Week 2 Textbook Flashcards

Question

what are the 2 ways that proteins be assisted to folod

Answer 1

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)

Answer 2

true they can be globular or fibrous (round or straight and thin) and can form filaments, sheets, rings, spheres

Answer 3

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

Answer 4

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

Answer 5

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

Answer 6

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

Answer 7

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

Answer 8

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

Answer 9

amyloid structures when done incorrectly can damage cells and tissues - alzheimers, parkinsons, huntingtons diseases

Answer 10

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

Answer 11

1. Primary structure - amnio acid sequence 2. secondary structures - alpha helix and beta sheets 3. tetriary structures - 3D conformation formed by the alpha and beta structures folded together (by the noncovalent bonds) 4. quanternary structure - more than 1 polypeptide chain held together by noncovalent bonds

Answer 12

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

Answer 13

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

Answer 14

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

Answer 15

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

Answer 16

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

Answer 17

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

Answer 18

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

Answer 19

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

Answer 20

any protein in which the polypeptide chain folds into a compact, rounded shape most enzymes are like this (quanternary and round)

Answer 21

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

Answer 22

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

Answer 23

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

Answer 24

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

Answer 25

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

Answer 26

1. alpha carbon which everything else is attached to 2. amnio group = NH2 3. carboxyl group = COOH 4. 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

Answer 27

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

Answer 28

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

Answer 29

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)

Answer 30

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

Answer 31

it is the nuclear subcompartment in which ribsomal proteins and ribsomal RNAs are assembled into ribsomes

Answer 32

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

Answer 33

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

Answer 34

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

Answer 35

1. breaking open the cell to release its contents, the result is slurry of cell homogenate or extract 2. initial fractionation procedure to separate out the class of molecules of interest (separating all the soluable proteins from the insoluable) 3. 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 4. examining the fractions to see which oen contains the protein of interest 5. more chromatography steps to get the protein in its purest form

Answer 36

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

Answer 37

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)

Answer 38

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

Answer 39

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

Answer 40

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

Answer 41

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

Answer 42

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

Answer 43

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

Answer 44

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

Answer 45

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

Answer 46

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

Answer 47

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

Answer 48

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

Answer 49

which bind to the regulatory sites elsewhere on the enzyme surface

Week 2 Textbook Flashcards

(76 cards)