Biology for Bioinformatics

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Biology for Bioinformatics
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The Big Picture of Biology

• What is Life?

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What is Life?

• NASA life is a self-sustaining set of chemical
  reactions capable of reproducing similar copies
  of itself.
• We can separate this into
• chemistry movement of electrons between atoms
• reproduction, which immediately leads to natural
  selection offspring that are better at surviving
  and reproducing end up taking over in future
  generations.

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Chemistry

• Life is applied chemistry. All living systems
  are based on the interactions of chemical
  compounds, the sharing of electrons between
  atoms.
• Life occurs in cells, with a membrane separating
  the inside from the outside.
• membrane is impermeable to almost everything (but
  not gasses or water).
• other molecules enter or leave using specific
  channels
• Homeostasis maintaining a constant internal
  state despite external changes. Homeostasis
  requires
• Metabolism capture matter and energy from the
  outside world, and use it to maintain, grow,
  reproduce.
• Irritability Detect and respond to
  environmental changes.

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All life on Earth is similar

• Current belief life originated on Earth at least
  3.5 billion years ago, not long after the Earths
  surface cooled.
• There may have been many forms of life early in
  our history, many semi-independent origins, but
  we believe all life on Earth today can be traced
  to a single common ancestor. Sometimes referred
  to as the Last Universal Common Ancestor (LUCA).
  
• All organisms are made of same molecules in
  similar structures DNA used for instructions and
  heredity, proteins do the necessary work, cells
  are surrounded by lipid membranes
• Many seemingly arbitrary decisions, such as the
  handedness of molecules and the genetic code, are
  identical in all organisms that have been
  studied.
• Individuals are born and then die, but each
  individuals life comes from previous life.
  Life is an unbroken chain of living cells
  extending back 3 billion years ago to our
  original common ancestor.
• DNAs point of view individuals exist merely as
  temporary carriers of the DNA.

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Reproduction

• All the information needed to produce a living
  thing is coded in its DNA.
• this is a well-supported belief, but as is usual
  in biology, there is some fuzziness around the
  edges
• To reproduce, organisms replicate their DNA, then
  use the DNA instructions to create a new
  organism.
• for microorganisms, this usually means growing
  large, and then splitting into 2 halves, each of
  which gets a copy of the DNA.
• fancier process in multicellular organisms

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Evolution by Natural Selection

• Offspring resemble their parents because the
  offspring are built from their parents genes.
• Random changes in the DNA (mutations) occur at a
  slow but steady rate. This produces a lot of
  variation within a species.
• Some members of a species are more fit better
  able to survive and reproduce than other members
  of the species. This is natural selection the
  more fit individuals are selected by Nature to
  reproduce more than the less fit individuals.
• this can also happen by artificial selection,
  where a human decides which individuals will be
  allowed to reproduce.
• The genes from the more fit individuals will
  slowly take over the species.
• Thus, the genes within a species slowly change
  (or occasionally, change rapidly).
• However, most mutations have no effect on
  fitness, and all organisms contain large numbers
  of DNA positions that are different from other
  members of their species.

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DNA Sharing

• An important consideration DNA is traded between
  different organisms, so innovations can spread
  very widely.
• which is the reason antibiotic resistance is so
  widespread among pathogenic bacteria.
• higher organisms use a formal sexual mechanism
  each offspring gets half its DNA from each
  parent. Also, DNA is almost always confined
  within a species.
• bacteria share DNA less formally, with small
  segments being passed around by several different
  mechanisms, often between species.
• cross-species transfer is called lateral or
  horizontal transfer
• This process is quite widespread, and I have
  heard estimates that up to 1/3 of all genes in
  bacteria have been transferred in from another
  species, as opposed to have come from the common
  ancestor by vertical transfer, regular
  parent-to-offspring descent.

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Diversity of Life

• Lots of different ways to make a living
• Several million different species
• Species a group of similar organisms that can
  reproduce with each other but not with others.
• Easy to define in sexually-reproducing organisms,
  but not in bacteria
• Speciation one species splits into two different
  species very easily
• Isolate two groups so they cant mate with each
  other
• Different random mutations quickly cause
  differences in sexual attractiveness and
  fertility
• When brought back together, the two groups no
  longer want to mate with each other, or they
  cant produce fertile offspring.
• They are now two different species.
• Phylogeny the branching pattern of descent of a
  species starting at the universal last common
  ancestor.
• a binary tree each parent node has 2 offspring
  nodes. Of course, any given species may be
  extinct.

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Basic Division of Life

• Prokaryotes simple cells with no internal
  compartments especially, no separate nucleus
  that contains the DNA.
• Eukaryotes more complex cells with internal
  compartments and membranes, with the DNA
  contained in the nucleus, a special
  membrane-bound compartment.
• Viruses have no metabolism, arent composed of
  cells, are parasites use cells to reproduce
• called bacteriophage or just phage in
  bacteria
• conventional theory viruses are escaped bits of
  cellular machinery
• but viruses often have genes with no homologues
  in living cells

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Major Sub-divisions

• Prokaryotes Eubacteria (common bacteria found
  everywhere) and Archaea (special forms found in
  extreme conditions such as hot, high salt,
  acidic).
• Eukaryotes Protists (single celled), Fungi
  (digest their food externally), Plants (produce
  food from sunlight), Animals (move under their
  own power for part of their lives).
• Protist is a catch-all group, containing many
  different lineages that are no more related than
  animals and plants are. Also, multicellular
  seaweeds are considered protists.
• In contrast, plants, animals and fungi each seem
  to have had a single common ancestor.

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(No Transcript)
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Older Trees
Above is Darwins original tree of life, from his
1837 notebook.
To the right is A tree from Haeckel (1866)
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Another View
I just like this one. I dont know its origin I
found it on a creationist web site.
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Ring of Life

• This is rather speculative, based on the idea
  that eukaryotes arose from a fusion of a
  bacterium and an archaean.
• Bacteria contributed the basic metabolic pathways
• Archaea contributed information handling system

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Biological Molecules
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Molecules in the Cell

• The most common molecule in cells is water, which
  is the universal solvent that all the other
  molecules are dissolved in.
• Various small ions, dissolved salts, keep the
  cell in osmotic balance.
• The main positively charged ions are sodium (Na)
  potassium (K), magnesium (Mg2) , and calcium
  (Ca2).
• The main negative ions are chloride (Cl-) ,
  bicarbonate (HCO3-) , and phosphate (PO4-).
• Four main classes of macromolecule nucleic
  acids, proteins, polysaccharides, and lipids.
  These molecules are usually in the form of
  polymers, long chains of similar subunits, which
  are called monomers.
• Miscellaneous small molecules that act as
  helpers (co-factors) in enzymatic reactions.
  Many of these are vitamins co-factors we
  humans cant synthesize for ourselves.

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Carbohydrates

• Sugars and starches saccharides.
• The name carbohydrate comes from the
  approximate composition a ratio of 1 carbon to 2
  hydrogens to one oxygen (CH2O). For instance the
  sugar glucose is C6H12O6.
• Carbohydrates are composed of rings of 5 or 6
  carbons, with alcohol (-OH) groups attached.
  This makes most carbohydrates water-soluble.
• Carbohydrates are used for energy production and
  storage, and for structure.
• Glucose, a simple 6-carbon sugar, is the primary
  fuel source for most living things. It is broken
  down by the process of glycolysis.
• Starches are glucose polymers, used to store
  fuel.
• Structural carbohydrates include cellulose
  (another glucose polymer) and chitin, the outer
  coating of insects and many fungi.

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Lipids

• Lipids are the main non-polar component of cells.
  Mostly hydrocarbonscarbon and hydrogen.
• They are used primarily as energy storage and
  cell membranes.
• Energy storage triglycerides (fats). Composed
  of glycerol attached to 3 fatty acid molecules.
  Fatty acids are long chains of carbon and
  hydrogen. Double bonds kink the chains and lower
  the melting temperature.
• Cell membranes are composed primarily of
  phospholipids. These have 2 fatty acids attached
  to glycerol, plus a phosphate-containing polar
  head group.
• The heads stick into the water outside the
  membrane, while the non-polar tails stay in the
  hydrophobic interior of the membrane. This acts
  as a waterproof coat that keeps most other
  molecules from passing through the membrane. The
  membrane consists of 2 layers of phospholipids
  the lipid bilayer.

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Proteins

• The most important type of macromolecule.
• Roles
• Structure collagen in skin, keratin in hair,
  crystallin in eye.
• Enzymes all metabolic transformations, building
  up, rearranging, and breaking down of organic
  compounds, are done by enzymes, which are
  proteins.
• Transport oxygen in the blood is carried by
  hemoglobin, everything that goes in or out of a
  cell (except water and a few gasses) is carried
  by proteins.
• Also nutrition (egg yolk), hormones, defense,
  movement
• Proteins are composed of linear chains of amino
  acids.
• There are 20 different kinds of amino acids in
  proteins. Each one has a functional group (the
  R group) attached to it.
• Different R groups give the 20 amino acids
  different properties, such as charged ( or -),
  polar, hydrophobic, etc.
• The different properties of a protein come from
  the arrangement of the amino acids.

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Protein Structure

• A polypeptide is one linear chain of amino acids.
  A protein may contain one or more polypeptides.
  Proteins also sometimes contain small helper
  molecules such as heme.
• Each gene codes for one polypeptide
• After the polypeptides are synthesized by the
  cell, they spontaneously fold up into a
  characteristic conformation which allows them to
  be active. The proper shape is essential for
  active proteins. For most proteins, the amino
  acids sequence itself is all that is needed to
  get proper folding.
• Proteins fold up because they form hydrogen bonds
  between amino acids. The need for hydrophobic
  amino acids to be away from water also plays a
  big role. Similarly, the charged and polar amino
  acids need to be near each other.
• The joining of polypeptide subunits into a single
  protein also happens spontaneously, for the same
  reasons.
• Enzymes are usually roughly globular, while
  structural proteins are usually fiber-shaped.
  Proteins that transport materials across
  membranes have a long segment of hydrophobic
  amino acids that sits in the hydrophobic interior
  of the membrane.

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Nucleic Acids

• Only 2 types DNA and RNA
• Both DNA and RNA are linear chains of nucleotides
• DNA 2 chains running anti-parallel twisted
  together into a double helix
• RNA usually 1 chain of nucleotides, with
  secondary structure caused by base pairing
  between nucleotides on the same strand.

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Nucleotides

• Each nucleotide has 3 parts sugar, phosphate,
  base.
• Sugar is ribose (RNA) or deoxyribose (DNA)
• Bases are attached to the 1 carbon of the sugar
• Base (sometimes called nitrogenous base) is
  purine or pyrimidine.
• Purines 2 carbon-nitrogen rings, adenine (A) or
  guanine (G)
• Pyrimidines 1 carbon-nitrogen ring, cytosine
  (C), thymine (T) (DNA only), uracil (RNA only)
• In the backbone, nucleotides are bonded together
  between the phosphate on the 5' carbon and the
  -OH on the 3' carbon.
• Thus each nucleic acid has a free 5' phosphate on
  one end and a free 3' -OH on the other.
• Used to write the polarity of the molecule
  each nucleotide chain has a 5 end and a 3 end.
• DNA has -H on 2' carbon of the sugar RNA has
  -OH.
• This difference makes DNA more stable and allows
  it to form a regular double helix structure

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Base Pairing

• A bonds with T (or U) G bonds with C. Held
  together by hydrogen bonds
• A-T has 2 hydrogen bonds G-C has 3. This makes
  G-C stronger and more stable at high
  temperatures.
• In DNA, 2 antiparallel chains are held together
  by this pairing.
• Implies that the amount of A amount of T, and G
  C in DNA.
• One characteristic of genomes is their GC
  content the percentage of G and C. This can vary
  between from about 20 to 70. Eukaryotes
  generally have GC contents around 40. Also,
  there are large scale variations in GC content
  along the length of chromosomes called
  isochores, which may be the result of
  horizontal gene transfer.
• RNA is usually single stranded and held in a
  folded conformation by base pairing within the
  RNA molecule. e.g. tRNA.

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Genetic Information Processing
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Central Dogma of Molecular Biology

• Concerns the flow of information in the cell.
• DNA is long term information storage
• RNA is produced from individual genes when needed
  by the cell
• Protein is the actual usable product of each gene

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Replication

• Main enzyme DNA polymerase. Several other
  enzymes also involved (see below)
• Replication is semiconservative
• DNA helix is opened up and unwound by a helicase
• Each old strand gets a new strand built on it.
• DNA polymerase can only add bases to the 3 OH
  group on a pre-existing nucleic acid that is
  base-paired with the template strand it is
  copying. This means that DNA synthesis starts
  with the enzyme primase synthesizing a short RNA
  primer. DNA polymerase then adds bases to this
  primer.
• DNA polymerase can only add new bases to 3' end,
  so one strand is synthesized continuously
  (leading strand) and the other is built up of
  short fragments discontinuous synthesis on the
  lagging strand.
• The short (100-1000 bp ) DNA fragments, called
  Okazaki fragments, are built in the opposite
  direction of fork movement and then ligated
  together (by DNA ligase).
• In eukaryotes, the whole process starts at
  several points on each chromosome and goes in
  both directions. Takes 8 hr to complete.
• In bacteria (which have circular chromosomes),
  there is a single origin of replication, with
  replication proceeding in both directions and
  meeting at the opposite side of the circular
  chromosome.

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Replication
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Transcription

• Transcription is making an RNA copy of a short
  region of DNA.
• Only part of the DNA is transcribed. A
  transcribed region is called a transcription
  unit, which is approximately equivalent to
  gene.
• most transcription units code for proteins
• However, some code for functional RNAs that never
  get translated into proteins (RNA genes).
• When transcription starts, the DNA double helix
  is unwound and only one strand is used as a
  template for the RNA.
• the template DNA strand is called the antisense
  strand, and the other DNA strand, not used in
  transcription is called the sense strand. This
  is because the sense strand has the same base
  sequence as the RNA transcript.
• Genes are oriented from 5' to 3' based on
  transcription direction (even though the template
  DNA is read 3' to 5'). Thus, 5' end of a gene is
  where transcription starts. Upstream and
  downstream also relate to this direction.
• In the scientific literature, only the sense
  strand is written, with the 5 end on the left.
• The antisense strand is implied.
• Sequences are written as DNA (using T) and not
  RNA (using U).

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Transcription Process

• The primary enzyme used for transcription is RNA
  polymerase
• RNA polymerase binds to a promoter sequence just
  upstream from the transcription start point, with
  the help of several proteins called transcription
  factors.
• some transcription factors are used for all
  transcriptions, but others are very specific for
  cell type, hormonal stimulus, developmental time,
  etc.
• RNA polymerase then moves in a 3 direction,
  adding new RNA nucleotides to the growing RNA
  molecule.
• New bases are always added to the 3 end of the
  growing RNA molecule
• In prokaryotes, transcription ends at a specific
  terminator sequence
• In eukaryotes, there is no definite transcription
  terminator, but the RNA molecules are cut off at
  a poly-A addition site (part of RNA processing)

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Gene Regulation

• What makes cells within an organism different
  from each other is which genes are being
  expressed and which are not gene regulation.
• Most of the control of gene expression occurs at
  the point of transcription.
• Transcription regulation is based on interactions
  between transcription factors (proteins) and DNA
  sequences near the gene .
• transcription factors are trans-acting they
  diffuse freely through the cell and affect any
  DNA sequence they can bind to.
• in contrast, DNA sequences near the gene are
  cis-acting they can only affect transcription of
  the gene they are next to. (and not, for example,
  the same gene on the other homologous
  chromosome).
• Types of cis-acting sequence
• promoters several short regions within 100 bp of
  transcription start, especially the TATA box,
  which are all similar to TATAAA.
• enhancers can be up to several kilobases from
  the gene, either upstream or downstream, and in
  either orientation. Increase transcription
  level.
• silencers similar to enhancers, but opposite
  effect.
• Regulatory sequences are short consensus
  sequences imperfect variants on a common
  sequence
• Genes are also affected by the region of
  chromosome they are in some areas are highly
  condensed and unable to be transcribed (depending
  on cell type).

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RNA Processing

• In prokaryotes, transcription and translation are
  essentially simultaneous translation of the
  messenger RNA starts before transcription is
  completed.
• In eukaryotes, transcription occurs in the
  nucleus (where the DNA is), and translation
  occurs in the cytoplasm. This de-coupling of
  transcription and translation requires several
  steps specific to eukaryotes RNA processing
• The initial RNA molecule produced by
  transcription is called a primary transcript.
  It is an exact copy of the DNA. Before it can be
  translated into protein, it must be processed,
  then transported to the cytoplasm. RNA
  processing has 3 steps
• Splicing out of introns, which are non-protein
  coding regions in the middle of protein-coding
  genes. . Most eukaryotic genes are interrupted
  by introns up to 99 of the gene in some cases.
  Exons are the regions of genes that code for
  protein. Primary transcript contains introns,
  but spliceosomes (RNA/protein hybrids) splice out
  the introns. There are signals on the RNA for
  this, but it can vary between tissues
  (alternative splicing).
• 5' cap a 7-methyl guanine linked 5 to 5 with
  the first nucleotide of the RNA.
• 3' poly A tail several hundred adenosines added
  to 3 end. The signal for poly A marks end of
  gene, but transcription continues past this
  without having a definite end point. All except
  histone genes have poly A. Stability of mRNA is
  probable reason for it.
• After processing, the RNA is called messenger
  RNA, and it gets transported to the cytoplasm.

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Intron Splicing and RNA Processing Overview
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Translation

• After transcription, the messenger RNA molecules
  are translated into polypeptides. That is, the
  base sequence of the mRNA is used as a code to
  construct an entirely different molecule, the
  polypeptide.
• The polypeptide is synthesized from N-terminus to
  C-terminus, based on free -NH2 and -COOH groups
  on terminal amino acids of the polypeptide. The
  polypeptide is collinear with the mRNA the
  N-terminal of the polypeptide corresponds to the
  5 end (beginning) of the mRNA. correspond to
  the ribosome moving down the messenger RNA from
  5 end to 3 end.
• Translation is performed by the ribosome, a
  protein/RNA hybrid structure.
• Each group of 3 RNA bases is a codon. Each codon
  codes for a specific amino acid.
• The ribosome starts translation at a start codon
• There are untranslated regions (UTRs) at both
  ends of the mRNA.
• Start codons are also used internally in the
  polypeptides.
• In eukaryotes, translation starts at first AUG in
  the messenger RNA, goes to first stop codon.
  (So, only one polypeptide per messenger RNA.)
• In bacteria (but not archaea, which are like
  eukaryotes in this), AUG, GUG, and UUG can all be
  used as start codons.
• The ribosome then moves down the mRNA, adding one
  new amino acid for each codon.
• Translation stops when the ribosome reaches a
  stop codon.
• Most mRNA molecules are translated multiple times.

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More on Translation

• A key actor in translation is transfer RNA
  short RNA molecules that act as adapters between
  codons on the mRNA and the amino acids.
• The ribosome holds the growing polypeptide chain
  attached to a transfer RNA, and it also holds a
  transfer RNA carrying the next amino acid.
• At each step in the synthesis process, the
  ribosome catalyzes the transfer of the growing
  polypeptide to the next amino acid

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Genetic Code

• Three bases of DNA or RNA code for 1 amino acid
  codon.
• Since there are 4 bases, there are 43 64
  codons. 61 of these code for amino acids, while
  the last 3 are stop codons that end the
  translation process.
• Most amino acids have more than 1 possible codon
  code is degenerate. Most variation is in third
  position of codon.
• Nearly all organisms use the same code, with
  minor variations mostly in mitochondria and
  chloroplasts.
• mitochondria often use a slightly altered genetic
  code
• All translations start with methionine (N-formyl
  methionine in bacteria), regardless of which
  start codon is used (only AUG in eukaryotes).

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Reading Frames

• Codons are groups of 3 bases. Since translation
  can start at any nucleotide, the same region of
  DNA can be read in 3 ways, starting one base
  apart. Each of these 3 modes is a reading frame.
  
• The DNA might also be read on the opposite
  strand, giving a total of 6 possible reading
  frames.
• Genes occur in open reading frames (ORFs), areas
  where there are no stop codons. Genes end at the
  first stop codon that exists in their reading
  frame.
• 3 out of every 64 codons is a stop codon, so
  large open reading frames are rare in random,
  unselected DNA. Since genes are under selection
  pressure, most long open reading frames contain
  genes.

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Protein folding

• After they have been synthesized, most proteins
  fold spontaneously to the most stable (lowest
  energy) configuration.
• Some proteins are assisted by chaperone proteins,
  which also assist in recovery from heat shock by
  causing re-folding to proper configuration.
• Thus, chaperone proteins are also often called
  heat shock proteins. (Actually, these proteins
  were first discovered in Drosophila as proteins
  synthesized in large amounts when the flies were
  given a heat shock.)
• However, predicting protein structure from the
  amino acid sequence is (so far) an unsolved and
  very difficult problem in biochemistry.

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Post-translational modification

• Various chemical modifications occur on many
  proteins
• Glycosylation adding sugars. occurs in smooth
  ER. Mostly for proteins that are secreted or on
  outside of plasma membrane or inside of
  lysosomes. Large blocks of sugars added.
  Proteins called glycoproteins.
• Phosphorylation adding phosphates. An important
  way to active various enzymes , especially for
  turning genes on and off. On serine, threonine,
  or tyrosine.
• Adding lipids so proteins get anchored to
  membrane. Various names depending on which lipid
  is added. For example, myristoyation,
  prenylation, palmitoylation, etc. Proteins
  called lipoproteins.
• Others as well.
• Cleavage. Often the N-terminal Met is removed.
  Other regions can also be removed middle region
  of insulin, removal of signal peptides.

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Localization

• How do proteins get to the proper location in the
  cell?
• Polypeptides often contain signal sequences that
  cause protein to end up in proper organelle, or
  be secreted, or become embedded in the membrane.
  Often a leader sequence (or signal sequence) at N
  terminus that is then removed.
• Best known is for secretion into ER, into
  membrane, and extracellular About 20 mostly
  hydrophobic amino acids at the N-terminus of the
  polypeptide. A Signal Recognition Particle
  (RNA/protein hybrid) recognizes this during
  translation and guides ribosomes to the rough ER
  where translation finishes.
• Also signals for nucleus, lysosome,
  mitochondria. Some are internal to protein and
  not removed.

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A Few Odds and Ends
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Operons

• In eukaryotes, each messenger RNA contains a
  single gene. Genes are scattered randomly
  throughout the genome, with no grouping of
  related genes.
• monocistronic having only 1 gene on a mRNA.
• In prokaryotes, genes that make different parts
  of the same structure or metabolic pathway are
  often grouped together and transcribed as a
  single unit. Several different proteins are
  independently translated from the same mRNA
  molecule. This group of genes is called an
  operon.
• polycistronic having several genes
  co-transcribed onto the same mRNA.

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Exceptions in Prokaryotes

• In addition to the 20 regular amino acids, two
  other amino acids coded in the DNA have been
  found selenocysteine and pyrolysine. Both of
  these use the UGA stop codon, with other bases
  around it used to signal that it is to be
  interpreted as an amino acid and not a stop.
• Bacteria have been seen (rarely) to use several
  other start codons, including CTG, ATA, ATC, and
  ATT.
• Regardless of which start codon is used, all
  bacteria (NOT Archaea) use N-formyl methionine as
  the first amino acid in the polypeptide.
• RNA editing is a process by which certain
  messenger RNAs are altered by adding, deleting,
  or altering certain bases. It seems rare and (so
  far) confined to eukaryotes (including
  mitochondria and chloroplasts).

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Reverse Transcription

• A few exceptions to the Central Dogma exist.
• Most importantly, some RNA viruses, called
  retroviruses make a DNA copy of themselves
  using the enzyme reverse transcriptase. The DNA
  copy incorporates into one of the chromosomes and
  becomes a permanent feature of the genome. The
  DNA copy inserted into the genome is called a
  provirus. This represents a flow of
  information from RNA to DNA.
• Closely related to retroviruses are
  retrotransposons, sequences of DNA that make
  RNA copies of themselves, which then get
  reverse-transcribed into DNA that inserts into
  new locations in the genome. Unlike
  retroviruses, retrotransposons always remain
  within the cell. They lack genes to make the
  protein coat that surrounds viruses.
• Some viruses use RNA for their genome, and
  directly copy it into more RNA without any DNA
  intermediate. The enzyme involved is called a
  replicase or RNA dependent RNA polymerase.