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MM16: genes and the genetic basis of metabolism and development - Coggle…
MM16: genes and the genetic basis of metabolism and development
Storing genetic information
protecting the genes
DNA doesn't participate directly in protein synthesis
messenger RNA (mRNA) carries info from DNA to the site of protein synthesis
most DNA is stored in the nucleus
protected by the nuclear envelope
histone proteins hold most nuclear DNA in an inert, resistant form
histone: special class of proteins found in all organisms that have a nuclei
5 types: H1, H2A, H2B, H3, H4
H2A, H2B, H3, H4 among the most highly conserved proteins known
DNases: DNA digesting enzymes
DNA + histone formed aggregates = nucleosome (spherical)
chromatin: H1 binds nucleotides into chromatin, so dense that enzymes can't penetrate
the genetic code
codons: nucleotides must be read in groups of 3, 64 possible triplets, made by using 4 nucleotides
surplus of 44 codons after each amino acid is paired with a codon
UAA, UAG, UGA: stop codons (signal that the ribosome should stop protein synthesis
AUG is the start codon
the genetic code is degenerate since multiple codons exist for most amino acids
the extra 40 codons also code for amino acids
20 types of amino acids used in synthesizing proteins
almost perfectly universal
the structure of genes
genes are composed of a structural region
the structural region codes for the amino acid sequence
structural region: contains 2 distinct types of regions: exons and introns
exon/expressed
sequences of nucleotides whose codons are eventually expressed
introns are sequences of nucleotides that aren't expressed, but instead intervene between exons
intron/intervene
promoter: a controlling region- regulating synthesis of mRNA from the structural region
located "upstream" from the structural region
TATA box: rich in A and T, about 6 to 8 base pairs long
if TATA box damaged, RNA polymerase II doesn't bind well
enhancer elements: other promoter sequences
after RNA polymerase II binds to the promoter it moves downstream towards the structural region
starts creating RNA when it moves 20-30 nucleotides below the TATA box
transcription of genes
RNA polymerase begins creating RNA
two strands of DNA separate from each other and free ribonucleotides diffuse to the region
C bonds with G, T bonds with A, U bonds with A, etc
transcription incorporates about 30 ribonucleotides per second
RNA continues this process until it encounters a transcription stop signal
hairpin loop, small kink affecting RNA
RNA polymerase transcribes introns and exons into hnRNA. Introns are kicked out, exons are spliced into RNA molecules
alternative splicing
sometimes only introns are removed and exons are spliced together
other times some exons are removed as well
one gene can produce 2+ types of mRNA
one thats all exons and one thats missing some exons
both are made into proteins as normal
these proteins can be very similar or very different
very common in human gene expression
Protein synthesis
ribosomes
small particles
composed of a smaller and larger subunit
made up of proteins and ribosomal RNA (rRNA)
"read" the genetic message from mRNA
construct proteins based on these instructions
ribosomes found in the cytoplasm: 80S (large and dense)
ribosomes of mitochondria, plastids, and prokaryotes: 70S (smaller and lighter)
once rRNA molecules are transcribed they combine with the ribosome, then that new molecule is broken down into the subunits of a ribosome
tRNA
amino acids are carried to the ribosomes by tRNA
codons cant interact directly with an amino acid
can only be read by an anticodon
ribonucleic acids called transfer RNA
all tRNA molecules have the same parts
anticodon and an amino acid attachment site at its 3' end, consisting of the sequence CCA
CCA: a special class of enzymes, recognizes each tRNA and attaches the correct amino acid to it
amino acid activation:
contain bases A, U, G, and C with some extra unusual bases
mRNA translation
translation: the synthesis of a protein molecule by ribosomes under the guidance of mRNA
initiation: the start of the codon AUG
codes for the amino acid methionine
two types of tRNA that carry methionine
initiator tRNA, binds to the ribosome small subunit pre-mRNA
frameshift error: reading nucleotides in the wrong sets of 3
Control of protein levels
(common) gene activity is controlled by transcription factors
transcription factors: proteins that bind to promoter or enhancer regions and activate genes
many have a sequence of amino acids that fits into the DNA double helix
most transcription factors must act as dimers
many can be identified by their structure
TATA boxes are cis-acting factors because they're actually apart of the gene structure
they are trans-acting factors bc they come from somewhere else and bind to DNA
also controlled by micro-RNAs
Analysis of genes and recombinant DNA techniques
nucleic acid hybridization
DNA hybridization/reannealing: rejoining double stranded DNA by cooling
DNA melting/DNA denaturation: separating the double helix by heating (the H bonds separate)
restriction endonucleases
restriction endonucleases: bacterial enzymes that recognize and bind to a specific sequence of nucleotides in DNA then cleaves the DNA
palindromes: the sequence recognized by a restriction endonuclease is present in both strands, running in opposite directions
DNA repair enzyme: DNA ligase
DNA prepared by adding DNA ligase to the mixture and having the cuts repaired so that the two fragments join together: recombinant DNA
identifying DNA fragments
after restriction endonucleases have acted, the DNA fragments can be identified and used (mostly to study the evolution of DNA)
restriction map: fragments separated by gel electrophoresis and then made visible by staining
the number of fragments reveals the number of PstI sites and the number of base pairs between them in the plastid DNA
restriction fragment length polymorphism (RFLP) easy, quick, and inexpensive , can be done with various restriction endonucleases
DNA cloning
placing DNA into bacteria
the colony containing the fragment can be cultured and grown easily
placing the original plant DNA fragments into bacteria is much easier than it seems
fragments are placed with bacteria, virus DNA, or plasmids (a short circular piece of DNA that occurs in bacteria and acts like a tiny bacterial chromosome)
several viruses are being used like plasmids
most plant chromosomes are hundreds of times larger than a typical bacterium
yeast artificial chromosomes (YACs) can be used instead
vectors (carriers)
polymerase chain reaction (PCR) a method of DNA cloning in which only enzymes are used
sequencing entire genomes
to sequence DNA the DNA must be cut into fragments
we may have a batch of perfectly sequenced several hundred genomes, but not know the order of the fragments
for the second batch we can align equivalent regions, and the third batch is verification
DNA sequencing
chain termination method: DNA to be sequenced is first cloned to obtain a large sample and is then divided into four batches
each batch all the enzymes and free nucleotides necessary to carry out DNA duplication are added
to one tube a small amount of dideoxyadenosine is also added
in this tube the DNA acts as a template and replication begins
pyrosequencing method: DNA is added to a solution with all the enzymes for replication, and other enzymes that release light when pyrophosphate is present
when the wrong nucleotide is introduced there is no flash of light, the sequencer records the lack of flash and washes the incorrect nucleotide away before introducing another
open reading frame (ORF): if a region of DNA is found to have these genelike features (promoters or enhancers, TATA boxes, AUG start sites, areas that might be boundaries between exons and introns)
genetic engineering of plants
recombinant DNA techniques have made it possible for botanists to identify, isolate, and study the structure and activity of many genes
allowing botanists to insert genes into plants that do not normally have these genes
if said gene protects the plant it could prevent as much as $100 million in crop losses annualy
CRISPR-Cas9: new tool for precisely editing DNA
a protein complex that binds to a short piece of RNA called guide RNA
causes CRISPR-Cas9 to bind to DNA at specific sites rather than at random
it has been modified not only to cut a section of DNA, but even add a new piece of DNA onto it
GMOs (genetically modified organisms)
Concepts
differential activation of genes
underlying developmental process when cells develop proteins
DNA (deoxyribonucleic acid)
linear polymer consisting of A, T, G, and C
gene
each region of DNA responsible of coding amino acid sequences in proteins
DNA sequence analysis
techniques used to locate genes of proteins
recombinant DNA techniques
genetic engineering