Download Prep 101

Bio 200 Equation Sheet
(Lasko / Fagotto)
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Biology 200 is a challenging course containing
lots of material and requires a full
understanding of the course content
Start studying early to be well prepared for the
exam
It is impossible to memorize all the information
without understanding it
Do not only rely on lecture notes – create a
summarized version of notes to study with by
using lecture notes, class notes and the text
book
The exam style is multiple choice - many
questions will not be straight forward but will
require the application of different parts of the
course
It is important to do as many practice
questions as possible to be comfortable with
approaching exam questions
MACROMOLECULES: PROTEINS,
NUCLEIC ACIDS,
CARBOHYDRATES AND LIPIDS
Key Terms
Coiled coil
Polypeptide
motif
α helix
Tertiary
β-pleated
Structure
sheets
Quaternary
Helix-loopStructure
helix
Purines
Ca2 Zinc
Finger
Pyrimidines
Nucleotide
Ribonucleic Acid
(RNA)
Deoxyribonucleic
acid (DNA)
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Lipid membranes composed of phospholipids
that are amphipathic. Have hydrophobic tail
and hydrophilic head
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Carbohydrates : Have the general formula
(CH2O)n
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Monosaccharides are linked together
via a glycosidic bonds forming
polysaccharides
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Sugars can also branch forming huge
polymers
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Proteins : Consists of one or more
polypeptide that have a defined 3-D structure
and have diverse biological functions
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Peptides have covalent bonds between
the amino group from one amino acid
with the carboxyl group of adjoining
amino acid
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There are 20 different amino acids
differing by their R group
Nucleic Acids: macromolecules composed of
a long chain of monomers known as
nucleotides.
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Nucleotides consist of : a Pentose
Sugar, 5-C sugar either deoxyribose or
ribose, a nitrogenous base either a
purine or pyrimidine and a phosphate
group
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Nucleotides are joined through 5’-3’
phosphodiester linkage
DNAs stores all genetic information in
genes
2 categories of RNA : Structural (tRNA,
mRNA, rRNA) and catalytic
TRANSCRIPTION
Key Terms
Primary
transcript
Capping
Poly (A)tail
Alternative
splicing
Operon
repressors
Activators
mutations
Enhancers
Protein-coding
region
Pre-Initiation
Complex
Transcription
factors
TATA-BOX
Regulatory
Sequences
Promoterproximal
elements
Deletion
analysis
Repression
domain
DNA-binding
Domain
Homeodomain
proteins
Zinc-Finger
proteins
Leucine Zippers
Basic
helix-loop-helix
proteins
(bHLH)
enhancesome
POST-TRANSCRIPTIONAL GENE
REGULATION
Key Terms
Capping
Polyadenylation
RNA-Binding
Domains
hnRNP
Proteins
RNA
recognition
motif(RRM)
RGG box
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Transcription a process by which the
polymerization of ribonucleotides is guided by
complementary base pairing with DNA
producing an RNA transcript of a gene
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Occurs in 3 steps :
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Initiation : RNA Polymerase binds
consist of multiple subunits, DNA
denatures, 2 ribonucleotides are
aligned, release of the σ subunit ends
initiation
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Elongation : Transcription bubble is
formed
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Termination: RNA sequences that
signal the end of elongation coded by
DNA. Terminator sequence stops RNA
Polymerase
Promoter is essential for transcription.
Prokaryotes and eukaryotes have different
polymerases
Prokaryotes regulate gene transcription via
operons and Two-component regulatory
systems
Eukaryotic gene regulation is much more
complex - each gene has its own promoter
unlike operons
Eukaryotic transcription factors bind the
promoter and other regulatory sequences
regulating gene expression.
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The DNA binding domain of
transcriptions factors contain a variety
of motifs that bind specific DNA
sequences
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Different combinations of factors can
form dimmers which bind different
regulatory sequences enhancing or
inhibiting transcription
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KH motif
Cleavage
Splicing
Spliceosomes
Self-Splicing
Alternative
Splicing
RNA Editing
Nucleocytoplasmic
export
Nuclear
localization signals
(NLS)
Nuclear Export
Signal (NES)
SR proteins
Exon-Junction
complex (EJC)
Eukaryotic transcripts go through several
processes before becoming mRNA
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5’ capping
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Poly A (tail)
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Alternative splicing
RNA processing occurs in the nuclei and only
mRNA is exported out to be translated
All post transcriptional modifications have
multiple steps and different enzymes are
involved which must be known
Cleavage and polyadenylation occurs in the
same process
Splicing occurs at introns and alternative
splicing can lead to different proteins from the
same transcript
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At introns/exon border there are is short
consensus sequences
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The splice reaction occurs in two transesterfication steps
Most splicing occurs via spliceosomes which
contain several small nuclear ribonucleotide
proteins (snRNPs) and have a specific series
of steps
RNA Editing :The sequence of pre-mRNA is
altered and mRNA sequence is different than
the genomic DNA sequence
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Deamination reactions changes A to I
and C to U
Nucleocytoplasmic export of RNA- ONLY
fully spliced mature mRNA gets exported to
the cytoplasm for translation
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Different proteins and receptors allow
transport through the nuclear pore
Protein import Nuclear Localization Signal
(NSL)
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Proteins that are destined for the
nucleus have a specific sequence
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NSL is recognized by specific proteins
that orchestrate import through the
nuclear pore
Nuclear Export Signal (NES)
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Proteins can exported through the
nuclear pore by recognition of the
nuclear export signal
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Specific proteins recognize the NES
and orchestrate export
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RNA POST-TRANSCRIPTIONAL
REGULATION II
Key Terms
Phosphorylation
Ferrtin
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Transferrin
receptors
(TfRs)
MicroRNAs
RNA
Interference
mRNA stability effects how long mRNA
persists and therefore the amount of protein
translated
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degradation of the poly(A) tail over time
leading to decapping and degradation
of mRNA by exonucleases
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AUUUA in the 3’UTR sequence
decreases the ½ life of mRNA
Cytoplasmic Polyadenylation and mRNA
Translation: Some mRNA must undergo
polyadenylation in the cytoplasm to become
translationally active
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They have a Regulatory sequence that
control translation are usual found with
the UTR at the 3’ or 5’ end
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Sequence-specific translational-control
proteins can bind to the 3’UTR of an
mRNA and function in a combinatorial
manner and in most cases repress
translation
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Phosphorylation allows translation to
occur
RNA Interference: dsRNA on the 3’end of a
target will silence the whole gene while dsRNA
on the 5’ end only target the region it
hybridizes with
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miRNA is formed by the processing of
≈70-nt pre-RNA that has a hairpin
structure with a few mismatched base
pairs in the stem
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siRNA are produced by cleavage of
long dsRNA (RNAi)
Iron regulation : Iron levels are kept at
equilibrium through Transferrin receptors
(TfRs) which mediate iron uptake and through
ferrtin an intracellular iron binding protein. A
brief overview :
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stability of TfRs mRNA and Ferrtin
mRNA is regulated by iron
concentrations
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TfR mRNA have Iron Response
Elements(IRE) that contain the AU-rich
degradation signals at the 3’ end
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Ferrtin mRNA has 5’ Iron Response
Elements(IRE)
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Control of mRNA for both occurs
through IRE-binding protein(BP) and
iron levels control mRNA levels of each
through binding of this protein
polymerase
T-antigen
helicase
RPA
Phosphodiester
bonds
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Key Terms
RNA primer
primase
DNA
Replication
bubble
Replication fork
Okazaki
fragments
Restriction
endonuclease
MCM
Helicases
Topoisomerase
DNA replication is a semi-conservative
process where newly synthesized DNA
contains a parental and daughter strand.
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Synthesis occurs in the 5’ to 3’ direction
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RNA primer is required which is added
by primase
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DNA polymerase proofreads and
removes any mistakes: DNA pol δ
make less mistakes that DNA pol α
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During elongation, RNA primers is
removed by DNA pol δ
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DNA pol δ (not DNA pol α) fills in the
gap
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DNA ligase seals the 3’ OH and 5’ PO4
nicks by catalyzing the formation of
phosphodiester bonds
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DNA pol δ is responsible for the
majority of replicating strand elongation
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Multiple enzymes and protein
complexes are involved
In Eukaryotes there are multiple Origin sites of
replication and replication occurs
bidirectionally
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Key Terms
tRNA
mRNA
rRNA
Ribosomes
AminoacyltRNA
synthetase
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Many amino acids have more than one
tRNA and many tRNAs can bind more
than one amino acid
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rRNAs are found in the ribosome which
catalyzes the formation of a polypeptide
chain
A ribosome is the site of translation
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Composed of a small subunit and a
large subunit
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Recognizes translation initiation start
site
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Has catalytic activity linking amino acids
to form polypeptide
Translation occurs in three defined and which
must be known
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Formation of the Pre-initiation
complex and translation initiation
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Translation elongation
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Translation termination
Polysomes allow simultaneous translation of
an mRNA by multiple ribosomes increasing
efficiency of protein synthesis
Protein degradation occurs through a series
of steps leading to a ubiquitin tag and
cleavage by proteosomes
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TRANSLATION
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DNA REPLICATION
Complementary
base-pairing
Wobble
MethionyltRNAi Met
Pre-initiation
complex
Internal
ribosome
entry site
(IRES)
P site
E site
A site
Polysomes
Ubiquitin
Proteosome
Translation is a cytoplasmic process in which
mRNA transcripts are translated into a
polypeptide sequence by ribosomal machinery
Different RNA’s have different roles in
translation
Three ribonucleotides of an mRNA make a
codon and carries the transcribed genetic
sequence
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mRNAs have three reading frames
usually only is read and codes for a
protein
tRNA has an amino acid attached to its 3’ end
by aminoacyl-tRNA synthetase and has an
anticodon sequence
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Methionyl- tRNAi Met : has a different
structure than regular tRNA that binds
methionine
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The AUG start codon is recognized by
tRNAiMet
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CHROMATIN AND
CHROMOSOMES
Key Terms
Chromatin
Nucleosome
Core
proteins
Linker
protein
Histone
Solenoid
Protein
scaffold
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MARs
SARs
Heterochromatin
Euchromatin
Acetylation
Centromeres
Telomeres
Gene Silencing
Hypoacetylated
Hyperacetylation
DNA is compacted into the nucleus by an
ordered chromatin structure which also can
regulate gene transcription and expression
DNA in the interphase state is complexed with
proteins this DNA-protein complex is called
chromatin
The smallest unit of chromatin is the
nucleosome which is associated with
histones
Solenoid is a coiling of nucleosome filament
into a higher-order, thicker filament
Protein scaffold is a higher order of
compaction of solenoids associated with
Scaffold-associated proteins (SARs) and
matrix attachment protein (MARs)
During cell division Chromosomes appear
which are a the most compact organization of
chromatin
Histones can be acetylated and
deacetylated : charges are altered, altering
the level of compaction of chromatin
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Deacetylation tight chromatin structure
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Acetylation loose chromatin structure
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regulates transcription; genes found in
tight chromatin cannot be transcribed :
Gene silencing i.e. yeast mating type
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Complexes can bind leading to
deacetylation and acetylation
suppressing and activating gene
transcription
Heterochromatin is more condensed areas,
Euchromatin less condensed areas
Stable inheritance of chromosomes during cell
division requires a centromeres, two telomeres
and multiple origins of replication
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Centromeres bind microtubules and are
important for chromosome separation
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Telomeres are added to prevent
shortening of chromosomes after each
replication round
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Transient
Transfection
Stable
Transfection
Western Blots
Probes
Ligation
Oligonucleotide
Klenow
fragments
Transgene
Knock Out
Knock In
Dominant
negative
Knock down
Microarray
Yeast twohybrid
Molecular techniques are a very important part
of this course and are the fundamental basis of
many of the questions on the exam
Understand the practical application as there is
a wide array of questions that can be asked.
You likely will be asked to apply a practical
technique to a situation as well as know what
is involved in each technique
Look through lecture notes and the text book
and ensure you have a full understanding if a
technique was applied to a given experiment
or what it can be used for
cDNA libraries
Screening
Recombinant
Transient
Transfection
Stable
Transfection
Western Blots
Probes
Restriction
Cutting
Transformation
Shotgun
Cloning
cDNA libraries
Screening
Recombinant
Protein Chips
GENE STRUCTURE AND FAMILIES
Key Terms
Genes
Mutations
Retrotransposons
Pseudogenes
Transposable
Elements
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PROTEINS
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CELL SIGNALLING
Key Terms
Endocrine
Signalling
Paracrine
signalling
Autocrine
Signalling
Key Terms
Chaperone
Native
conformation
Chaperonines
Protein
Modifications
Glycosylation
Ubiquitin
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G protein –
coupled
receptors
Cytokine
receptor
TGF-β
receptors
Receptor
tyrosine
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Retrovirus
Exon
shuffling
Alu
sequences
Transposase
Minisatellite
Simple
Sequence
Repeats
(SSRs)
Microsatellite
Paralogs
Orthologues
Autocrine Signalling : The signalling cells
respond to a signal they produce themselves
Cell Surface Receptors : G protein –coupled
receptors, Cytokine receptor, Receptor
tyrosine kinases, TGFß receptors, Receptor
guanylyl cyclases, Receptor phosphotyrosine
phosphatases, T-cell receptors
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MOLECULAR TECHNIQUES
Key terms
Gel
Electrophoresis
DNA Sequencing
Polymerase
Chain Reaction
(PCR)
RT-PCR
DNA Cloning
Vector
Plasmid
Bacteriophage
YAC
BAC
Transformation
Shotgun
Cloning
FISH SDS-Gel
A gene is a region of DNA that controls a
distinct hereditary character or the entire
nucleic acid region that is required to
produce a functional protein
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Genes can be present in the genome as
single copies or there can be found in
duplicates or multiple copies
Mutations in genes
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Mutations in control regions can lead to
higher, lower or no expression of that
gene
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In an exon they can lead to no change,
an amino acid substitution, frame-shift
or insertion of a stop site
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In introns can lead to new splicing sites
and altered alternative splicing patterns
Gene families : related genes that have been
duplicated
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Orthologues genes are genes that
evolved form a common ancestor in
different species through speciation and
will have similar function
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Paralogs are genes that are related in
the same genome through duplication
Simple Sequence Repeats :Simple sequence
repeats (SSRs) are short sequence that
contain short repeats
Tandem Repeats: rRNA and snRNA : these
genes produce nearly identical copies
Minisatellite DNA : composed of tandem
repeats units which are 6-100 bp long and are
found in centromeres and telomeres
Microsatellite DNA are <150 bp repeats are
1-4 bp long and are sometimes found in
transcription units
Transposons =Mobile elements=
Transposable elements are moderately to
highly repetitive DNA that can move in the
genome and interrupt genes
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Know the mechanism of transposons
and Autonomous elements and
Nonautonomous elements
Interdispersed Elements: mobile elements
that do not disrupt gene expression but can
have crossing over occur as they have similar
sequences. Example Alu
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Endocrine Signalling: The signalling
molecules are hormones that can act on
cells far from the site of synthesis
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Paracrine signalling : Signalling molecules
targets are in close proximity, many diffuse
away from the signalling cell , concentrations
gradients of the signals invoke different
responses in target cells
Specificity
Affinity
Antibody
Enzymes
Protein Kinases
Phosphorylation
Allostery
Signal
Recognition
Particle
(SRP)
Translocon
Crosslinking
Cooperativity
Know the mechanisms for how protein are
targeted for intracellular organelle
membranes and secretion pathways
The amino acid sequence of a polypeptide
dictates how a protein will fold into a 3-D
conformation the native conformation
Chaperones help proteins fold, know the
mechanisms
Following synthesis nearly every protein is
chemically modified
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Alter the activity, lifespan or cellular
location
The covalent modification of a lysine with a 76residues ubiquitin polypeptide, tags the protein
for degradation by a proteosome
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Know the ubiquitin pathway and all it’s
components
Some Neurodegenerative diseases are
caused by aggregates of stably folded
proteins in an alternative conformation.
example Bovine spongiform encephalopathy
(BSE)
What effects protein-ligand binding
Enzymes catalyze the chemical alteration of
substrates by lowering the activation energy
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Learn PKA and how it catalyzes a
reaction
Motor proteins convert chemical energy from
ATP hydrolysis or electrochemical gradients
into mechanical linear or rotary movement
What is allostery and cooperativity and how
do they alter a enzyme activity of a protein
Learn all the different way in which proteins
can be regulated
Know how different techniques use certain
characteristic of proteins to purify them
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