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Genes and the Genetic Bases of Metabolism and Development - Coggle Diagram
Genes and the Genetic Bases of Metabolism and Development
Concepts
Plants are composed of numerous types of cells. Each cell type is unique because it has a distinct metabolism based largely on proteins such as enzymes microtubules and membrane proteins. All cells create a fundamental metabolism involving respiration, amino acid synthesis, and so on, some of the reactions in each cell type differ from those in the other cell types.
The information needed to construct a type of protein is stored in genes, but because an organism grows by mitosis (duplication and division) all of its cells have identical sets of genes
Differential Activation of genes– as each cell differentiates and develops a unique set of proteins this is the underlying developmental process
Enzymes involved in synthesis the flower color pigments are present in petal cells but not in the cells of roots, wood, and bark.
The pattern of wall deposition varies by a pattern of protein microtubules in the protoplasm.
During
Protein Synthesis,
the correct amino acids must be incorporated in the proper sequence because this determines both the structure and all other properties of the protein.
DNA (Deoxyribonucleic acid)
- An information archive that holds the sequence information for all its proteins
Gene
- Each region of DNA that is responsible for coding the amino acid sequence in a particular protein and each type of protein has its own gene.
DNA Sequence Analysis
- Genes can be isolated in vitro, duplicated, and their nucleotide sequence revealed
Similar techniques make it possible to alter the DNA sequence then insert the gene back into a plant cell. As the cell grows, divides, and differentiates, the altered DNA either produces an altered protein if the coding region was changed or produces the protein at an unusual time or place if it's control site was changed. This is also known as
Recombinant DNA Techniques
or
genetic engineering
Understanding this process is helping scientists produce plants that are more resistant to insects and producing seeds and fruits that are more nutritious for humans
Storing Genetic Information
Protecting the Genes
It is vital that the information in DNA be stored accurately for a long time. If the storage is not safe the information produced by the DNA will be inaccurate and probably useless or even harmful. There are several ways in which DNA is kept relatively inert and safely stored
DNA does not participate directly in proteins synthesis, instead DNA produces a messenger molecule
messenger RNA (mRNA)
, which carries information from DNA to the site of 14 synthesis. If mRNA is damaged it can be replaced with more copies
Most DNA is stored in the nucleus, protected from the cytoplasm by the nuclear envelope. The DNA of plastids and mitochondria is protected from cytosol enzymes by being located within plastids and mitochondria themselves
Histone proteins hold most nuclear DNA in an inert, resistant form. Histones are a special class of proteins found in all organisms that have nuclei (plants, animals, fungi, algae, and protozoans) there are five types. Histone proteins are so essential that virtually any change in the amino acid sequence causes the organism to die or at least not reproduce
Nucleosome- A spherical structure formed when histones form aggregates and DNA wraps around them.
Histone H1 then binds its nucleosomes into a tightly coiled configuration. In this mode, the DNA-protein structure
chromatin
is so dense that enzymes cannot penetrate it, and DNA is relatively inert
DNases
or
DNAases
-DNA digesting enzymes
The Genetic Code
20 types of amino acids are used in synthesizing proteins, but only four different nucleotides are present in DNA or mRNA; consequently, it is not possible for one nucleotide alone to specify one amino acid because 16 amino acids would be left without nucleotides to code for them
Codons
- a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule.
Stop Codon
- Signal that the ribosome should stop protein synthesis.
UAA, UAG, UGA
Start Codons
- signals the point in which mRNA should begin protein synthesis
AUG
Degenerate
- 2 codons code for the same amino acid. Degeneracy protects DNA because if a mutation occurs and changes, for example UUU to UUC, they will both code to the same thing
Reading nucleotides in the wrong sets of three is a
Frameshift error
The Structure of Genes
Most genes only need to be activated and read when the cell needs a particular enzymes they code for. Each gene must have a structure that allows controlling substances to recognize the gene, bind to it, and activate at the proper time
Genes are composed of a
structural region
that actually codes for the amino acid sequence, and a
promoter
, a controlling region involved in regulating the synthesis of mRNA from the structural region
The structural portion of genes contains two distinct types of regions: Exons and Introns. Exons are sequences of nucleotides whose codons are eventually expressed (Exon, expressed) as sequences of amino acids in proteins, and introns are sequences of nucleotides that are not expressed, but instead intervene between exons.
TATA box- A short sequence about 6 to 8 base pairs long, rich in A and T. If the
TATA box
is damaged by either mutation or experimental treatment, the RNA- synthesizing enzyme
RNA polymerase II
does not bind well
Transcription of Genes
After RNA polymerase binds and encounters the start signal, it begins actually creating RNA, a process called
transcription
Hairpin Loop
- RNA transcribed from DNA nucleotides doubles back on itself and hydrogen bonds to another part of itself.
RNA Polymerase transcribes both introns and exons into a large molecule of
heterogeneous nuclear RNA (hnRNA)
that is rapidly modified by nuclear enzymes.
Alternative Splicing-
https://www.youtube.com/watch?v=aVgwr0QpYNE
Protein Synthesis-In this process ribosomes bind to mRNA and "read" its codons. Guided by the information in the nucleotide sequence of the mRNA, the ribosomes catalyze the polymerization of amino acids in the order specified by the gene from which the mRNA was transcribed
Ribosomes- Small particles that read the genetic message an mRNA construct proteins guided by that information. Each is composed of two subunits, one larger than the other, and each is made up of both proteins and
ribosomal RNA
Ribosomes found in the cytoplasm of eukaryotes are designed
80s
, meaning that they're relatively large and densee. Ribosomes of plastids, mitochondria, and prokaryotes are smaller, lighter,
70s ribosomes
All cells need large numbers of ribosomes. Most genes are present in a diploid nucleus as only 2 copies, but just 2 copies would be inadequate for producing hundreds of thousands of rRNAs needed. Instead, they're highly amplified and many copies are present.
tRNA- During protein synthesis, amino acids are carried to ribosomes acids called
transfer RNA (tRNA)
. They are necessary because a codon cannot interact directly with an amino acid; the genetic code can be read only by a ribonucleic acid that has a three-nucleotide sequence, called an
anticodon
Amino Acid Activation
- A step where a special class of enzymes recognizes each tRNA and attaches the correct amino acid to it.
mRNA Translation
The synthesis of a protein molecule By ribosomes under the guidance of mRNA is called
translation
Protein synthesis begins with a complex
initiation
process involving the start codon AUG.
Eukaryotic initiation factors (eIFs)
- proteins that bind to the small subunit
Elongation of the protein chain
At the time Of initial binding, the small subunit already contains initiator tRNA in the
P channel
(P for protein). The adjacent
A channel
(A for amino acid) is empty, but numerous molecules enter it at random. Some are activated tRNAs, but if they're anticodons do not complement the exposed codon at the bottom of the A channel, they defuse out.
Control of Protein Levels
As cells undergo differentiation and morphogenesis, their metabolism and structure become different from those of other cells because of the presence of proteins, especially enzymes, unique to that cell type. The central question developmental biology is the mechanism by which the states all types control activities in chains so that they undergo the proper differentiation obtain the proper sort of proteins. Many enzymes and structural proteins are present in a cell in an inactive form
We know very little about control of transcription in eukaryotes, especially plants, but our knowledge is increasing rapidly. In many cases, do you know activity is controlled by
transcription factors
, proteins that bind to promoter or enhancer regions in activate genes.
Because transcription factors come from somewhere else in button to DNA, they are said to be
trans-acting factors
; promoters, enhancers, and totter boxes are part of the gene itself enters our
cis-acting factors
.
Analysis of Genes and Recombinant DNA Techniques
Nucleic acid hybridization
The 2 halves of a DNA double helix can be separated by heating them just enough to break the hydrogen bonds between complementary bases. This separation, which produces a solution of single-stranded DNA molecules, is called both
DNA melting
and
DNA denaturation
.
DNA hybridization
, also called
reannealing
is the reformation of double-stranded DNA by cooling a solution of single-stranded DNAs
If DNA is broken into small pieces, denatured, and allowed to cool, the reannealing is extremely slow
Restriction Endonucleases
DNA is far too long to work with it easily. It is chemically broken down into more manageable sizes. It is critical to cut it at specific known sites so that repeat experiments can yield the same pieces as the first experiment.
Restriction endonucleases
- Each one recognizes and binds to specific sequence of nucleotides in DNA and then cleaves the DNA. Because of these properties, we always know exactly where DNA will be cut by a particular restriction endonuclease, and when two identical batches of DNA are treated with the same restriction endonuclease, the resulting fragmentations are always the same
Palindromes
- sequences that can be read backwards and forwards
DNA Ligase- DNA repair enzyme
Recombinant DNA- DNA prepared by this method
Identifying DNA Fragments
Restriction Map
- made by gel electrophoresis and made visible by staining.
Reverse Transcriptase
- a virus enzyme that synthesizes DNA using RNA as a template.
Complementary DNA (cDNA)
- complementary to the exons of the gene
Expression Profiling
- Uses cDNAs to examine gene expression during development in one species with that in another.
DNA Cloning
- The method of placing DNA fragments into bacteria, as just described, it is an extremely useful technique
Genetic Engineering of Plants
this can help reduce food waste and protect crops from things such as caterpillars.
CRISPR-Cas9
- A new tool for precisely editing DNA. It is a protein complex that binds short piece of RNA called a guide RNA. The guide RNA is complementary to a particular region of DNA, so CRISPR-Cas9 does not bind to DNA at random but rather at specific sites. After binding, it cuts both strands of the DNA, clearing it completely into.
https://www.youtube.com/watch?v=rx953M-tpp4
