The General Timeline For The Evolution Of The Earth Essay

The General Timeline for the Evolution of the Earth Essay
know the elements of life – and how the reduction and oxidative of some of these drive
bioenergetics oxidize carbon (i.e. glucose source) and reduce oxygen (electron acceptor) (CHNOPS)
and iron (Fe; trace element; Fe also important to obtain cellular energy). Nutrition: CHNOPS Trace
Elements: Iron (Fe), Ni, Mg, Mo, Mn, Ca (important in humans due to osteoblastic activity), Co
Occupancy: beat out others for a spot to live, e.g. microbiota (normal flora) Resistance: defend
against microbes, eukaryotes and anything taking over your niche; biofilms can contribute to
resistance towards antibiotics or antiseptics Energy can be derived from reductive and/or ... Show
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An example of a closed genome is B. anthrasis (Anthrax) Core genomes are the essential genes in
all genomes and is conserved across all pathogenic species; these genes are very often involved in
metabolism and growth. These genomes hardly change because they are central to the microbe and
slight changes may kill the organism. A pan–genome is the entire gene pool for that pathogen
species, and includes genes that are not shared by all strains. Pan–genomes may be open or closed
depending on whether comparative analysis of multiple strains reveals no new genes (closed) or
many new genes (open) compared to the core genome for that pathogen species. Short stuff: Open
genome = C. difficile = many different isolates and strains. There are large variations between same
genus, species (new genes + core genome). Closed genome = B. anthracis = very, very little
variation when different isolated have been sequenced. Pangenome = all the genes that have ever
been sequenced from E. coli. Also known as microbial Pangaea. All the genes in that genome.
Archaea are usually found in what kind of environments? How does this support Woese's hypothesis
for three domains of life? What does this likely say about early evolution on Earth? They are found
in extreme environments exhibiting extreme temperatures, osmotic pressures, pH, and
concentrations of inorganic molecules (often toxic to other forms of life). This supports Carl Woese
in that he posited that if
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Chapter 13 Review
When lactose becomes available the genes encoding β–galactosidase and lactose permease are
upregulated in E. coli.
true 2
Different globin polypeptides are expressed at similar levels during the embryonic and fetal stages
of mammalian development.
false 3
RNA polymerase can bind to the promoter region of the DNA even when the lac repressor is bound
to the operator site.
true Hide
4
Both eukaryotes and prokaryotes require a promoter region for gene transcription.
true 5
Eukaryotic genes are almost always organized in groups, similar to operons in prokaryotes.
false Advertisement
Hide ads ($1).
6
Unmethylated CpG islands are correlated with inactive ... Show more content on Helpwriting.net ...
Transcriptional start site : where transcription beings
2. TATA box : 25 base pairs, determines precise starting point for transcription
3. Response elements: where regulatory proteins bind 51
3 types of proteins that are needed for basal transcription at the core promoter:
RNA pol II
5 general transcription factors mediator 52
Glucocorticoid
– activates transcription of specific genes
– hormone released into bloodstream after meals
– into cytosol
– releases proteins called chaperones and exposes NLS
– Directs receptor to travel into nucleus 53

Domains or portions of domains with similar structures in different proteins motif 54
DNA methylation
– attaches methyl groups
– usually inhibits transcripiton
55
2 ways Methylation can inhibit transcription
1. Methy. of CpG islands prevents an activator form binding
2. Convert chromatin form open to closed 56
DNA methylation
is associated with transcriptional repression. 57
In eukaryotes, the most common nucleotide to be methylated is
CYTOSINE 58
Which of the following statements is true?
In

Cell Biology Final Essay
Name: _Leroy Johnson __________________________________ Date:
______________Comprehensive Study Guide. Test will only be Multiple choice
1. The feature that most clearly separates eukaryotes from prokaryotes is the presence of _______ in
eukaryotic cells. A) ribosomes B) oxidative phosphorylation C) DNA molecules –D) a nucleus
2. Cytoplasmic organelles are
– A) absent in prokaryotic cells; present in eukaryotic cells. B) present in both prokaryotic and
eukaryotic cells. C) present in prokaryotic cells; absent in eukaryotic cells. D) absent in both
prokaryotic and eukaryotic cells.
3. Eukaryotic chromosomes contain _______ DNA molecules. A) single linear B) single circular –
C) multiple linear D) ... Show more content on Helpwriting.net ...
A) True B) False
22. The two major groups of prokaryotic cells are the _______ and the _______, which diverged
early in evolution. archaebacteria; eubacteria
23. Connective tissues of animals include _______, _______, and _______. bone; cartilage; adipose
tissue
24. List four significant differences that distinguish prokaryotic cells from eukaryotic cells.

25. The formation of a phospholipid bilayer membrane around a set of macromolecules was an
important step in the origin and early evolution of life. What two advantages of such a system are
thought to have allowed the first cells to grow and evolve? (1) The membrane forms a
(semipermeable) barrier between the interior of the cell and its environment, and (2) it allows a cell
to grow and evolve as a unit, instead of existing as isolated molecules.
26. E. coli is a good model system for molecular biology studies because A) it has a small genome.
B) it reproduces rapidly. C) mutants can easily be isolated from culture dishes. D) All of the above
27. A yeast cell divides in culture about every A) 20 minutes. B) 2 hours. C) 12 hours. D) 24 hours.

28. How many genes does the yeast nuclear genome contain? A) 1000 B) 6000 C) 10,000 D) 20,000
29. The adult nematode worm Caenorhabditis elegans consists of _______ somatic cells. A) 95 B)
959 C) 9,590 D)

Protein Synthesis : Transcription And Translation
Protein synthesis is defined as "The creation of proteins by cells that uses DNA, RNA, and various
enzymes." The synthesis of proteins takes two steps: transcription and translation. Transcription
takes the information that is coded in DNA and codes it into mRNA, which heads out of the cell's
nucleus and into the cytoplasm. During translation, the mRNA works with a ribosome and tRNA to
synthesize proteins. When trying to understand the process of protein synthesis, basic terms are
necessary. DNA is the backbone of life as we know it. DNA stands for deoxyribonucleic acid and it
is necessary to life on earth. The basic unit of DNA is called a nucleotide which is also known as a
base. DNA is a double stranded helix that is made of these bases. DNA makes thousands of proteins
using only four different basis. These bases are labeled as A, T, G, and C. These letters stand for
adenine, thymine, guanine, and cytosine. These bases make pairs. A Pairs with T and G pairs with
C.The same goes for RNA except thymine is replaced with uracil and RNA is single stranded. A
continuous strand of DNA is called a gene. Genes are used to make functioning strands of RNA or
proteins. The first step in protein synthesis is transcription which is when the cell makes an RNA
copy of the information from DNA in the nucleus. The first step of transcription is called initiation.
This is when the RNA polymerase binds to the promoter which contains the transcription start point.
The polymerase binds

Expanded Genetic Code Research Paper
What is the Expanded Genetic Code?
By Jonas Wilson, Ing. Med.
There are 20 canonical amino acids that are encoded by the genetic code of nearly all known
organisms. There are only very few exceptions. In order to add novel building blocks to this existing
repertoire, unique aminoacyl–tRNA synthetase and tRNA pairs are required, in addition to the
specific amino acid codon as well as a source of the amino acid. In terms of biological evolution, it
is known that our ensemble of 20 amino acids has remained unchanged over a period of 3 billion
years. This is demonstrated by the fact that all living organisms have adopted it.
While the possibility of amino acid to analog replacement could theoretically occur owing to the
existence of analogs ... Show more content on Helpwriting.net ...
There is some redundancy in the code as most of the amino acids may be encoded by more than one
codon. Moreover, the code can be expressed as RNA or DNA codons with the former being used
during translation (i.e. creation of proteins) after acquiring its sequence of nucleotides from the latter
during transcription (i.e. copying of DNA into mRNA).
While it may be regarded as a common language shared between nearly all organisms, the genetic
code is imperative for the interpretation of genes and the production of proteins. In addition to this,
it precisely guides how the genome is put together via a series of fundamental and biochemical
constraints. This has allowed the code to be fairly refractory to change and enables it to shape how
mutations that arise affect the evolution of the genome.
Changes anywhere within codon function must be capable of being tolerated genome–wide. This
means that compensatory changes throughout the rest of the genome must occur if there are small
changes to the genetic code. Random mutagenesis is unlikely to cause such stable changes.
However, contemporary feats in engineering are enabling the possibility of making rational changes
to the genetic code.
Expanding the genetic

Ncldv Virus Research Paper
In the last two–decade, numbers of giant dsDNA, icosahedral viruses have been discovered and
assigned to the NCLDV clade. The major capsid proteins of these viruses consist of two consecutive
jelly–roll domains, assembled into trimers, with six fold symmetry. The capsomers are assembled
into arrays that have either p6 as in Paramecium bursaria Chlorella virus 1 or p3 symmetry as in
Mimivirus (Xiao & Rossmann 2011).
Mimivirus has a capsid (icosahedral) diameter of 400 nm with protein filaments of 100 nm from the
surface of the capsid, comprising the total length of the virus up to 600 nm. While most of the other
discovered large viruses size varies between 400 nm and 800 nm (Xiao et al., 2009). Mimivirus
shares similar morphological characteristics with all members of the NCLDV group of viruses. The
central core of the virion appears as a dark region under the electron microscope. An internal lipid
layer surrounding the central core seen in all other NCLDV viruses this features present in
Mimivirus (Xiao et al., 2009). ... Show more content on Helpwriting.net ...
However, the virions of P. sibericum like pandoraviruses morphologically but are still being the
largest (1.5 μm in length), with a 60 nm thickness of the enveloped hexagonal structure that missing
in pandoraviruses. Pandoravirus and P. sibericum both have the apical pore. Wile, the virion of M.
sibericum is a spheric shape covered with 2 to 4 layers of fibers. Faustovirus virions have an
icosahedral capsid without fibers. As for virions of all previous giant viruses, the internal lipid
membrane surrounding the core and fuses with the vacuole membrane is to release the dsDNA

The Regulation Of Transcription Of Most Aminoacyl Trna...
The regulation of transcription of most aminoacyl tRNA synthetase genes in Gram–positive bacteria
is controlled by a common transcription anti–termination system (cite?). This anti–termination
system is formed by the T–box riboswitch, which is characterized by a conserved RNA sequence
and secondary structure elements. T–box riboswitches are located in nascent 5 ' RNA transcripts
(leader RNA) of these aminoacyl tRNA synthetase genes. Synthesis of the full–length mRNA
requires stabilizaton of the anti–terminator motif. This is facilitated by RNA–RNA interactions
between cognate uncharged amino–acyl tRNAs and leader RNA (Grundy et. al, 1994). Specifically,
in the case of glycine tRNA synthetase, the specifier sequence (GCC) of the leader RNA base–pairs
with the tRNA anticodon (CGG), and the antiterminator element pairs with residues in the 3 '
acceptor end of the tRNA. Interestingly, only cognate uncharged tRNAs promote antitermination
(Grundy et. al, 1994). For example, the tyr–tRNA synthetase gene is only transcribed when
uncharged tyr–tRNA 's are present (Grundy and Henkin, 1993). Thus, transcription is induced in
response to high levels of uncharged tRNA 's due to a deficiency of the corresponding amino acid or
aminoacyl–tRNA synthetase. This logical regulation of transcription thereby tries to restore levels of
charged amino–acyl tRNA synthetases. The exact requirements for these tRNA–leader RNA
interactions that induce transcription have not yet been fully defined,

Protein Synthesis Lab Report
Scientists found out that the formation of proteins (polypeptide chains) are dictated by the
expression of DNA. The DNA dictates the types of proteins that will be formed by making the
sequence of nitrogen–containing bases. Each three base sequence has an equivalent code for the
amino acid that will make–up the formation of protein (polypeptide). For example; the sequence of
the three bases CCA is a code for using the amino acid Proline (Pro), CTT is for the amino acid
Leucine (Leu), TCT is the code for the amino acid Serine (Ser), and so on. After coding, each of
these amino acids will be used to form long chains of amino acids called polypeptide chain. These
chains will make up the proteins. The synthesis of protein is a very complex process. The two major
steps in protein synthesis are (I) Transcription and (II) Translation. These are the process in the
synthesis of protein from the information expressed by genes. The figure below illustrates the
synthesis of proteins in a cell. ... Show more content on Helpwriting.net ...
Transcription. In this process, the information from the DNA sequence is copied to a complementary
RNA sequence. The type of RNA that is involved in this process is the messenger RNA (mRNA).
During a transcription process, when a sequence of DNA is expressed, one of the two DNA strands
is copied into the mRNA based on the base–pairing rules. For example, in base–pairing in DNA,
Adenine (A) is paired with Thymine (T), and Cytosine (C) is paired with Guanine (G. But when it
comes to base–pairing rules in RNA, Adenine (A) is paired with Uracil (U) instead of Thymine (T),
and Cytosine(C) is paired with Guanine (G). Figure __ illustrates the transcription of DNA sequence
into the mRNA codons. It also shows the transfer RNA (tRNA) anticodon that is complementary to
mRNA codon

Synthesis Of Messenger Dna
DNA is found inside the nucleus of cells. It has two complementary, antiparallel strands. The strands
contain nucleotides, which each have a phosphoric acid, deoxyribose sugar and a base. There are
two groups of bases purine and pyrimidine; adenine and guanine are purine bases, and cytosine and
thymine are pyrimidine bases. A purine must pair with a pyrimidine, a purine can't pair with another
purine nor can a pyrimidine pair with another pyrimidine, this is in order to ensure that the 'rungs in
the ladder' remain the same width. The two strands are bonded together through hydrogen bonds
between the corresponding bases; adenine and thymine pair together with two hydrogen bonds, and
guanine and cytosine pair together with three hydrogen bonds. ... Show more content on
Helpwriting.net ...
The ribosome is made up of two subunits and the smaller subunit will attach to two codons. The first
codon will always contain the bases in order: adenine, uracil and guanine. A tRNA molecule which
contains the anticodon for this codon (the bases uracil, adenine and cytosine) will form a bond with
the codon on the mRNA strand. Adenine on the codon will pair with uracil, uracil with pair with
adenine and guanine will pair with cytosine. In order for this bond to be formed an enzyme called
aminoacyl synthetase is needed as a catalyst and energy from ATP is also required. This will form an
amino

Transfer RNA Synthesis Lab Report
Aminoacyl transfer RNA synthetases catalyze the formation of "charged" transfer RNA. This means
the Aminoacyl transfer RNA synthtaseses attach an amino acid to the transfer RNA. A specific
aminoacyl transfer RNA synthestase binds a specific amino acid and a molecule of Adenosine
triphosphate to the active site. The bond is broken between the amino acid and Adeonsine
monophosphate and the Adenosine monophosphate is then released. At the same time, a covalent
bond is formed between the amino acid and the 3' end of the transfer RNA. A specific transfer RNA
has an anticodon that corresponds to the amino acid then binds to the synthetase. The RNA sequence
in the anticodon region, as well as other parts of the transfer RNA molecule, are important ... Show
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The first being, the attachment of a given amino acid to a specific transfer RNA establishes the
translation of the genetic code. The genetic code has several important properties, without these
properties life could not exist. When an amino acid is linked to a transfer RNA, it will be assimilated
into a growing peptide chain at a location ordained by the anticodon of the transfer RNA. The
second reason the linkage of an amino acid to a transfer RNA is so important is, the formation of a
peptide bond between amino acids is not thermodynamically favorable. The amino acids need to be
activated for the reaction to continue, once activated they are amino acid esters. These intermediates
have the carboxyl group linked to either the 2′– or the 3′–hydroxyl group of the ribose unit at the 3′
end of tRNA. This is called the aminoacyl–tRNA synthetase. Tyrosyl tRNA synthetase is a dimeric
enzyme, that is comprised of two indistinguishable sub–units. Tyrosyl transfer RNA synthetase
catalyzes the formation of tyrosyl transfer RNA in a two–step reaction. Tyrosine is first activated by
reaction with Adenosine triphosphate. This forms the enzyme bound intermediate, tyrosine
adenylate. Although the enzyme is a dimer, only one molecule of tyrosine is bound per

E. Cois Lab Report
Specific Objective #2: Stalling, collision, and ribosome recovery in E. coli protein translation. It has
long been known that when a ribosome encounters clusters of rare codons, the ribosome can be
"rescued," where a specialized tmRNA molecule allows the ribosome to abort translation of the
current peptide chain via the simultaneous completion of the polypeptide with a fast–degradation tag
and cleavage/degradation of the mRNA molecule at the site of stalling69–71. Ribosome rescue is a
fundamental process that allows cells to recover unproductive ribosomes, e.g. when the cell is under
stress and lacks a sufficiently large number of tRNA molecules for translation. These fast
degradation tags found on tmRNA are themselves of interest, as they ... Show more content on
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The original model included certain features, such as the finite footprint of ribosomes on mRNA,
and collective crowding effects (one ribosome cannot pass another). However, the model did not
explicitly consider mRNA dynamics, and more seriously, it did not consider the influence of
ribosome rescue on protein and mRNA stability. For this proposed work, we have developed custom
python code (based on the efficient Gibson–Bruck algorithm74) for stochastic simulation of both
mRNA dynamics and ribosome rescue. This model allows ribosomes to initiate ribosome rescue and
associated mRNA cleavage either with a constant rate or with a reaction rate that is nonzero only if
two ribosomes are immediately adjacent (Fig. 5A). Preliminary investigations of this model reveal
that collision based initiation of ribosome rescue leads to strongly tunable ribosome rescue and
mRNA stability depending on the translational elongation rate. To match our experimental system,
we consider a system with 6 rare codons (a gate) in the middle of the transcript (Fig. 5B). Passage to
the late portion of the transcript is heavily controlled by the gate, which allows for differential
translational output from the transcript.
To develop an analytic understanding, we will also investigate effective queueing models that keep
track only of the number of ribosomes upstream of this gate, where the gate acts as a server. This is
analogous to the theoretical system in Fig.

D1 Protein Synthesis
D1 task 1; protein synthesis
Transcription:
DNA consists of two strands. One is the coding strand and the other is the template stand. In
transcription there is an enzyme called RNA polymerase that 'unzips' the two strands. This allows
RNA nucleotides (uracil, adenine, guanine and cytosine) to enter the DNA and connect to the
corresponding DNA nucleotides (thymine, adenine, guanine and cytosine) on the template strand.
After the nucleotides have been paired, phosphodiester bonds, bond the RNA nucleotides together
and this creates a continuous strain of mRNA which is capable of leaving the cell's nucleus, whereas
the DNA cannot as the molecule is too big. Once the mRNA has moved out of the nucleus it moves
to a ribosome. (1)
Translation:
Translation

Expanded Genetic Code Analysis
Applications of the Expanded Genetic Code
By Jonas Wilson, Ing. Med.
The genetic code consists of 64 triplets of nucleotides called codons. With the exception of three
codons, each codon encodes for at least one of the 20 canonical amino acids and most of the amino
acids are encoded by more than one codon. The genetic code may be seen as a universal language
shared by all living organisms.
It is imperative for the interpretation of genes and the production of proteins. Moreover, it is a
precision guide that constructs the genome along fundamental and biochemical constraints. This
played a key role in allowing the code to be conserved over the course of 3 billion years and enables
it to shape how mutations affect the evolution of the genome. ... Show more content on
Helpwriting.net ...
In addition to this, they may be able to function as intracellular protein modifiers and can be used to
directly introduce novel or enhanced catalytic properties to proteins. Selective chemistries that can
be used to engineer such novelties include oxime condensation reactions and click chemistry.
Among others, UUAs may also be used as heavy atoms for determining the structure of X–rays,
redox–active reagents and probes of hydrogen bonding as well as interactions in proteins.
Therapeutics
UUAs may be widely used for therapeutic purposes. They are particularly useful in cases where
large quantifies of a modified protein is required for production. For instance, immunogenic amino
acids may be used to generate vaccines against self–proteins by the breakdown of immunological
tolerance in conditions, such as inflammation or cancer. UUAs can also be used to generate vaccines
against the conserved epitopes of diseases like HIV and malaria, which are fairly difficult to target
with our traditional vaccines.
Sources

Protien Molecules Research Paper
The production of protien molecules happends in two stages, transcription and translation.
Transciption takes place in the nucleus. First, DNA in the nucleus,its double stranded in eukaryote
cells. DNA molecule unfolds forming two templates of DNA. RNA polymerase attaches itself to a
template of DNA and synthesizes mRNA. DNA contains the cistrons/genes which code for specific
polypeptides. The part of the strand that forms the cistron is called the transcribing strand. It acts as
a template and is transcribed to mRNA. The complementary strand which does not carry the cistron
is called the non–transcribing strand. An enzyme RNA polymerase attaches itself to the promoter
site next to the cistron on the DNA and initiates transcription. The enzymes ... Show more content
on Helpwriting.net ...
During the process of transcription, an enzyme called RNA polymerase binds to DNA at a gene's
promoter, then begins unwinding the DNA and making a complementary strand of RNA from the
exposed DNA template. Depending on the gene being transcribed, the result can be a molecule of
mRNA (messenger RNA), tRNA (transfer RNA), or rRNA (ribosomal RNA). Each type of RNA
performs a specific function later in translation. Ribosomal RNA (rRNA) along with ribosomal
proteins make up ribosomes, the "workbenches" on which polypeptides (proteins) are synthesized. It
turns out that it is actually rRNA, and not a protein, in the large subunit of the ribosome that
performs the peptidyl transferase function of linking amino acids together via peptide bonds. In
eukaryotes, the genes coding for rRNAs are located in the nucleolus of the nucleus. A ribosome has
3 binding sites: an A (aminoacyl) site, a P (peptidyl) site, and an E (exit) site. The message carrying
the information needed to make a particular polypeptide exists in the mRNA molecule. It binds with
a ribosome and the ribosome starts reading it one codon – 3 consecutive mRNA bases – at a

Explain The Two-Step Aminoacylation Reaction Between Aars...
The two–step aminoacylation reaction that is required to attach an amino acid to the tRNA is
displayed in Figure 6.
Figure 6: Word equation for the 2–step aminoacylation reaction within aaRS's. Please note that aa
(amino acid), aaRS (aminoacyl tRNA synthetase), and aaRS.aa–AMP (amino acyl adenalate) are the
abbreviations within the word equation. Adapted from Ibba, M 2000:
Within the first step of the reaction, the binding of the ATP to the enzyme induces a conformational
change, allowing the specific amino acid to bind to the aaRS, thus forming the active amino acid
AMP complex (aaRS.aa–AMP). The amino acid binds to the aaRS such that the carboxy terminus of
the amino acid is bound to the tRNA in step 2, and a O=C–O bond is formed between the OH group
of the 3' end of the tRNA and the amino acid. The DHU loop and the anticodon nucleotides are
important structural features that determine the specificity between the amino acid and tRNA. A
covalent bond is formed ... Show more content on Helpwriting.net ...
To prevent incorrect amino acid joining to a tRNA, an editing domain is required. The 3.90.740.10
(connecting–peptide domain) is a post–transfer editing and proofreading domain, which hydrolyses
the misacylated tRNA, and is found in ValRS, IleRS and LeuRS. For example, isoleucine is larger
than valine by just one methyl group, therefore these aaRS's need to distinguish between the smaller
amino acids to ensure the correct amino acid is transferred to the tRNA. The 3.90.740.10 domain is
inserted into the catalytic core and if valine enters the editing domain, it will be hydrolysed and
broken down, as is too small to accommodate the binding of isoleucine (Arnez. J, 2009).
1.10.730.10 (Orthogonal bundle) is another example of an editing domain, and helps with the
binding of the correct bases to the anticodon (Sugiura et al.

The General Timeline For The Evolution Of The Earth Essay

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The General Timeline For The Evolution Of The Earth Essay