small interfering RNA
(siRNA): similar in size and function to miRNAs, cause
RNAi
(interference)
Researchers monitor expression of specific genes
nucleic acid hybridization
: the base pairing of one strand of nucleic acids to complement another to help understand where in the organism corresponding mRNA to a gene is
DNA microarray
: a small number of different single-stranded DNA fragments attach to a grid to represent genes in a cell
Signal transduction pathways
a series of molecular changes that converts a signal on a target cell’s surface to a specific response inside the cell
New signals can trigger the translation of a new protein
Cloning of Plants and Animals
Plant cloning
shows differentiated cells can retain all genetic potential. Root cells can be cultured into adult
some cells are
totipotent
: a cell that is capable of producing every kind of specialized cell in an organism (ex. Plants)
Seen
regeneration
(the regrowth of lost body parts) in animals
clone
: an individual created by asexual reproduction and genetically identical to the one parent
Biologists can clone animals through
nuclear transplantation
need a donor cell and host egg to transplant a nucleus to clone animal, easier to have successful if donor cell is not very differentiated (take from embryo, not tadpole)
This cloning is reproductive cloning (the resulting offspring from nuclear transplantation)
nucleus is removed from egg cell, somatic cell from adult donor is added, cell grows to produce blastocyst, which is then implanted in surrogate mother so clone can be born
Therapeutic cloning
: using cloning to produce cells for medical purposes to treat somebody
embryonic stem cells
are the most totipotent
Adult stem cells
can also be used. Farther down road to differentiation so only give rise to few related types of cells
The Genetic Basis of Cancer
cancer results from mutations that control cell division
proto-oncogene
: a normal gene that has the potential to become an oncogene and cause cancer
oncogene
: can cause cancer when present in single copy of a cell
Tumor-suppressor genes
: cells who contain normal products that inhibit cell division and prevent uncontrolled growth
Genetic changes in chromosomes
oncogene is activated = increased cell division
tumor-suppressor gene is inactivated = growth of polyp (benign tumor)
second tumor-suppressor gene is inactivated = growth of a malignant tumor
faulty proteins can interfere with signal transduction pathways
hyperactive relay proteins produce product even in absence of growth factor, overexpressing protein
nonfunctional transcription factor can't trigger transcription
Lifestyle choices reduce cancer risk
carcinogens
: agents that alter DNA and make cells cancerous, a type of mutagen