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54 Cards in this Set
- Front
- Back
- 3rd side (hint)
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what has happened through evolution regarding amino acids
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a conservation of amino acids in protein domains with similar function
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what does rhodopsin do?
y special? |
it is the visual pigment in invertebrates and vertebrates eyes that absorbs light
30% identical amino acids despite difference in eye structure (compound vs. single lens eye). |
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protein families
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proteins with a similar function that have similar, conserved motifs
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give one example of a protein family
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the myosin family of motor proteins
-over 100 members exist that drive movement of organelles, cytoskeleon and muscles |
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name 3 ways of obtaining protein sequences
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-cDNA libraries
-Genomes -Direct sequencing of purified proteins |
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how do u create a cDNA library
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-grind up tissue
-create cDNA by adding reverse transcriptase+nucleotides to synthesize from mRNA -Insert cDNA fragments into DNA of phage virus vectors -amplify phage vectors in bacterial hosts -grow mutant colonies...often times a antibiotic resistent gene can be used to help grow only these colonies |
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vector
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delivers something
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how do u analyze a cDNA library
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-sequence phages extracted from each clone
-use data base to compare cDNA with other cDNA -assign possible identies to each clone -confirm identity |
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the last step of analyzing a cDNA library is confirming the identity..how is this done
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-express each sequence in cell lines or engineered organism
-test its function -localize both mRNA and protein to cells and tissues |
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probe
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a molecule that will bind to a second molecule so that the second molecule can be tracked by following the first
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how would you isolate specific protein sequences froam a cDNA library without sequencing the entire library:
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-use an existing cDNA sequence as a probe (from another organism)
-plate out colonies and determine which colonies have a probe. (probe is complementary to the wanted DNA) -sequence phages from these colonies -or use PCR |
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what can pcr be used for
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PCR amplifies CdNA fragments with out the need for bacterial cells
-takes advantage of heat-resistant DNA polymerase |
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what are 2 alternates to cDNA librarys
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1)purify protein and use mass spectometry
2)sequence the entire genome of an organism and splice together exons to create cDNA |
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what is different about cDNA
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it does not have introns
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where can information about proteins be accessed on the web?
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from the ncbi website
national center for biotechnology information |
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how would you access information about a protein in a protein database?
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-publication abstracts
-cdna or mrna sequence -translated sequence -structure |
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what can protein database blast search do
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-compare one sequence with others
-compare protein to protein sequences -used to classify unknown cDNA sequences obained from a tissue |
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what are ways that proteins can be covalently modified
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1)phosphorylation
2)addition of sugars or glycosylation 3)addition of lipids or glycolipids |
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what is phosporalation
amino acids? |
-addition of negatively charged phosphate to R group
-must have an alcohol group -serine, threonine, tyrosine - |
a sea of ties and trees was fast
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R= -CH2-OH what will happen to this after phosporalation?
serine |
R= -CH2-O-PO3 (2-)
phosphoserine |
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where does phosphate usually come from?
byproduct of phosporalation |
atp
phospho-amino acid + Adp |
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what is phosporalation catalyzed by?
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enzymes known as kinases
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what effects can phosporalation have?
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profound structural and functional consequences
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gly sister had nice lips
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glycosylation examples
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carbohydrate chains can be joined to OH group of serine or NH2 group of asparagine (N-linked)
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benefits of glycoproteins
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-added carbohydrates stabilize protein structure in aqueous environments and protect against proteases
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protease
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enzyme that causes proteins to go through prolysis(degredation of proteins)
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where are glycoproteins often found?
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extracellular surface of proteins in cell membranes-glycocalyx
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glycocalyx
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carbhoydrate coat
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besides protective functions, what other functions can glycoproteins have?
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signaling functions
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Addition of _____ to form lipoproteins.
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lipoproteins
phosopholipids and fatty acids to cysteine or an N-terminal glycine residues to form |
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what can the addition of lipids to proteins do?
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can insert into the hydrophobic core of biological membranes anchoring the protein to the membrane
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What is energy used to do?
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work
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different types of work
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mechanical-movement of cells
electrical- seperation of plus an minus charges formation/breaking of chemical bonds heat production light production |
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how can energy be stored
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-chemical bonds
-electrical potential differenes -chemical concentration gradients |
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what is the first law of thermodynamics
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conservation of energy
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enthalpy
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heat content: H
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internal energy...enthalpy equation and meaning of values
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ΔH = ΔE + PΔV
H=enthalpy E=energy P=pressure V=volume |
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for most biological reactions ΔH equals
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ΔE
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if internal energy of products is less than internal energy of of reactants...what?
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ΔH is negative
difference is given out as heat or may be used to do work |
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free energy
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ΔG
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free energy equation
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ΔG = ΔH -TΔS (ΔS = entropy change)
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what is free energy
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what is the amount of energy from the reaction that is available to do work?
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ΔG
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ΔG = G(products) –G(reactants)
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what reactions occur spontaniously?
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ones with negative ΔG
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free energy is negative what way does reaction go
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reaction goes to the right
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if free energy is positive what way does reaction go
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reaction goes to the left
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if free energy is 0 what does it mean
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equilibrium
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At equilibrium is the [A] necessarily equal to [B]?
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no
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How can we determine which way a reaction will “go”or if it is at equilibrium?
make out equation from start to finish For the reaction A <->B |
ΔG = RT ln( [B] pr/[A] pr) –RT ln( [B]eq/[A]eq)
Now define an equilibrium constant Keq= [B]eq/[A]eq ΔG = RT ln([B]pr/[A]pr) –RT ln(Keq) [A] pr is what exists at the moment now factor in standard... ΔGo’= -RT lnKeq ΔG = RT ln([B]pr/[A]pr) + ΔGo’ |
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Ln(1) equals what?
Ln above 1? |
zero
above zero |
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what are standard conditions
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when
all [ ]pr= 1M (except water), T = 298 degrees K, P = 1 atm, pH7 |
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what would this keq equation be?
A+B <--> C+D |
Keq= [C]eq[D]eq/ [A]eq[B]eq
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what would free energy equation be for this reaction?
A+B <--> C+D |
ΔG = RT ln([C]pr[D]pr/ [A]pr [B]pr) +ΔGo’
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how does a reaction inside a cell with positive free energy occur?
describe |
coupled reactions
1)removal of product through a reaction with a negative delta G 2)activated intermediate |
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