Week 2 Textbook Flashcards
what are amnio acids
small organic molecules with one defining property = all have carboxylic acid group like -COOH and an amino group like -NH2
- they are both attached to the central atom alpha-C
- they build proteins
what is a peptide bond
a covalent bond that is between 2 AA in a protein chain to form a polypeptide which is a long chain of these amnio acids
usually 50 AA long
how are peptide bonds formed?
they are formed by condensation reactions that link one A to the next A
- always has N-terminus and C-terminus standing for amnio and carboxyl
- having different ends gives the polypeptife a different structural polarity
How many types of amnio acids are commonly found in proteins ___
20
- each of them have a different side chain attached to the alpha-C
- mystery for evolution - why are these specific types successful?
what are L-forms
sugars that exist in optical isomers such as D and L-forms
- L-forms are only found in proteins
what are D-forms
D-amnio acids occurs as part of the bacterial cell wall in antibiotics
D-serine = signal molecule in the brain
Out of the 20 standard important AA, how many can be charged
5 AA - lysine and glutamic acid can have side chains that form ions in solutions and can carry a charge
what makes amnio acids have diverse functions to proteins
the fact that some are uncharged, charged, nonpolar + hydrophobic, polar + hydrophilic
what does the general amnio acid look like
H
|
H2N - C - COOH
|
R
where the R is one of the 20 different side chains
at pH 7 the 2 functional groups are ionized (H2N = +, COO = - )
the way it is drawn now is the L-form (proteins exclusively)
when it is flipped so COO- and NH3+ is on opposite sides = D-form
aspartic ___ and glutamic ___
they are both acidic side chains
aspartic acid and glutamic acid
- since both of these have NH2 at the end of the R chain it is NOT charged at 7 pH but it is still POLAR
T/F any amnio acid with an -OH as an R group is polar
true
T/F any AA side chains endings with CH3 are polar
false
they are nonpolar
(alanine, valine, leucine, isoleucine, etc)
what is a disulfide bond
it can form between 2 cystenine side chains in proteins
CH2 - S - S - CH2
(the bond between 2 sulfurs)
what are proteins + list their functions
they are the main building blocls from which cells are assembled
proteins = most of the cells DRY mass
- enzymes = proteins
(active site + substrate)
- transporters and channels in membrane
- carry messages from cell to cell
- motors to propel organelles in cytosol
- specialized proteins = antibodies, toxins, hormones, antifreeze molecules, elastic fibers, luminescence generators
what is the function of an enzyme
made from proteins to catalyze covalent bond breakage or formation
- EX: pepsin degrades dietary proteins in the stomach
EX: DNA polymerase copies DNA
EX: protein kinase adds a phosphate group to a protein molecule
list the function of proteins and give examples
- STRUCTURAL PROTEINS
- provide mechanical support to cells and tissues (collagen, elastin to form fibers in tendons and ligaments, tubulin = microtubules, actin = filaments, keratin forms fibers in hair - TRANSPORT PROTEINS
- carry small molecules or ions (hemoglobin carries oxygen, glucose transporters shuttle glucose into and out of the cell) - MOTOR PROTEINS
- generates movement in cells and tissues (myosin in skeletal muscle cells = force for humans to move) - STORAGE PROTEINS
- stores amnio acids or ions (iron is stored in the liver by binding to the small proein ferritin, casein in milk is a source of amnio acids for baby mammals) - SIGNAL PROTEINS
- carry extracellular signals from cell to cell (insulin controls glucose levels in the blood, nerve growth factor stimulates nerve cells to grow axons) - RECEPTOR PROTEINS
- detect signals and trasmit them into the cells response machinery (rhodopsin in the retina detects light, insulin receptor allows a cell to respons to the hormon by taking up glucose) - TRANSCRIPTION REGULATORS
- bind to DNA to switch genes on or off (lac repressor in bacteria sliences genes to degrade the sugar lactose, DNA binding proteins that act as genetic switches to control organisms) - SPECIAL PURPOSE PROTEINS
- high variation of purposes (marine organisms secrete glue proteins to stick them to a rock, antifreeze proteins in cold fishes protect their blood from freezing, green fluorescent proteins from jellyfish make then release green light)
what is the significance of an amnio acid sequence
for each protein type like insulin = hormone they have a unique AA order
- every human has the same amnio acid sequence for human insulin
what is the polypeptide backbone
it is formed from a repeating sequence of the core atoms - N - C - C -
-because the ends of rach amnio acid are chemically different, they have directionality
N terminus, C terminus
which part of the amnio acid gives it its identity
the side chains (R groups) attached to the alpha C
- alanine = methyl group as its side chain
- also gives them unique properties like nonpolar and hydrophobic or polar and hydrophilic, +/- charges, chemically reactive, etc
explain how long chains of proteins can be flexible and fold up to become many different structures
because noncovalent bonds (ionic, van der waals, hydrogen bonds) are weaker than covalent bonds it is hard to fold and bend the chain and maintain the shape it is holding by using H bonds, electrostattic attractions and van der waals
- it takes many types of noncovalent bonds in different areas of the polypeptide chain to = strong
having electrostattic attractions, VDW and Hbonds in one corner of the fold = strong
explain how the hydrophobic force works
weak interaction
hydrophobic molecules like all the nonpolar side chains and forced together to minimize their distruptive effect on hydrogen bonded water molecules
- it is important in the folding of large polypeptides to see the distribution of polar and nonpolar AA
- the nonpolar + hydrophobic AA tend to cluter inside the folded protein tucked away to avoid contact with aqeuous environment
- thepolar side chains are likely to arrange themselves on the outside of the fold to interact with other polar molecules and aqueous fluids
- they usually are hydrogen bonded to other polar amnio acids or to another polypeptide backbone to = final folded structure of the entire protein
what is a conformation/final folded structure
precise, 3D shape of a protein or macromolecule based on the spital location of its atoms in relation to another
- it is determined by its ability to minimize its free energy (G)
- the folding process is energetically favoured as it releases heat and increases the disorder of the universe
- G = spont = + S= - H
how can a protein be denatured
denatured = unfolded by a tratement of solvenet that disrupt the noncovalent bonds (attractions, VDW, Hbonds) = lost its natural shape
- can even denature in unfavourable conditions, too hot, too cold, pH, etc
what is renaturation
in the lab when they denature it they give the protein its proper conditions and then it re forms and they study it
they way it goes back into its original conformation = renaturation
- the fact that it can go back to how it was before proves that the shape of the protein is coded in the amnio acid sequence
what are the 2 ways that proteins be assisted to folod
CHAPRONE PROTEINS
inside the cell, proteins are assisted by chaperone proteins to fold together proteins in the msot energetically favourable way (spont)
ISOLATION CHAMBERS (still a chaprone just isolated in a box)
- other proteins form isolation chambers in which single polypeptide chains can fold without the risk of forming aggregates in crowded conditions in cytosol
- the purpose of the helpers are to make the process more effiicent + minimize G = spont
- *when the protein interacts with other molecules of the cell is may slightly change its conformation)
T/F proteins are the most structually diverse macromolecules in the cell
true
they can be globular or fibrous (round or straight and thin) and can form filaments, sheets, rings, spheres
what are the 4 different protein structures in the bacterial transport protein; HPr
small, 88 AA long
1. BACKBONE MODEL
- primary structure
2. RIBBON MODEL
- alpha and beta sheets
secondary structure
3. WIRE MODEL
4. SPACE FILLING MODEL
- shows all the atoms - the radius of the spheres represent the van der waals radius in the atom
what are the 2 regular folding patterns found in many different proteins
ALPHA HELIX
a folding pattern when a single polypeptide chain twists around itself to form a rigid cylinder stabilized by Hbonds between every 4th AA
- found in alpha keratin which is abundant in skin, hair, nails, horns
BETA SHEET
- neighbouring regions of the chain associate side by side with each other through hydrogen bonds to give a rigid and flattened structure
- adjacent chains runs in antiparallel directions
- found in fibroin, the major constituent of silk
*these folding patterns are particulary common because they result from hydrogen bonds that form between N-H and C=O in polypeptide backbone
- they adopt a regular repeating form
how are helices formed
the helix formation is formed by hydrogen bonding between the backbone of the carbonyl group of one amnio acid + backbone of amnio group of another amnio acid
amnio + carbonyl (n + 4) 4 position away from amnio 1 group
the hydrogen bonds then form a helix structure and spin and grow
what is a coiled coil
when 2 or more alpha helices twist repeatedly around each other
- stable and rod like protein structure
- this structue forms when the alpha helices have most of their nonpolar side chains on one side adn they twist facing the interior
- alpha-keratin + myosin = long rod like coiled coils
what are the 2 structures of beta sheets
antiparallel B sheets
- when the neighboring segments run in opposite directions
parallel B sheets
- when the neighboring segments run in the same orientation from N-terminus to C-terminus
what properties do B sheets have
they form amyloid structures - where they are stacked together in long rows and the amni acid side chains form teeth like a zipper
- these structures can = specialized secretion
= these are efficient in packaging, and they unfold once they get outside the cell
what happens when there is a misfolding of amyloid protein structures
amyloid structures when done incorrectly can damage cells and tissues
- alzheimers, parkinsons, huntingtons diseases
what are prions
creutzfeldt-jakob disease in humans can occur when misfold of proteins called prions
- they are infectious bc the amyloid form of the portein can convert properly folded moelcules of the protein, into the abnormal ones
- these infections occur when tissues containing prions are introduced into the food chain - after eating, they find their way into the brain = death
normal protein –> abnormal prion –> they bind together to get infected –> converts normal to abnormal –> they multiply and create an amyloid fibril which is a stack of infectious prions
what are the 4 levels of organization in proteins
- Primary structure
- amnio acid sequence - secondary structures
- alpha helix and beta sheets - tetriary structures
- 3D conformation formed by the alpha and beta structures folded together (by the noncovalent bonds) - quanternary structure
- more than 1 polypeptide chain held together by noncovalent bonds
what is the importance of the organizational levels in proteins
the organizational unit = protein domain = any segment of a polypeptife chain that can fold independently into a compact stable structure
40-350 AA folded into alpha helix and beta sheets = modular unit from which other bigger proteins are made from = domain
- proteins can be made with more than 1 domain (smaller units being bonded together to make bigger ones but they are all unique sections)
- the bacterial catabolite activator protein (CAP) has 2 domains, a small domain that binds to DNA and a large domain that binds to cyclic AMP –> when it binds, conformational changes occur
what are unstructured regions of a protein
some small proteins only have 1 domain
large proteins can have lots of domains that are connected by small unstructured polypeptide chains
- the unstructured regions can have lots of functions
why are only a few polypeptide chains useful in the cell
bc most biological functions depend on proteins with stable 3D conformations - they also must be well behaved and not engage in associations with other proteins in the cell forming
- restricts alot of the other protein chains
- due to NS the amnio acid sequences have evolved to adopt a stable conformation
- due to evolution some polypeptides have stayed the same and some have evolved to change their structure and function
what are protein families
grouping present-day proteins by amnio acid dequence and 3D conformation that closesly resemvle thoses of other family members
- they reflect a common evolutionary origin
- usually have related but unique functions
- the serine proteases = a family of protein enzymes - they have nearly the same AA sequences, almost same folds and structures
what is a binding site
on a protein where they have noncovalent bonds, when interacting with another molecule thru these bonds = binding site and when it recognizes the surface of another protein to bind = a large protein
- each polypeptide chain in a large protein made up of many is called a subunit
what is a dimer
two identifical polypeptide chains form a symmetrical complex of 2 protein subunits = dimer
- CAP = bacterial protein = dimer
= 2 identifical copies of the protein subunit = 2 domains
- other proteins contrain 2 or more different polypeptide chains = hemoglobin = 2 globin subunits and 2 identifical beta globin subunits
how is actin filament made
due to long helical proteins that can extend on either side = long, helical structure formed from many molecules of the protein actin
- one of the major filament systems of the cytoskeleton
- other identifical proteins can bind together to form tubes, mictrotubules etc bc they can form into chains, helix, rings, etc
T/F all molecules that have complicated structures get instructions on how to build themselves from somewhere esle
false all the infromation is contained in the macromolecule themselves, in the DNA of the cells of the coding of the AA
- bc they can be ripped apart and independently put back together in the right conditions
what are globular proteins
any protein in which the polypeptide chain folds into a compact, rounded shape
most enzymes are like this (quanternary and round)
what are fibrous proteins
these proteins have roles that require them to span a large distance
simple elongated 3D structure
- alpha-keratin molecule is a dimer of 2 identifical subunits with long helices of each subunit forming a coiled coil (capped at either end) = assemble a roplelike intermediate filaments = cytoskeleton that gives the cells the mechanical strength
what is the function of fibrous proteins
they are used alot outside the cell
- this helps bind the cells together to form tissues
- collagen is the most abundant of these fibrous extracellular proteins in animal tissues
(it is made up of 3 long polypeptide chains - each of them have a nonpolar amnio acid glycine at every third position)
- many collagen molecules bind side by side and end to end to create long overlapping collagen fibrils = strong
collagen= triple helix that is coiled around each other
what is the structure and function of elastin
it is a molecule formed loosly and unstructured polypeptife chains that are covalently cross-linked into a rubberlike elastic meshwork
= elastic fibers = skin and other tissues to stretch and recoil without tearing
T/F many protein molecules are attached to the surface of the cell membrane or secreteed as part of the extracullular matrix
true
- when they are secreted out of the cell they are often stabilized by covalent cross-linkages
these linkages can either tie together 2 amnio acids in the same polypeptide chains in a large protein complex
- the most complex covalent cross links in proteins are sulfurs = disulfide bonds S -S bonds
what is a disulfide bonds function
S - S bond that is covalently cross linked between the sulfhydryl groups on 2 cystenine side chains
- used to reinforce a secreted proteins structure or to join 2 different proteins together
- they do not change the conformation but act as a staple to = most favoured conformation
- lysozyme, saliva can disrupt bacterial cell walls and maintains antibacterial acitivty for a long time bc it is stabilized with dissulfide links
*oxidization of the 2 cystenine polypeptides = bond forms, reduction of the 2 = breaks bond
- these bonds are formed outside of the cell bc there is alot of reducing agents that convert bonds back into cyeteine -SH groups
what are the parts of an amnio acid and how do they link (video)
- alpha carbon which everything else is attached to
- amnio group = NH2
- carboxyl group = COOH
- side chains that differentiates them
2 amnio acids bind together bc the OH of the carboxyl reacts with the H atom on another amnio acid to = water (OH + H –>h20) and then the result in a strong covalent peptide bond (C-N)
- the R groups are not involved in the formation of peptide bonds
- they keep forming this until they keep the N-terminus and the C-terminus
- once AA are into polypeptide chain they are now residues
- more C-N = spining and helix structure
what are motor proteins
uses energy from the hydrolysis of ATP to propel itself along a protein filament or other molecules as directed along the cell
- myosin
- generate the forces responsible for muscle contraction
- power intercellular movements
- they help move chromosomes to oppositeends of the cell during mitosis (anaphase)
- it can move by having conformational changes with a driver = undirectional
how can motor proteins move in one direction for long periods of time
the conformational changes must be unidirectional and irresversivle
the irresversibility is achieved by coupling one the conformational changes to the hydrolysis of an ATP molecule, this why motor proteins rely on ATP
- alot of free energy is released when ATP is hydrolyzed, this allows reasurance that the protein will not go backward (bc it needs ATP hydroylsis to be reversed as well which is energentically unfavoured)
- myosin walks along actin filaments rapidly
what is a proteins machine
assembly of protein molecules that operates as a cooperative unit to perform complex tasks such as replicating DNA
- enzymes catalyze the highly coordinated ones
- the hydrolysis of ATP drives a lot of reactions(splitting into ADP and phosphate group)
what are scaffold proteins
how do proetins locate their partners
- complexes are brought together by scaffold proteins, large molecules that contain binding sites recognized by multiple proteins
- a scaffold can greatly enhance the rate of particular chemical reactions or cell process
- EX: nerve cells use scaffold proteins to organize the specialized proteins that locialize at the synapse between one nerve cell and the next - they cluster under the plasma memebranes for communicating with nerve cells (transmit and respond when stimulated to do so)
- the structure of these proteins are elastic and long to bend and sway
- long molecules of RNA can also be a scaffold protein
what is the nucleolus
it is the nuclear subcompartment in which ribsomal proteins and ribsomal RNAs are assembled into ribsomes
what does biomolecular condensate mean
the term used to descrive such assemblies that contain RNA in addition to protein
- creating a region with special biochemistry without the use of an encaspsulating membrane
- each contains at least one type of scaffold protein or scaffold RNA that interact with specific molecules called clients, which become concentrated there
- the scaffold molecules = weak interactions with ech other = liquid like structure in which connections are being made and broken ( weak interaction network allows molecules to come nad go while the condensate as a whole remains intact and separated from its surroundings = phase separation
explain how biomolecular condensates can be made when needed and disappear when not needed
the nucelolus - froms during interphase and then disappears when they actively start dividing
- these factories appear when and where each of these process take place when needed
what does phosphorylating a protein mean
addition of a phosphate group to a protein
- it can increase or decrease the protein activity depedning on the site of phosphorylation
adding a phosphate group induced change in a proteins conformation
what are the steps in purification of a protein from cells or tissue
- breaking open the cell to release its contents, the result is slurry of cell homogenate or extract
- initial fractionation procedure to separate out the class of molecules of interest (separating all the soluable proteins from the insoluable)
- isolate the desired protein, through chromatography - which uses different materials to separate the individual componetns of a complex mixture based on the properties of the protein like size, shape or charge
- examining the fractions to see which oen contains the protein of interest
- more chromatography steps to get the protein in its purest form
what is chromatography
a technique used to separate the individual molecules in a complex micture on the basis of their properties, like size, charge or ability to bing to other chemical groups
- the mixture is run through a column filled with a material that binds the desired molecule - then it is eluted from the column with a solvent gradient
what is affinity chromatography
it is a process that is the most efficient forms of protein chromatography - it separates polypeptides ont he basis of their ability to bind to a particular molecules
- if large amounts of antibodies that recognize the protein are avaliable they can help extract the protein from a mixture
- it can also be used to isolate proteins that interact physically
- the purified protein of interest is attached tighly to the column matrix and can be removed by chaing the composition of the washing solution (high salt or change in pH)
what is electophoresis
a mixture of proteins is loaded onto a polymer gel and subjected to an electic field, the polypeptides will migrate through the gel at different speeds depending on their size and net charge
- yield bands or spots visualized by staining
what is the significance of having a protein in its pure form
it can be used in biochemical assays to study the details of its activity
- can be subjected to techniques that reveal its amnio acid sequence and 3D structure
how did they used to determine the protein sequence
they would purifiy the protein first and break it down into smaller pieces using protease (trypsin)
- then the identities of the amnio acids in each fragment were determined chemically
the first protein to be sequenced this way was insulin
what is mass spectrometry
it is the faster way to determine the amnio acid sequence of proteins
- it determines the exact mass of each peptide fragment in a purified protein which then allows the protein to be identified from the database that contains a list of every protein that was thought to be encoded by the genome
explain the process of mass spectrometry
the peptides are blasted with a laster and heat
this causes them to be ionized and ejected as a form of gas
- they fly towards the detector in gas form - based on the time it takes for them to arrive, we can determine its mass
- slowly = bigger protein
- faster = more highly charged
EX: the peptides produced by tryptic digestion
- to analyze more complex proteins, they are passed through a second mass spectrometer after being broken into smaller fragments
what are methods that are used to determine the STRUCTURE of purified proteins
x-ray crystallography (shows protein from many angles - can help identify the position of each amnio acid sequence to identitfy the position of each amnio acid)
nuclear magnetic resoance spectroscopy
cry-electron microscopy
what does understanding the structure and code of a protein help us with
knowing a proteins exact surface contours at the atomic level facilitates the design of small molecules that can serve as drugs to alter metabolic pathways or infections
- used to treat covid
T/F scientists have found that most proteins belong to families of one domain or a mix of both
true
T/F bacteria, yeast and cultured mammalian are still unknown on how to use to produce a varity of therapeutic proteins
false
it has given rise to the biotechnology industry
- these organisms have allows us to mass-produce a variety of therapeutic proteins like insulin, human growth hronome, fertility enchanving drugs
T/F genetic engineers have found a way to produce new proteins and enzymes
true
they made proteins/enzymes that metabolize toxic waste, synthesizing life-saving drugs
- we are still learning
- they have built a synthetic protein that opens like a latch when exposed to the compound that serves as a molecular key
- can be used to deliver a molecule on a target gene or used to trigger cell death of a cancer cell
T/F determination of a proteins structure by xray crystallography requires prior knowlegde of its amnio acid sequence
true
what is an enzyme and how do we measure its activity
proteins that control the machinery that drives the cell, protection from diseases
- measuring them in a test tube - how rapidly its reaction proceeds in the presecne of a fixed amount of enzyme and different concentrations of substrate
- the rate should increase as the amount of substrate rises until max velocity
- measure how quickly the substrate is consumed = spectrophotometer
competitive inhibitors
which complete directyl with the substrate for binding to the enzymes active site
- when the CI binds to the enzyme at the active site it acts as a blockage
- can be overcome by adding enough substrate so that the enzyme knows to bond to the subtrate instead of the inhibitor
- the inhibitors affinity for its enzyme must be very low for a compount to be considered viable as a potential therapeutic
noncompetitive inhibitors
which bind to the regulatory sites elsewhere on the enzyme surface
