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COLORADO / OTHER / MCDB 3145 / What motor proteins are associated with microtubules?

What motor proteins are associated with microtubules?

What motor proteins are associated with microtubules?

Description

School: University of Colorado at Boulder
Department: OTHER
Course: Molecular Cell Biology 2
Professor: Gia voeltz
Term: Spring 2017
Tags: Cellular and Biology
Cost: 50
Name: MCDB 3145: Midterm 1 Study Guide
Description: This study guide is all the information covered from the first two powerpoints she presented on. Only the 2 powerpoints will be on the exam.
Uploaded: 02/04/2017
9 Pages 28 Views 1 Unlocks
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MCDB 3145 – Exam 1 Study Guide


What motor proteins are associated with microtubules?



Section 1 Notes

Prok

aryot

es

-Bacteria & Archaea

-Extremophiles: live in extreme in hostile environments

-1 um  

-Floating DNA, no organelles

-Structures:  

- Nucleoid: is an irregularly shaped region within the cell of a  prokaryote that contains all or most of the genetic material.  - Capsule: polysaccharide layer that surrounds the cell wall  - Pilus: organelles of adhesion allowing bacteria to colonize  environmental surfaces or cells and resist flushing. (she didn’t  cover this)

Both

-Plasma membrane similarly constructed  

-Genetic information encoded in DNA

-Similar mechanisms for transcription/translation/ribosomes -Shared metabolic pathways

-Similar way to use ATP for chemical energy

-Similar mechanism of photosynthesis

-similar mechanism for inserting/synthesizing membrane proteins -proteasomes  

-Structures

- Plasma membrane: outermost cell surface which separates the cell  from the environment  

- Cytoplasm: semi-liquid substance that composes the volume of the  cell  

- Ribosome: makes proteins  

- Flagellum: a slender threadlike structure, especially a microscopic  whip like appendage that enables many protozoa, bacteria, sperm,  etc., to swim.

- DNA

- Cell Wall: contains chitin, provides support, helps cell resist  mechanical strain, not solid

Euka

ryote

s

-fungi, plants, animals, amoeba, yeast, trees, starfish

-50 um

-Nuclear envelope separates nucleus from cytoplasm

-Chromosomes: the DNA is able to compact with histones

-Complex organelles in cytoplasm (ER, Golgi, lysosomes, endosomes,  peroxisomes)

-Aerobic respiration organelles: mitochondria, chloroplasts  -Complex cytoskeletal system: microfilaments (actin & myosin-changes in cell shape), intermediate filaments (prevents cell from being torn apart),


What forms microtubules during cell division that are used for separating chromosomes?



We also discuss several other topics like What are some examples of culture bound syndromes?

microtubules (highway) and associated motor proteins

-Complex flagellum and cilia  

-Phagocytosis, Cell division using microtubule-containing mitotic spindle  that separates chromosomes  

-2 copies of genes per cell (diploid)  one from each parent -RNA polymerases

-Sexual reproduction requiring meiosis and fertilization  

- Structures:

- Lysosome: demolition of materials

- Plasma Membrane: phospholipid bilayer surrounding rest of cell - Golgi Complex: packages products and sends them (like FedEx) - Smooth ER: no ribosomes present. Regulates and releases Ca ions - Rough ER: Has ribosomes attached. Makes products (proteins) - Mitochondria: power house/energy

- Nucleus: DNA—control center of the cell  

- Cytosol: semi-liquid material between organelles  

-Examples in Human Body of cells

- Red blood cells, smooth muscle cells, fat (adipose) cells, intestinal  epithelial cells, striated muscle cells, bone tissue with osteocytes,  bundle of nerve cells, loose connective tissue with fibroblasts


How does the plasma membrane stay attached to the rest of the cell?



Don't forget about the age old question of What is the atomic number for the atom?

Four Major Types of Biological Molecules  

Protein

-Protein complexes

Carbohydrat e

Lipid

-Membranes

-Long term energy storage in animals  

-Triacylglycerol (triglyceride)  

-Phospholipid

Nucleic Acids (DNA and  

RNA)

Don't forget about the age old question of What is the definition of a dependent variable in science?

Protein Folding

- The path that a protein takes to fold is hard to predict  

- A protein has only 1 structure…it will fold back how it’s supposed to fold o Rare folding of proteins=disease (sickle cell anemia—Change GluVal)

- Protein unfolds when chemicals (ex: urea + mercaptoethanol) are present.  They will refold normally when washed and the chemicals are gone.  o Denatured RNase spontaneously folds into its native conformation  o Chemicals break disulfide bonds to disrupt native conformation o When denatured RNase is returned to native conformation it will  spontaneously refold to its native conformation.  Don't forget about the age old question of What is the main difference between mass and weight?

- How do they fold?  

o Noncovalent bonds

 Vander Waals Forces

 Hydrogen bonds  

 Ionic Bonds

- What can change protein conformation?  

o Phosphorylation, mutations, dimerization, binding to nucleotide  - Shuffling Domains

o Can piece together the function of a protein based on domains that  make it up similar/same to other domains  

Primary Structure

-Unfolded, Amino Acid Sequence

Secondary Structure

-Alpha helixes

- Maximum # of H-bonds

-Beta Base

- H-bonds perpendicular to  

backbone

Tertiary Structure

-3D

-Multiple beta sheets to form a beta  barrel

Quaternary Structure

-Protein & DNA, protein & RNA

-Helps things bind to others

-Ex: hemoglobin  

-Ex: Myoglobin—first solved—only alpha helix

-Cytochrome C

Don't forget about the age old question of What is the difference between a reinforcer and a punisher?

Amino Acids (Included are some ways I remember them)

Polar Charged (5)

Hydrophilic side  

chains  

Form Ionic bonds

-Arginine (+): arrrrrggg like a pirate  

-Lysine (+): Lydia is positive  

-Histidine (+): He/his should be positive  

-Aspartic Acid (-): acids are negative

-Glutamic Acid (-): acids are negative

Polar Uncharged  (5)

Hydrophilic side  

chains: have a  

partial charge…lets

(Three Silver Tyes)- These can be phosphorylated – have  OH groups  

-Threonine

-Serine

-Tyrosine  

These are opposite/similar to the polar charged acids:

them form H-bonds  as associate with  water

-Asparagine

-Glutamine

Ionic (nonpolar)  (7)

Nonpolar=not  

moving/just chilling

Hydrophobic side  chains,  

Tend to form inner  core of soluble  

proteins

-Valine: like Vaseline, it stays where you put it

-Phenylalanine: pH 7 is neural  

-Methionine: meth heads aren’t going anywhere in life so  they don’t move

-Leucine: twins are nonpolar/equal (no pull of a charge) -Isoleucine: twins are nonpolar/equal (no pull of a charge) -Alanine: Alyson likes to chill

-Tryptophan: you don’t move after eating Thanksgiving  turkey because of the tryptophan in it.

Special (3)

-Proline: this amino acid is pro, it can form kinks and ring  structures—hydrophobic  

-Glycine: glorious, little/hidden like secrets, can fit into  either hydrophobic or hydrophilic environments  -Cysteine: ssss like a snake—forms diSulfide bonds—polar  uncharged character

We also discuss several other topics like What are the measures of spread or dispersion?

Chaperones

- Assist protein folding in a cell  

- Hsp 70 --Heat shock proteins  

o Binds exposed hydrophobic patches on nascent polypeptide

Chaperonins

- Hsp 60-- Heat shock proteins

o Provides Aquarium/forms channel/chamber. This provides a protected  environment for the protein to fold

o GroEL/GroES

- These are upregulated during the presence of heat

- This helps proteins not be denatured

- 2 heptameric rings form the chamber  

- System:

o 1. Unfolded protein goes into chamber  hydrophobic patches o 2. ATP binds GroEL

o 3. GroES lid binds the top to close chamber (only 1 lid at a time) o 4. Chamber expands—conformation change

o 5. Hydrophobic side chains retract in the chaperonin, allowing protein  to fold

o Takes only 15 seconds—ATP burns up in 15 seconds  

Proteasome  

- Degrades misfolded proteins and just proteins

- Similar to GroES/GroEL

- Composed of 2 caps, 2 a-subunits, 2 b-subunits

- System:

o 1. Misfolded protein is poly-ubiquitinated (need 4 or more)

 Lysine side chain accepts ubiquitin, 1 at a time

o 2. Poly-ubiquitin binds to the cap outside of proteasome

o 3. Cleavage factors cuts off Poly-ubiquitination  

o 4. ATPase (a-ring)—uses energy to unfold protein and protein goes  single file into chamber

 Degrades proteins on the inside (in the b-rings)

o 5. Amino Acids are spit out to be reused

- Ubiquitin: a little protein

o Need 4 or more to got to proteasome

o These bind initially to lysine residue  

- Poly-ubiquitin: 4 or more ubiquitin targets protein to proteasome  

Protein mis-folding diseases (BAD)

- Neurodegenerative Diseases  

o Alzheimer’s  

 Neurofibrillary tangles: these accumulate –caused by changes in microtubules –really dense protein that makes a mess  

 Amyloid plaques: between cells and prevent communication  from one cell to another –lot of crap builds up

Amyloid Hypothesis

- Amyloid Precursor Protein (APP) is cleaved incorrectly –gets exported to  cytoplasm  

- APP is synthesized in the ER

- B-secretase specifically cleaves APP  

- AB40 peptide=normal: function is unknown

- AB42 peptide=mutated: goes to create/form plaques and cause disease – cleaved wrong  

- Incorrect cleavage of APP is because there is too much APP present and B secretase is overwhelmed. Also could be from a mutation in the B Secretase and cuts the APP wrong

- The cleaved peptide adopts a beta sheet structure—these then interact  between beta sheets to become more stable

Progressive Neurodegenerative Disease  

- Mad Cow disease: you get some of that misfolded protein—normal folding  adopts bad folding structure and then becomes normal  contagious

Prion Disease:

- Took infectious materials—treated it with protease and it killed the disease —led to the fact that it’s a protein that causes disease  

- Prion Hypothesis: Wild Type Globular a-helix structure 95% of the time, 5%  beta sheet structure. Mutated square (protein) only causes disease when it  is added to the secondary structure in the B-sheet conformation.  Normal/healthy protein if it is added to the a-helix conformation - Amyloids=long polymer fibers (B-sheet structures)

Kuru:

- Fatal neurodegenerative disease  

- Progressive dementia and ataxia  

- Disease incidence: 1% of population—tends to run in families –genetic –but  also contagious from eating brains of infected people

Creutzfeldt-Jakob Disease (CJD)

- Ground up infected brain, put in into healthy individuals, they then got the  disease

PrP: A Host encoded proteins

- 1985: isolation of PrP cDNA

- 1986: cloning of PRNP gene  

- If the PRNP gene causes scrapie, it should only be isolated from individuals  with disease, but PRNP was present in both healthy and diseased  individuals  

- Test for scrapie: knockout WT PRP gene, inject little bit of mutant PRP no  disease  

- You need PRP, but WT PRP has no known function

Other/Definitions:

- Ribonuclease=RNase: an enzyme that promotes the breakdown of RNA into  oligonucleotides and similar molecules  

- Halophiles: an organism, especially a microorganism, that grows in or can  tolerate saline conditions.

- Amphipathic: hydrophobic and hydrophilic

o Ex: Phospholipids, integral membrane proteins, liposomes, membrane  bilayers  

Section 2 Notes: Ch. 4—The Plasma  Membrane

The  

Plasma  

Membran e

Advantages:  

- Barrier

- Regulation of concentrations between environment and inside  of cell

- Form tissues

- Smaller than entire volume of cytoplasm—this provides a  greater chance of finding binding partners (enzymes  

concentrated on surface)

- Stores metabolites (lipids)

Composition

- Very fluid! Fluid mosaic model, membrane items float about - Different phospholipids on inside vs. outside of membrane  - Distance: about 20 hydrophobic Amino Acids  

- Phospholipids—amphipathic: hydrophilic polar head group,  hydrophobic tails (2)—these pack very tightly  

- Phosphoglycerides: PI & PS (-) charge on head groups, PE &  PC: neutral  

- These 4 phospholipids make up the plasma  membrane  

- PS, PE & PI on cytoplasm side—PC on outside of cell  Integrate Membrane Proteins

- N-term faces cytosol

- 1st transmembrane domain determines topology of entire

protein  

- Cannot be washed with salt

- Passes all the way through Plasma Membrane

Peripheral Membrane Protein  

- Can be washed off with salt  

- Binds cytoplasmic side  

- Noncovalent bonded to head groups or to an integral protein  Diffusion & Localization  

- Green Florescent Protein (GFP)—helps to look at the  localization and diffusion or proteins in the membrane

Liposome

- Used to study how protein channels work—study trafficking,  transport, topology  

- Spontaneous, most favorable, membrane bilayer

FRAP

- Florescent recovery after photo bleaching

- Bleach just one area

- If color is replaced, then IT is mobile

- If it stays black, then not mobile  

- The recovery of color is related to the rate of diffusion

FLIP

- Florescent Loss in Photo bleaching

- After hitting the box in one spot over and over for 1 minute,  the whole cell will go dark

- Continuous photo bleaching to test continuous-ness  - Test: to determine if a membrane or something in the  membrane is continuous  assumes its mobile  

- If it is continuous  everything will eventually go black - If NOT continuous  only a section of the whole will go black

Semi

Permeabl e  

Membran e

- Can diffuse freely: Gases (O2, CO2) Hydrophobic molecules  (estrogen), small polar molecules (H2O, ethanol) PASSIVE - Needs something to help them transport: Large polar  molecules (glucose), charged molecules (Ca2+, H+, Cl-)  ACTIVE  

- Osmosis: H2O molecules will move from hypotonic (low salt) to hypertonic (high salt)

Gated  

Channels : Na+/K+  pump

- 3 Na+ pumped out, 2 K+ pumped in –through the same  channel—1 ATP per time

- ATP binds and allows 3 Na+ ions to go through, pump then  loses the phosphate group due to 2 K+ binding, allows a  change in conformation and 2 K+ ions to come IN  

- ATP phosphorylates channel

- Cells use a HUGE amount of ATP to do this

Voltage  

Gated

K+ Channel (Bacteria)

- Voltage gated –Tetramer (4 subunits) alpha helix -- activated  by change in membrane potential  

- Let’s K+ go down concentration gradient (Low outside & high  inside)

- Allows only it’s specific ion to pass through –PERFECT SIZE  - 4 double bonded Oxygens line up 4 Angstroms apart—Ion fits  inside  

- Channel has a kink in the middle with a proline Amino Acid— K+ will flow out fast –M2 domain  

- Inactivation Peptide: plugs up hole after open

K+ Channel (Drosophila Channel)

- Voltage gated--6 alpha-helixes— activated by change in  membrane potential  

- S6 is like the M2 domain—it feels a change in potential of ions  across the membrane –then changes conformation and twists  to open up allowing ions through  

- Let’s K+ go down concentration gradient (Low outside & high  inside)

Na + Channel

- Voltage Gated: activated by change in membrane potential  - VERY SIMLIAR TO K+ CHANNEL  

- Na+ high outside the cell, low inside the cell

Neurons  & Action  Potential s

- Dendrites: receive incoming information from external sources - Axons: conducts outgoing impulses away from the cell body  - Myelin sheath: insulators, layers around axons  

- Purpose: muscle contraction

- More (-) charge on inside of cell  

- Region of action potential: has experienced a change in  membrane potential

- Moves in the direction of terminal knobs—only between myelin sheaths

- Depolarization: Na+ comes into cell  

- Repolarization: K+ goes out of cell  

Terminal Knob Process

- Membrane potential reaches terminal knobs

- Voltage gated Calcium ions flow through channel, into the cell, causing synaptic vesicles fuse with PM to release  

neurotransmitters.  

- Neurotransmitters (ligands) float into synaptic cleft (the space) to reach the receptors which then allows different ions to  come into the cell (ex: Na+)

- This causes a depolarization of muscle  

- Neurotransmitters act as ligands and are degraded after used  - Ex: Ligand Gated Sodium Channel

Glucose  

Transport (Large

Facilitated diffusion

- down glucose gradient  

- Glucose high concentration in cells –import against gradient

Polar  

Molecule s)

Active Glucose Transport

- Na+/glucose—2 Na+ ions and 1 glucose molecule bind and go  through.  

- HIGH Na+/low glucose OUTSIDE CELL. Low Na+/High glucose  INSIDE CELL

- Transporter mediated –can work in both directions

- Na+/glucose transporter uses the energy in Na+ to pull  glucose across the PM against its concentration gradient

What to study:

- Everything she taught and talked about in class

- Features and categories of Amino Acids

- Different levels of protein folding

- Domains of proteins

- Protein folding diseases  

- Bonds that form between proteins

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