Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
152 Cards in this Set
- Front
- Back
|
When did life start according to 12C/13C isotope ratios?
|
3.8 billion years ago.
|
|
|
How does 12C/13C dating work?
|
Living organisms prefer 12C over 13C. When there's a composit in the rock that has a high 12C/13C ratio, it means that's probably life. 13C depletes over time so the higher ratio you have, the older it is.
|
|
|
Earliest fossil is of...
|
cyanobacteria 3.5 billion yrs ago.
|
|
|
What is the "top down" method for the origin of life?
|
DNA sequence analysis
|
|
|
What is the "bottom up" method for the origin of life?
|
chemistry, nucleotide and protein synthesis
|
|
|
How does phylogeny work?
|
In the 60s Zuckerkandl and Pauling sequenced amino acids of hemoglobin of several species and found the differences in species related to the estimated time of the common ancestor.
|
|
|
What does LUCA stand for?
|
Last Universal Common Ancestor
|
|
|
What are the 4 assumptions of phylogenetic trees?
|
1. DNA codes for the aa sequence found in all cell proteins.
2. DNA is passed down vertically from one generation to another. 3. More closely related species will have more similar DNA. 4. DNA is passed down as a whole set of chromosomes; it should not matter what genes are used to reconstruct a family tree. |
|
|
2 problems with DNA sequence comparisons:
|
1. Long branch attraction
2. Lateral gene transfer |
|
|
What is long branch attraction?
|
Rapidly mutating DNA can change and then change back - it doesn't follow the chronological order.
|
|
|
What is lateral gene transfer?
|
A gene is transferred between organisms. Genes are lost and acquired through this.
|
|
|
What are the three main divisions of life?
|
Eubacteria
Archaea Eukaryotes |
|
|
Which divisions of life are prokaryotes?
|
Eubacteria
Archaea |
|
|
Name 7 things Prokaryotes have:
|
1. flagellum
2. mesosome 3. ribosomes 4. DNA 5. plasma membrane 6. cell wall 7. capsule |
|
|
How are archaea similar to eukaryotes?
|
They have more similar proteins.
|
|
|
How are bacteria similar to eukaryotes?
|
They have similar metabolic pathways.
|
|
|
5 ways prokaryotes, mitochondria, and chloroplasts are similar.
|
1. 1 single, circular DNA
2. replication through binary fission 3. 70S ribosomal subunit 4. e- transport chain found in the plasma membrane 5. 1-10 micron size |
|
|
Describe the symbiosis theory.
|
Eukaryotes are a product of symbiosis where a mitochondria comes from an engulfed bacteria.
|
|
|
3 origin hypotheses from chemistry
|
1. vesicle first
2. metabolism first 3. RNA world hypothesis |
|
|
Explain vesicle first.
|
Vesicles form from lipids concentrate materials inside.
|
|
|
Explain metabolism first
|
Formation of biochemicals that act as catalysis of small molecules to make cycles.
|
|
|
Explain RNA world.
|
RNA can be both an enzyme and template. A self-replicating RNA could evolve.
|
|
|
3 main chemical components of a cell.
|
1. amino acids
2. nucleotides 3. lipids |
|
|
What's the problem with the Urey experiment?
|
It made D and L amino acids and life generally only uses L.
|
|
|
Name two negatively charged acids:
|
1. D (aspartic acid)
2. E (glutamic acid) |
|
|
3 positively charged basic aa's:
|
1. K (lysine)
2. R (arginine) 3. H (histidine) |
|
|
2 uncharged polar aa's:
|
1. N (asparagine
2. Q (glutamine) |
|
|
10 nonpolar aa's:
|
1. A (alanine)
2. V (valine) 3. L (leucine) 4. I (isoleucine) 5. G (glycine) 6. C (cysteine) 7. P (proline) 8. F (phenylalanine) 9. M (methionine) 10. W (tryptophan) |
|
|
In what kind of atmosphere can you make organic compounds?
|
Reducing atmosphere (CO2, O2, NO2, H2O)
|
|
|
What does Miller's exp. show us?
|
You need a reducing atmosphere to create organic molecules. It is thought the atmosphere was derived from volcanoes, but that's neutral and not reducing.
|
|
|
What's the problem with the prebiotic soup?
|
The scale would have to be huge and there would have to be evidence of huge deposits of carbon from non-living sources.
|
|
|
4 points for the RNA world hypothesis:
|
1. RNA can act as a catalyst (ribozymes)
2. RNA can make additional RNA molecules. 3. Self-replicating RNA could be the first step toward a living cell. 4. No one has made self-replicating RNA, but they have made RNAs replicate each other. |
|
|
What is the RNA relic?
|
A ribosome. Cells depend on RNA enzymes. The information molecule used to be RNA, then got switched to DNA, but the ribosome is an example.
|
|
|
What is the high magnification of a light microscope?
|
100 microns = 10^-6 m
|
|
|
How many lenses does a light microscope have?
|
1. the objective lens
2. the condensor lens |
|
|
What does the objective lens do?
|
It collects a cone of light to create an image.
|
|
|
What does a condensor lens do?
|
It focuses the cone of light onto each point of the specimen.
|
|
|
What is the resolution equation?
|
r = 0.61lamda/(Nao + Nac)
|
|
|
What is NA?
|
= index of media sin 1/2 the angle of light
|
|
|
The wider the ray of light the...
|
greater the resolution.
|
|
|
Why do you use immersion oil?
|
It increases the NA.
|
|
|
2 ways you can better the resolution:
|
1. Increase NA
2. Decrease the wavelength |
|
|
Even with resolution, what else do you have to do to see a cell?
|
Contrast.
|
|
|
2 ways to use contrast:
|
1. incident (white) light -- uses staining
2. incident (green) light -- uses phase shift |
|
|
4 kinds of light misroscopy.
|
1. bright field
2. phase 3. DIC 4. Dark field |
|
|
What is fluorescence?
|
When a molecule absorbs light in one wavelength and reemits it in a different, longer wavelength.
|
|
|
What is Stokes Shift?
|
The difference between the excitation and emission wavelength.
|
|
|
Describe a fluorescence microscope.
|
1. first barrier filter: lets only blue light through.
2. beam-splitting mirror: reflects light only below 510nm 3. second barrier filter: cuts out unwanted fluorescent signals. |
|
|
4 steps for directing proteins for immunofluorescence.
|
1. immobilized antigen A
2. primary antibody: to attack antigen A 3. secondary antibodies: have a fluorescent marker on them and attack the primary antibodies. 4. it fluoresces. |
|
|
Advantages and disadvantages of immunofluorescence.
|
Adv: easy, can be applied to separate cell lines or tissues, sensitivity.
dis: cells have to be dead. |
|
|
5 things about antibodies:
|
1. made by b cells
2. highly specific binding 3. can be modified by fluorescent molecules 4. heavy chain on inside 5. light chain on outside |
|
|
What is GFP?
|
Green fluorescent protein: a protein isolated from jelly fish that can be expressed in any organism.
|
|
|
How do you use GFP?
|
You genetically modify the organism so that the gene for GFP comes before the gene for the protein you want to study. multiple colors can be used in one cell.
|
|
|
How does GFP confocal microscope work?
|
1. Shine a laser on the specimen.
2. The emitted fluorescent light from the in-focus point is focused at a pinhole. 3. Out of focus light at the pinhole is mostly excluded. |
|
|
How does electron microscopes work?
|
An electron beam acts as a light beam and its wavelength is 2.5E-12m so it's much shorter than visible light. Atoms are at 10E-10 so EM can see atoms.
|
|
|
Name and define two strong bonds.
|
1. covalent bonds: the sharing of electrons
2. ionic bonds: the transfer of electrons |
|
|
When are ionic bonds weak?
|
In water.
|
|
|
Define H bonds:
|
Very weak bonds in which partially positive H on the donor molecule binds to partially negative atom on the acceptor molecule.
|
|
|
Define Van de Waals bonds.
|
Molecules polarize and attract when they approach a certain distance known as the Van der Waals radius.
|
|
|
Define hydrophobic interactions.
|
Hydrophobic molecules stick together because of Van de Waals and are forced out of water because of water's H bonds.
|
|
|
What is the equilibrium constant?
|
Keq[L][R] = [RL]
|
|
|
What is Kd?
|
The disassociation constant that gives 50% occupied receptor.
Kd = [L][R]/[RL] |
|
|
The lower the Kd, the _____ the binding.
|
stronger
|
|
|
What is the relationship of Kd, Ka and Keq?
|
1/Kd = Ka
Ka = Keq |
|
|
What is Gibbs free energy?
|
The free energy of the reaction.
|
|
|
What's Gibbs' relationship to Keq?
|
G = -RTlnKeq
|
|
|
The bigger the Keq...
|
the more negative the G and the more favorable the rxn.
|
|
|
Name the types of weak bonds.
|
1. Ionic bonds in water
2. H bonds 3. Van der Waals 4. Hydrophobic interactions |
|
|
Name 3 hydrophobic aa's:
|
L, I, V
(leucine, isoleucine, valine) |
|
|
What is the isoelectric point of a protein?
|
The point at which the protein has no net charge.
|
|
|
Why is cysteine so special?
|
They have an SH group that can create disulfide bonds to stabilize proteins. It's the strongest kind of bond used to stabilize.
|
|
|
What is peptide bond formation?
|
two amino acids come together and kick out water to produce a C-N bond with an O on the C and an H on the N.
|
|
|
Name the 4 steps of protein folding:
|
1. primary
2. secondary 3. tertiary 4 quaternary |
|
|
3 things involved in primary protein structure.
|
1. the covalently bonded structure
2. sequence of amino acids 3. disulfide bonds |
|
|
What is the beginning and ending of the protein sequence?
|
N terminal = beginning
C terminal = ending |
|
|
In a peptide bond, which is a H bond acceptor and donor?
|
carbonyl = acceptor
N-H = donor |
|
|
What structures are involved in the secondary protein structure?
|
1. H bonds
2. alpha helix 3. beta sheets |
|
|
Tertiary structure is due to...
|
interactions between R groups.
|
|
|
What is the structure of transmembrane proteins?
|
alpha helices
|
|
|
Define domains.
|
Stable units of protein structures that fold autonomously and function independently.
|
|
|
What is exon shuffling?
|
When exons move around the genome.
|
|
|
How do you prove that proteins must fold to be functional?
|
If you put them in a high concentration of urea, they're denatured and the function stops. Remove the urea and the protein reforms.
|
|
|
4 things that denature proteins.
|
1. heat
2. agitation 3. agents that compete for H bonds 4. detergents |
|
|
2 enzymes that help proteins fold correctly.
|
1. molecular chaperones
2. chaperonins |
|
|
What are molecular chaperones?
|
Enzymes that bind and stabilize proteins as they come out of the ribosome during synthesis.
|
|
|
What are chaperonins?
|
Enzymes that massage misfolded proteins. They look like big barrels.
|
|
|
What does HSP-70 do?
|
They bind to hydrophobic parts of proteins as they are being made and prevent folding until the protein is finished.
|
|
|
Why are unfolded proteins a problem for the cell?
|
The hydrophobic groups on the outside will stick to other denatured protein. ex: prion disease, Alzheimer's, Parkinson's
|
|
|
How does mad cow disease work?
|
Denatured prion proteins stick together and are insoluble in the brain. Deformed prions induce incorrect folding in sister proteins which creates a domino effect. They're incredibly resistant.
|
|
|
What happens to unfolded cytosolic proteins?
|
They're targeted for destruction through ubiquitination. They get tagged with ubiquitin by ubiquitinating enzymes which take them to proteasomes which break them up.
|
|
|
Describe the steps of ubiquitylation.
|
1. Uses ATP to create a thioester
2. ubiquitin ligase binds 3. ubiquitin activating enzyme leaves 4. ubiquitin ligase primed with ubiquitin 5. ubiquitin ligase binds to protein 6. first ubiquitin added to protein 7. repeat process to add multiple ubiquitin |
|
|
The proteasome cap contains...
|
unfoldase which denatures proteins with ATP.
|
|
|
How is ubiquitylation regulated?
|
It is turned on by a kinase which attaches a phosphate group.
|
|
|
How is the degradation signal of a protein activated?
|
phosphorylation of a kinase which unmasks the protein.
|
|
|
What does single ubiquitylation mean?
|
It's used as post-translational modification to change their properties. ex: histones.
|
|
|
What is the function of multiubiquitylation?
|
Endocytosis.
|
|
|
What are the functions of polyubiquitylation?
|
1. proteasomal degradation
2. DNA repair |
|
|
How does SDS-PAGE work?
|
If you add SDS, the molecules wrap around the protein backbone and denature it. SDS molecule has a negative charge and the number of SDS will attach according to the protein size. Proteins then move through the gel according to mass.
|
|
|
How does 2D gel electrophoresis work?
|
Proteins move through the gel based on their charge to found their isoelectric point.
|
|
|
Describe western blots:
|
1. SDS-PAGE
2. Protein blot on nitrocellulose 3. Label with a specific antibody 4. Detect the antibody |
|
|
What is an enzyme?
|
A molecule that lowers the activation energy of a reaction, but doesn't affect the equilibrium.
|
|
|
Enzymes bind best to...
|
the transition state. They help the transition state to form and do not care what happens to the transition state.
|
|
|
What is the 4 point of proof that enzymes bind to the transition state?
|
1. Stable transition state analogs inhibit enzymes.
2. Antibodies that are generated against the transition state are catalytic and act like enzymes. |
|
|
Enzymes provide a special environment that...
|
cannot exist in free solution.
|
|
|
How are enzymes regulated?
|
1. by an activator
2. via phosphorylation |
|
|
Why can enzymes have a lot of other inactive sections?
|
To regulate the enzyme.
|
|
|
Name 3 neutral lipids:
|
1. triglycerides
2. prenyl lipids 3. steroids |
|
|
Name 5 phosphatides:
|
1. head groups
2. amphipathic 3. fluidity 4. phospholipases 5. inflammation |
|
|
7 sphingolipids
|
1. sphingosine
2. ceramides 3. glycolipids 4. sugar interactions 5. rafts 6. the glycosynapse 7. ABO blood groups |
|
|
Name 12:0
|
lauric acid
|
|
|
Name 14:0
|
myristic acid
|
|
|
Name 16:0
|
Palmitic acid
|
|
|
Name 18:0
|
Stearic acid
|
|
|
Name 20:0
|
Arachidic acid
|
|
|
Name 16:1
|
Palmitoleic acid
|
|
|
Name 18:1
|
Oleic acid
|
|
|
Name 18:2
|
Linoleic acid
|
|
|
Name 18:3
|
Linolenic acid
|
|
|
Name 20:4
|
Arachidonic acid
|
|
|
Which unsaturated fatty acids does our body not make?
|
omega-3 linolenic acid
omega-6 linoleic acid |
|
|
What do cis double bonds do to fatty acid packing?
|
The kinks keep the chains from coming together and prevent van der Waals bonds.
|
|
|
Where to trans fats come from?
|
Trans fats come from partially hydrogenating unsaturated oils. Occasionally, things get messed up and you get a trans fat.
|
|
|
What are triacylglycerols and glycerophospholipids made up of?
|
Fatty acid esterified to glycerol
|
|
|
What are triacylglycerides used for?
|
Food and energy storage ex adipose (fat) cells
|
|
|
What is the derivitive of steroids?
|
cholesterol
|
|
|
Many steroids are...
|
hormones that trigger transcription of certain genes.
|
|
|
What does cholesterol do to cell membranes?
|
It keeps the lipid tails straight and prevents holes. It also prevents the tails from binding to each other.
|
|
|
What is bad cholesterol?
|
It's cholesterol carried in the blood by ApoB (LDL) where there is less lipoprotein to cholesterol. This complex can clog up your arteries.
|
|
|
What is good cholesterol?
|
It's ApoA-1 or the HDL which has a high density of protein.
|
|
|
4 kinds of phosphatide
|
1. phosphatidylcholine
2. phosphatidylethanolamine 3. phosphatidylserine 4. phosphatidylinositol |
|
|
4 kinds of sphingolipids
|
1. sphingomyelin
2. ceramides 3. cerebrosides 4. gangliosides |
|
|
What are the 3 components of a phosphatide?
|
1. fatty acids
2. glycerol 3. phosphate ester |
|
|
What are 3 things that phospholipids turn into in water?
|
1. micelle
2. liposome 3. bilayer sheet |
|
|
What can liposomes be used to treat?
|
It can be used to treat cystic fibrosis which is due to a mutation in a chloride transporter. A liposome could be filled with the gene for the good transporter, but usually they just put the transporter into the liposome for temporary relief.
|
|
|
What's the consistency of saturated lipid bilayer?
|
gel-like
|
|
|
What's the consistency of an unsaturated lipid bilayer?
|
fluid-like
|
|
|
As the temperature goes up, your bilayer is likely to contain more...
|
saturated fatty acids
|
|
|
What is homeoviscous adaption?
|
It's the remodeling of the membrane in response to changing temperatures. Colder temperatures lead to lipids with shorter fatty acid chains and more double bonds.
|
|
|
What are the components of sphingomylein?
|
1. sphingosine
2. phosphocholine 3. oleic acid |
|
|
Sphingolipids segregate out into..
|
patches in the membrane (rafts).
|
|
|
What kind of protein join to membrane rafts?
|
Lipidated proteins and GPI-linked proteins.
|
|
|
2 functions of glycosphingolipids.
|
1. bring together proteins
2. can serve as a signaling complex. |
|
|
Where do phospholipases cut?
|
A1, A2, C, D
|
|
|
Arachidonic acid is a precursor for...
|
lipid hormones prostaglandin, thromboxane, and HETE
|
|
|
What is phospholipase D do?
|
A signal for growth and change in the cytoskeleton.
|
|
|
What does cortisone do?
|
It inhibites phospholipase A2.
|
|
|
What do NSAIDs do?
|
They inhibit Cox, the first step to make prostaglandins and thromboxanes.
|
|
|
What do platelets do?
|
They bind to collagen when the tissues are damaged and it leaks out. It sends out a signal to repair. Ca2+ increases, thromboxane is made and platelets plug the wound.
|
|
|
What is the glycocalyx?
|
It's all the sugars on the surface of the cell.
|
|
|
4 kind of proteins in the membrane.
|
1. integral
2. peripheral 3. membrane anchored 4. GPI-linked proteins |
|
|
Where are sugars found when attached to the membrane?
|
Outside the cell.
|
|
|
What kind of bonds do the sugars have outside the cell?
|
disulfide bonds
|
