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The cell (from Latin cella, meaning "small room") chloroplast.

plast. Each is separated from the rest of the cell by


is the basic structural, functional, and biological unit of a double membrane. The nucleus contains most of the
all known organisms. A cell is the smallest unit of life. DNA of the cell and is the site of RNA synthesis. The
Cells are often called the "building blocks of life". The mitochondria contain enzymes that catalyze important
study of cells is called cell biology, cellular biology, or energy-yielding reactions.
cytology. Chloroplasts, which are found in green plants and green
Cells consist of cytoplasm enclosed within a algae, are the sites of photosynthesis. Both mitochondria
membrane, which contains many biomolecules such and chloroplasts contain DNA that differs from that found
as proteins and nucleic acids. Most plant and animal in the nucleus, and both carry out transcription and
cells are only visible under a microscope, with protein synthesis distinct from that directed by the
dimensions between 1 and 100 micrometers. nucleus.
Organisms can be classified as unicellular (consisting Other organelles play specific roles. They include the
of a single cell such as bacteria) or multicellular Golgi apparatus, lysosomes, and peroxisomes.
(including plants and animals). Most unicellular In the five-kingdom classification scheme, prokaryotes
organisms are classed as microorganisms. have a kingdom to themselves (Monera). The remaining
Cells are of two types: eukaryotic, which contains four kingdoms – protists, fungi, plants, and animals –
a nucleus, and prokaryotic, which do not. Prokaryotes consist of eukaryotes.
are single-celled organisms, while eukaryotes can be In the three-domain classification schemes, eukaryotes
either single-celled or multicellular. have a domain to themselves. Two domains consist of
Biochemistry and the Organization of Cells prokaryotes. Eubacteria are the commonly encountered
Biochemistry describes the molecular nature of life prokaryotes. Archaea are organisms that live in extreme
processes. In living cells, many chemical reactions take environments such as those that were found on the early
place simultaneously. Earth.
Cells of all types have so many fundamental features Many theories about the rise of eukaryotes from
in common that it is reasonable to say that they all prokaryotes focus on a possible role for symbiosis.
had a common origin. The idea of endosymbiosis, in which a larger cell engulfs
Life is based on compounds of carbon. This is the a smaller one, plays a large role in scenarios for the
subject matter of organic chemistry. development of organelles in eukaryotic cells.
The reactions of organic compounds are those of The sun is the source of energy for all life on Earth. It
their functional groups, which are specifically linked provides the energy for photosynthesis, which produces
atoms that react in similar ways under many different carbohydrates as well as oxygen. Carbohydrates can be
conditions. Our solar system, including the Earth, is processed in chemical reactions that release energy.
postulated to have been formed from chemical Reactions that release energy are favored and thus are
elements produced by first-generation stars. The early likely to occur. Thermodynamics is the branch of science
Earth had an atmosphere that consisted of simple that predicts the likelihood of reactions.
chemical compounds. A spontaneous reaction is one that will take place
The atmospheric conditions of the early Earth without outside intervention. This point does not specify
allowed the formation of molecules, such as amino the reaction rate. Some spontaneous processes can take a
acids, that play a role in life processes. long time to occur.
Several theories describe the origin of living cells The change in free energy (ΔG) that accompanies a
from component molecules. All require explanations reaction determines whether that reaction is spontaneous
for coding and for catalytic activity, and all assign an at a given temperature and pressure.
important role to RNA. A negative free energy change (ΔG<0) is characteristic of
All cells contain DNA and are separated from their a spontaneous reaction. A positive free energy change
environment by a cell membrane. Prokaryotic cells do (ΔG>0) indicates that the reaction is not spontaneous, but
not have significant internal membranes, but the the reverse process is spontaneous. When the free energy
larger cells of eukaryotes have an extensive change is zero (ΔG = 0), the reaction is at equilibrium.
membrane system. The internal membranes mark off Living things are ordered assemblies of molecules. They
the organelles, portions of the cell with a specific represent a local decrease in entropy. Because the
function. entropy of the universe increases in spontaneous
Prokaryotes have a nuclear region, which contains processes, this local decrease in entropy is offset by a
DNA, and ribosomes, the site of protein synthesis, as larger increase in the entropy of the surroundings. There
their main features. They have a cell membrane but is an increase in total entropy.
do not have an internal membrane system.
Three of the most important organelles in eukaryotic
cells are the nucleus, the mitochondrion, and the
Water is tasteless, odorless, and The three-dimensional structures of many
transparent. In small quantities, it is also important biomolecules, including proteins and
colorless. Water is capable of dissolving a nucleic acids, are stabilized by hydrogen bonds.
variety of different substances, which is why Acids are proton donors, and bases are proton
it is such a good solvent. And, water is called acceptors.
the "universal solvent" because it dissolves Water can accept or donate protons.
more substances than any other liquid. The strength of an acid is measured by its acid
This allows the water molecule to dissociation constant, Ka. The larger the Ka, the
become attracted to many other different stronger the acid and the more H+ dissociates.
types of molecules. Water molecules are The concentration of H+ is expressed
polar, so they form hydrogen bonds. This conveniently as the pH, which is the negative
gives water unique properties, such as a log of the hydrogen ion concentration.
relatively high boiling point, high specific A similar expression, pKa, can be used in place
heat, cohesion, adhesion, and density. Water of the Ka. pKa = -log Ka.
is directly involved in many chemical
The pH of a solution of a weak acid and its
reactions to build and break down important
conjugate base is related to the concentration of
components of the cell. Conversely, water is
the acid and base and the pKa by the Henderson-
required for the reverse reaction that breaks
Hasselbalch equation.
down these molecules, allowing cells to
In aqueous solution, the relative concentrations
obtain nutrients or repurpose pieces of big
of a weak acid and its conjugate base can be
molecules.
related to the titration curve of the acid.
Water: The Solvent for Biochemical
Reactions In the region of the titration curve in which the
pH changes very little upon addition of aid or
Water is a polar molecule, with a partial
base, the acid/base ratio varies within a narrow
negative charge on the oxygen and partial
range (10:1 at one extreme and 1:10 at the other
positive charges on the hydrogens.
extreme).
There are forces of attraction between the
Buffer solutions are characterized by their
unlike charges.
tendency to resist pH change when small
Polar substances tend to dissolve in water,
amounts of strong acid or strong base are added.
but nonpolar substances do not.
Buffers work because the concentration of the
The properties of water have a direct effect
weak acid and base is kept in the narrow
on the behavior of biomolecules.
window of the acid titration curve.
There are several different types of forces
Many experiments must have a buffered
based on the charge that will be seen
system to keep a stable pH.
frequently. These include, from strongest to
There are many physiological buffers, such as
weakest, ionic bonds, ion-dipole bonds,
dipole-dipole bonds, dipole-induced dipole the bicarbonate blood buffer or the phosphate
bonds, induced dipole-induced dipole bonds. buffer that help maintain physiological pH.
A hydrogen bond is a special example of a
dipole-dipole bond.
Water molecules are extensively hydrogen-
bonded.
The ability to form strong hydrogen bonds
is responsible for the many unique
characteristics of water, such as its very high
melting point and boiling point for a
molecule of its size.
The central dogma of molecular biology describes The organization of promoters and enhancers is more
the flow of genetic information in cells from DNA to complicated with eukaryotes. An important promoter element is
messenger RNA (mRNA) to protein. It states that genes the TATA box at -25.
specify the sequence of mRNA molecules, which in turn Initiation of eukaryotic transcription is also much more
specify the sequence of proteins. Information from a gene is complicated. In addition to the polymerase and the promoter,
used to build a functional product in a process called gene there are 6 general transcription factors involved in forming the
expression. A gene that encodes a polypeptide is expressed in initiation complex.
two steps. In this process, information flows from DNA → Two other RNA polymerases, pol IV and V, are poorly
RNA → protein, a directional relationship known as the understood but are involved in producing small non-coding
central dogma of molecular biology. RNA’s.
Genetic information is passed from generation to Control of eukaryotic transcription includes many of the same
generation through inherited units of chemical information (in concepts seen with prokaryotic transcription.
most cases, genes). Organisms produce other similar The use of enhancers and silencers is more extensive and the
organisms through sexual reproduction, which allows the line promoters are more complicated.
of genetic material to be maintained and generations to be A protein called Mediator is involved in activation of
linked. transcription. Mediator bridges the promoter region and specific
Transcription of the Genetic Code: Biosynthesis of RNA enhancers or silencers.
Transcription is the process of using a DNA template to Activation of eukaryotic transcription is also based on the
produce RNA repression of transcription caused by chromatin structure. The
There are many types of RNA produced, such as messenger chromatin must be relaxed in order for polymerase to access the
RNA, transfer RNA, ribosomal RNA, micro RNA, small DNA.
interfering RNA, and small nuclear RNA. Chromatin remodeling complexes and histone-modifying
A primer is not needed for RNA synthesis enzymes are involved in the relaxation of the chromatin.
As does all polynucleotide synthesis, the reaction proceeds Histones and DNA are modified by methylation,
in the 5’ to 3’ direction. phosphorylation, ubiquitinylation, and acetylation.
Prokaryotic transcription is catalyzed by RNA polymerase, Many control mechanisms are based on response elements,
which is a 470,000 Dalton enzyme with 5 types of subunits. enhancers that respond to some metabolic signal, like heat, heavy
RNA polymerase moves along the template strand of DNA metals, or other specific molecules such as cAMP.
and produces a complementary RNA sequence that matches One very important response element is the cyclic AMP
the coding strand of DNA. response element (CRE). A specific transcription factor called
RNA Polymerase recognizes specific DNA sequences called CREB and a mediating protein called CBP are involved in many
promoters and binds to the DNA. The promoters tell the metabolic processes in eukaryotes.
polymerase which DNA should be transcribed. Most of the transcription of DNA to RNA does not lead to
The  subunit is loosely bound to RNA polymerase and is RNA’s that code for proteins, rather it leads to non-coding RNA
involved in promoter recognition. The two principal types of non-coding RNA’s are micro RNA’s
Transcription can be divided into three parts – initiation, (MiRNA) and small interfering RNA’s (SiRNA)
elongation, and termination. Micro RNAs are about 22 nucleotides long, and are cut from a
There are four principal control mechanisms for prokaryotic longer, hairpin-shaped RNA by the enzyme Dicer. MiRNAs bind
transcription – alternative factors, enhancers, operons, and imperfectly to specific mRNAs and block their transcription.
transcription attenuation. Biosynthesis of RNA 3
Alternative  factors can direct RNA polymerase to SiRNAs are formed in a way similar to miRNA, by the enzyme
different promoters, altering the choice of RNA product. Dicer. When a cell detects specific double-stranded RNA
Enhancers and silencers are DNA sequences usually found molecules, Dicer cuts them into small pieces of 21–25
upstream of promoters that stimulate or reduce transcription, nucleotides. These then bind to mRNA molecules in the process
respectively. These sequences bind to specific proteins called known as RNA interference (RNAi), targeting them for
transcription factors. destruction.
Operons are groups of genes involved in a common Proteins such as transcription factors that bind to DNA often
metabolic process that are controlled as a group. A common have recognizable structural motifs.
example is the lac operon that produces -galactosidase and Common motifs are the helix-turn-helix, zinc fingers, and basic-
other enzymes involved in metabolism of lactose. region leucine zippers.
With an operon, a regulatory gene produces either an The fact that many transcription factors and other DNA binding
inducer or a repressor of the operon. A metabolite acts as a proteins have such motifs has aided in the identification of these
co-inducer or co-repressor to affect the transcription of the proteins when they are initially discovered.
structural genes. In addition to binding DNA, many proteins involved in
Transcription attenuation controls transcription after it has transcription bind to other proteins.
begun by adjusting the level of transcription based on the Many protein-protein binding domains also have identifiable
quantity of a related metabolite. For example, in the trp motifs, such as acidic domains, glutamine-rich domains, and
operon, the level of tryptophan affects the transcription of the proline-rich domains.
genes that produce the enzymes that make tryptophan. After being transcribed from DNA, many RNA molecules are
Eukaryotic transcription is far more complicated than the modified, often extensively, before they arrive at their final form.
prokaryotic version. Several modifications are common with tRNA and rRNA, such
There are 3 principal RNA polymerases in eukaryotes, of as trimming, the addition of terminal sequences, and base
which Pol II produces mRNA. modification.
Pol II is a large protein with at least 12 subunits. Some of Messenger RNA is modified by putting a cap on the 5’ end and a
the subunits share homology with the subunits of prokaryotic poly-A tail on the 3’ end.
RNA Polymerase as well as with eukaryotic Pol I and Pol III.
Messenger RNA is also modified by the removal of methionine in the peptidyl transfer reaction. In a translocation
intervening sequences, or introns. step, the ribosome then moves one codon leaving a dipeptidyl-
The reaction that removes introns involves the formation of tRNA in the A-site and moving the uncharged tRNA to the exit
a lariat as an intermediate. Splicing also depends on a site. The components continues with a new aminoacyl-tRNA
separate type of RNA called a small nuclear entering the P-site. The uncharged tRNA is then ejected from the
ribonucleoprotein, or snRNP (pronounced snurp). E-site.
Alternative splicing of mRNA helps account for the fact that When the ribosome encounters a stop codon, the chain is
there are more proteins produced in eukaryotes than there are terminated in a process requiring GTP and three protein release
separate genes. factors.
Proteins are not the only biological molecules with catalytic The ribosome is actually a ribozyme. There are no amino acids
properties. Some RNAs, called ribozymes, also catalyze at the active site where the peptidyl transferase reaction occurs.
certain reactions. Specific bases on the rRNA are believed to catalyze the reaction.
Group I ribozymes require an external guanosine for Eukaryotic translation involves many more protein factors than
reactivity. Group II ribozymes do. the corresponding translation in prokaryotes
Protein Synthesis: Translation of the Genetic Message Both the 5’-Cap and the 3’ poly-A tail are involved in orienting
Protein translation involves 3 types of RNA and many the ribosome close to the correct AUG used as the start codon.
protein factors. There is no Shine-Dalgarno sequence in eukaryotic mRNA.
Amino acids are activated via enzymes called aminoacyl- Once bound, the ribosome moves down the mRNA scanning for
tRNA synthetases. the correct AUG until it finds one that is in the correct context,
The formation of a protein takes place in four steps called which is identified by a small mRNA sequence around the AUG
activation, initiation, elongation, and termination. is called a Kozak sequence.
The genetic code is based on a series of three bases coding Eukaryotic chain elongation is similar to the prokaryotic
for an amino acid. counterpart. With chain termination, there is only one release
The code is nearly universal in all organisms from viruses factor that binds to all three stop codons.
through humans. The code has no punctuation, meaning the It has recently been found that there is some coupled
mRNA is read three bases at a time with no spaces in transcription and translation in the nucleus of eukaryotic cells.
between. The code is non-overlapping as well, meaning that It has also been recently found that in certain circumstances
each base is part of only one codon. found in the immune system, AUG is not the start codon, rather
The genetic code was determined by a variety of techniques, CUG, leaving leucine as the N-terminal amino acid.
such as using synthetic mRNA with known sequences to see Proteins are usually modified after their initial translation.
what proteins would be translated from them. Protein modification includes removal of the N-formyl-
While there are 64 combinations of three bases leading to 64 methionine from prokaryotic proteins, cleavage of specific amino
codons, there are fewer types of tRNA anticodons. This acids, and addition of signal sequences.
means that standard Watson-Crick base pairing must be Non-protein components can be added to some proteins, such as
broken on occasion. The wobble model of codon-anticodon the heme group added to hemoglobin.
base pairing shows that some bases at the 5’ end of the Proteins must also be folded properly into their correct form.
anticodon of the tRNA can base pair with multiple bases on Protein molecules called chaperones help many proteins fold into
the codon. their correct form.
While there may be many codons for a particular amino It was recently found that in some cases, the ribosome itself acts
acid, not all potential codons are represented equally. as its own chaperone and that proteins translated apart from
Before amino acids can be incorporated into a peptide, they ribosomes fold differently than proteins translated with
must be activated. ribosomes.
Amino acids are activated through a reaction with ATP Proteins are degraded in subcellular organelles, such as
yielding an amino acid bonded to AMP. The AMP-bound lysosomes, or in macromolecular structures called proteasomes.
amino acid is then reacted with a tRNA to yield an aminoacyl Many proteins are targeted for destruction by being bound to a
tRNA. protein called ubiquitin.
The enzymes responsible for activation are called The nature of the amino acid sequence at the N-terminus is often
aminoacyl-tRNA synthetases. very important to control of the timing of the destruction of a
The unique and elegant structure of the ribosome allows the protein.
binding of aminoacyl-tRNA molecules and mRNA. The
ribosome catalyzes the nucleophilic attack of one amino acid
upon the next, allowing for protein synthesis
Protein synthesis begins at an AUG codon on the mRNA.
The ribosome and mRNA forms an initiation complex that
includes the two main ribosomal subunits, the mRNA, GTP,
and three initiation factors, IF1, IF2, and IF3.
The ribosome locates the correct AUG to start translation by
binding to a consensus sequence called the Shine-Dalgarno
sequence.
The first aminoacyl-tRNA bound to the ribosome carries N-
formyl-methionine, and it is initially bound to the P-site of
the ribosome.
In chain elongation, the second amino acyl-tRNA binds to
the A-site. This amino acid’s -amino group performs a
nucleophilic attack on the carbonyl group of the N-formyl-
Nucleic acid is an important class of The two strands of the double helix can be separated
macromolecules found in all cells and viruses. The by heating DNA samples. This process is called
functions of nucleic acids have to do with the denaturation. DNA denaturation can be monitored by
storage and expression of genetic information. observing the rise in ultraviolet absorption that
Deoxyribonucleic acid (DNA) encodes the accompanies the process. The temperature at which
information the cell needs to make proteins. A DNA becomes denatured by heat depends on its base
related type of nucleic acid, called ribonucleic acid composition; higher temperatures are needed to
(RNA), comes in different molecular forms that denature DNA rich in G-C base pairs.
participate in protein synthesis. Nucleic acids are Four kinds of RNA—transfer RNA, ribosomal RNA,
long chainlike molecules composed of a series of messenger RNA, and small nuclear RNA—are involved
nearly identical building blocks called nucleotides. in protein synthesis.
Each nucleotide consists of a nitrogen- Transfer RNA transports amino acids to the sites of
containing aromatic base attached to a pentose (five- protein synthesis on ribosomes, hich consist of
carbon) sugar, which is in turn attached to a ribosomal RNAs and proteins.
phosphate group. A nucleotide is made up of three Messenger RNA directs the amino acid sequence of
components: a nitrogenous base, a pentose sugar, proteins. Small nuclear RNA is used to help process
and a phosphate group. The two main types of eukaryotic mRNA to its final form.
nucleic acids are deoxyribonucleic acid (DNA) and RNA interference, which requires short stretches of
ribonucleic acid (RNA). siRNA, exerts control over gene expression. Nucleic
Nucleic Acids: How Structure Conveys Information Acid Biotechnology Techniques
The two principal kinds of nucleic acids are DNA In order to study nucleic acids, we must have a way to
and RNA. The primary structure of nucleic acids is separate and identify them.
the order of bases. The secondary structure is the The most common separation technique is gel
three-dimensional conformation of the backbone. electrophoresis. DNA pieces separate on a gel-based on
The tertiary structure is the supercoiling of the size.
molecule.
DNA can be visualized on a gel via autoradiography, a
Two kinds of nitrogen-containing nucleobases, procedure where the DNA has incorporated radioactive
pyrimidines and purines, are joined to sugars to nucleotides.
form nucleosides.
DNA can also be seen using fluorescence, often with a
The sugar is deoxyribose in DNA and ribose in compound called ethidium bromide, which glows
RNA. orange under UV light when bound to DNA. The
The addition of phosphate groups to nucleotides disadvantage is that ethidium bromide is a strong
gives rise to nucleotides, which are the monomers of carcinogen.
nucleic acids. Other dyes, such as SyBr green, that are not
When nucleotides are joined by phosphodiester carcinogenic, are now being used to avoid
bonds, they form a sugar-phosphate backbone, environmental hazards. Restriction endonucleases are
giving rise to DNA and RNA. enzymes produced by bacteria that hydrolyze the
The sequence of bases is a very important feature phosphodiester backbone of DNA at specific sequences.
of the primary structure of nucleic acids because the The sequences targeted by restriction endonucleases
sequence is the genetic information that ultimately are palindromes, meaning their sequence reads the same
leads to the sequence of RNA and protein. on both strands going in the same direction.
The double helix is the predominant secondary Most restriction enzymes cut DNA in a way that
structure of DNA. The sugar–phosphate backbones, leaves sticky ends that are very useful for recombining
which run in antiparallel directions on the two DNA from different sources.
strands, lie on the outside of the helix. Pairs of
Cloning refers to creating a genetically identical
bases, one on each strand, are held in alignment by
population.
hydrogen bonds.
DNA can be combined by using restriction enzymes
The base pairs lie in a plane perpendicular to the
that create sticky ends in the DNA. This recombinant
helix axis in the most usual form of the double
DNA will have a target DNA sequence that the
helix, but there are variations in structure.
experimenter is interested in.
The tertiary structure of DNA depends on
The target DNA sequence is carried in some type of
supercoiling. In prokaryotes, the circular DNA is
vector, usually a bacterial plasmid or a virus.
twisted before the circle is sealed, giving rise to
The target DNA sequence is inserted into a host
supercoiling. In eukaryotes, the supercoiled DNA is
organism and the natural doubling time of the organism
complexed with proteins known as histones.
is used to create many copies of the target DNA Differences in DNA patterns between different
sequence. individuals are based on different base sequences of
Those organisms that are carrying the target DNA their DNA. These base sequence differences mean there
are identified through a process called selection. will be different restriction sites leading to different
Selection often involves antibiotic resistance. length fragments.
Genetic engineering is the process of inserting DNA can be sequenced by using several techniques.
genes of interest into specific organisms for either a One of the most common is called the chain termination
medical or purely scientific benefit. method.
Gene therapy is the process of inserting a missing Dideoxy nucleotides are used to terminate DNA
gene into an organism. synthesis. Multiple reactions are run with a different
Bacteria are often used as the factories to produce a dideoxynucleotide in each reaction mix.
protein from a cloned gene. This has led to the The reactions produce a series of DNA fragments of
production of human proteins such as insulin and different length that can be run on a gel and the
erythropoietin. sequence determined by tracking the different length
To produce the protein product of a gene of fragments in the lanes with the 4 different
interest, the gene must be cloned into an expression dideoxynucleotide.
vector, usually a plasmid with special features that As more DNA sequences become available, it
allows it to be transcribed and translated in a host becomes possible to compare those sequences. Of
cell. particular interest is any pattern that may emerge from
In agriculture, genetic engineering is used to genes that encode proteins with similar functions.
produce crops that are resistant to insects or have Important medical applications are emerging, and new
long shelf lives. A DNA library is a collection of methods are making it possible to analyze large
clones of an entire genome. quantities of data. Complete protein: protein interaction
The genome is digested with restriction enzymes maps are now available for eukaryotes.
and the pieces are cloned into vectors and The proteome is the protein version of the genome. It
transformed into cell lines. refers to all the proteins being expressed in a cell. The
Specific radioactive probes to a sequence of study of proteomics is becoming very important in the
interest are reacted to filters that have copies of the life sciences.
bacterial colonies in the library. The probe will bind A very powerful technique in vogue these days is the
to the sequence of interest and the colony’s location use of DNA or protein microchips. With these chips,
can be seen via autoradiography. thousands of samples of DNA or proteins can be
A cDNA library is constructed by using reverse applied and then checked for binding of biological
transcriptase to make DNA from the mRNA in a samples.
cell. This cDNA is then used to construct a library The binding is visualized by using fluorescently
similar to a genomic DNA library. labeled molecules and scanning the chip with a
Polymerase Chain Reaction (PCR) is a computer. The pattern of fluorescent labels then gives
sophisticated, automated technique for amplifying an indication of which mRNA or proteins are being
DNA from very small amounts of samples. The expressed in the samples.
DNA to be amplified is mixed with specific primers,
dNTPs, and a heat stabile form of DNA polymerase.
The mixture undergoes 20-40 rounds of DNA
polymerization via cycling the temperatures so that
the DNA strands separate, the primers anneal, and
the polymerase fills in the DNA. Each cycle doubles
the target DNA.
The technique has revolutionized forensic science
as DNA can be amplified from just a few cells and
then the DNA is analyzed and identified
A newer PCR technique, called quantitative PCR
(qPCR) can be used to measure the original amount
of DNA in a sample being amplified.
A DNA fingerprint is created by digesting DNA
with restriction enzymes, separating the pieces on a
gel, and then visualizing some of the pieces by using
labeled probes.

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