Study Guide: Cell Physiology Exam 1

What are the examples of Polymers?

Dr. Wilk’s class

Examples of Polymers:

∙ Enzymes

∙ Molecular motors

∙ Membrane Transporters

∙ Cytoskeleton

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Polymers: Augment function of molecules

5 Molecules:  

∙ Water

∙ Proteins  

∙ Nucleic Acids

∙ Carbohydrates  ∙ Lipids

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∙ Translation: Genes to Protein

∙ Only needed genes are transcribed

∙ mRNA->amino acid

∙ Happens in cytosol

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∙ What are Codons?

∙ mRNA triplets made by DNA transcription in nucleus

∙ Leaves nucleus to cytoplasm and binds to ribosome

∙ Anticodons?

∙ tRNA triplet in cytoplasm

∙ Translation amino acid

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∙ What will happen in the cell in lysine deficiency?

∙ If lysine cannot be added to the chain, then translation could not add a  lysine or any amino acid that comes after it

What do post translational modifiers do?

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∙ How do proteins get in the body?

∙ DNA

∙ Infected  

∙ Injected  

∙ Eaten

∙ Defective DNA Defective Protein

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∙ How are polymers formed? Dehydration reaction

∙ How are polymers broken down? Hydrolysis

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∙ What are the Bond types?

1. Peptide bond: Protein

2. Glycosidic bond: Carbs

3. Phosphodiester: Nucleic Acids

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∙ What are genes?  

∙ Ordered sequence of nucleotide

∙ Make ONE protein

∙ Segment of DNA (made from structural blocks called nucleotides) ∙ Instruction manuals

∙ Unit of heredity example eye color

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∙ Thought blob:

∙ Actinmade from a combination of the 20 amino acidsamino acids  made from codons and anticodons codons come from  

DNA/RNAsequence of nucleotides-->nucleotides are made from  nucleic acid molecules  

What are examples of cell membrane proteins?

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∙ What are functional domains? We also discuss several other topics like meat lab auburn

∙ Noncovalent bonds between regions in the linear sequence. ∙ Each domain forms a 3D structure

∙ Can be 25-500 amino acids  

∙ Often form functional units

∙ Think Zinc Fingers

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∙ Why are amino acid chains linear/unbranched?

∙ Linkage formed from dehydration synthesus

∙ +H3N amino group of one amino acid to COOH- carboxyl ∙

∙ What are the special amino acids?

1. Proline

2. Glycine

3. Cysteine

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∙ *They’re special because they contribute to the 3D structure and  bending sites

∙ Cystein forms S-S disulfide bonds

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∙ Amino acids shapes/properties = shape = function

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∙ How many levels of structure determine protein shape? 4 ∙

∙ Primary structure? Linear sequence of amino acids. Secondary is  interaction with neighbors

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∙ Secondary Structure? Peptide chain folding into a helix or b sheet ∙

∙ Difference between a helix and B sheet?

∙ a helix: spiral of strong H bonds, a carbons that form helix shape ∙ b sheet: planar made of 2 or more b strands—bound by h bonds ∙

∙ Tertiary Structure? Functional domains and motifs such as coiled coil,  helix loop helix, and zinc finger. Attributed to hydrophobic interactions  between aa and disulfide bonds

∙ Coiled coil: 2 or more helices together. Dimerization (2 subunits  making a dimer)

∙ Helix loop helix: Occurs in calcium binding. Loop around Ca2+  ion

∙ Zinc-finger: present transcription factor proteins. Zn2+ ion  between b strands and a helix

∙ Domains localize activity.  

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∙ Quaternary Structure?

∙ 2 or more polypeptides making a multimeric protein  (macromolecular)  We also discuss several other topics like suuds

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∙ Sickle-cell: substitution from Glu to Val  

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∙ Why is protein destination important?

∙ To perform proper function

∙ MUST KNOW: Receptors go to plasma membrane

∙ DNA Polymerase goes to nucleus

∙ Catalase goes to peroxisome

∙ Insulin is secreted outside cell

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∙ Cellular Destination  

∙ Cytosol We also discuss several other topics like chm 103

∙ Nucleus  

∙ Membranes

∙ Mitochondria, chloroplasts

∙ Peroxisomes

∙ Lysosomes

∙ Outside

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∙ ****Come up with a list of 3 proteins for each destination, and how  they get there. Watch videos

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∙ How do proteins know what’s their destination?

∙ They have an intrinsic coding sequence. The delivery address  (targeting signal sequence) is part of the polypeptide (chain of amino  acid). They start heading to their destination once the sequence is  translated and out the subunit tunnel

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∙ EXCEPTION: All proteins are translated in cytosol. Those who plan to  stay don’t need a targeting signal sequence!!!

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∙ Where is the targeting signal located?

∙ Part of polypeptide: N-terminus, C-terminus, or the middle of the  protein. Often later cleaved by signal peptidase.  

∙ Where does targeting signal bind? Receptor

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∙ Who is Gunter Blobel? 1999 he discovered that proteins have intrinsic  signal that govern localization

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∙ What is needed to sort proteins to destination?

1. Targeting signal sequence

2. Specific receptor on destination organelle to bind

3. Translocation channel

4. Energy

5. Chaperones (sometimes)

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∙ ALL Proteins are synthesized o Free Cystolic Proteins. Some  have an extra stop to the ER

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∙ Which are translocated POST Translation?

∙ Proteins going to nucleus, mitochondria, and peroxisomes ∙

∙ Which are CO-Translational?

∙ Proteins that are secreted, integral membrane proteins, lysosomes ∙

∙ What happens if no targeting signal sequence (coding sequence about  where the final destination)? Released into cytosol after finishing ∙ If you want to learn more check out rachel spigler

∙ Are proteins that are going to be inside organelles post-translational or  co-translational?

∙ Co-translational—they are translocated inside of ER unless they are  going to the nucleus, mitochondria, or peroxisome

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∙ Where does decoding and synthesis take place? Cavity between  ribosomal subunit

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∙ What’s SRP? (Signal Receptor Particle) It’s a small cystolic protein that  drags the start sequence to the receptor. It also swings a little which  opens the translocation channel

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∙ What is the first amino acid EVERY protein makes in cell? Start codon  AUG Met (amino acid)

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∙ What destroys the targeting sequence? Peptidase

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∙ Once a stop codon is reached it markes the end. Ribosome open, and  protein starts to fold in ER (if secretory pathway protein) ∙

∙ What are the two fates of secretory pathway proteins? 1. They are  secreted outside (no coming back) 2. They cling to ER and stay due to  post translational enzymes. For example, Golgi proteins. ∙

∙ What do post translational modifiers do? They enable proteins to stick  to certain organelles post translation in ER.

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∙ Integral Membrane Proteins? If a protein is to become a part of a cell  membrane, it enters the ER. The inside portion of the protein in the ER  becomes the outside portion of the cell membrane. The position is kept during transport

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∙ What are examples of cell membrane proteins? Receptor proteins such  as Insulin receptor We also discuss several other topics like define multifinality

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∙ For secretory pathway protein production, what targets the ribosomal subunit to the ER? SRP We also discuss several other topics like ginzberg's career choice theory

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∙ What are the basic steps of synthesis of secretory proteins? 1. Translation on cystolic ribosome

2. Signal sequence emerges from ribosomal tunnel

3. SRP binds to signal sequence and causes translational arrest 4. SRP drags complex to ER membrane

5. SRP binds to receptor “swings a little”

6. Opens translocon channel and ribosomes docks to translocon 7. SRP dissociates

8. Translation of peptide while it translocates into ER hence “co translational”

9. Once in ER, signal sequence cleaved by signal peptidase ∙

∙ What assists in folding? Chaperons

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∙ What are topogenic sequences?

∙ They direct insertion of proteins into membranes

∙ Examples include:

∙ 1. N-terminal signal sequence

∙ 2. Stop-transfer: stops translocation

∙ 3. Signal anchor: begins translocation towards ER

∙ 4. Internal sequences: N-terminal signal sequence is usually cleaved  while internal sequences are not. Internal transfer sequences become  transmembrane domains

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∙ What topogenic sequences does an insulin receptor have? N-terminal  Signal sequence to guide it to ER. Stop-transfer sequence to stop  translocation and insert into the membrane

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∙ How is asiasoglycoprotein receptor different? C-terminus outside cell  membrane. Needs internal signal anchor start transfer sequence to do  so.

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∙ Fun Fact: Type IV receptor or multiple transmembrane domains require  multiple signal sequence. Each internal sigal-anchor sequence or stop  becomes transmembrane domain.  

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∙ **Example: Ion channels, receptors, transporters

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∙ How to know if N-terminus is OUTSIDE membrane or INSIDE membrane of final destination

∙ For N-terminus to be outside. Signal sequence must be localized at N terminus and cleaved later

∙ For N-terminus to be in cytosol, signal sequence must be internal ∙

∙ “MCAT question answer”: Insulin is a N-terminal ER targeting sequence ∙

∙ What are post translational modifications?

1. Folding: Disulfide bond formation

2. Glycosylation: Adds carbs

3. Proteolytic Cleave: Activates protein by cleaving off fragments ∙ Freshly Ground Powder (for) Coffee (Pneumonic)

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∙ What is often the first post translational modification? ∙ Removal of signal peptide (proteolytic cleavage)

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∙ Examples of post translational modifications in ER?

∙ Glycosylation

∙ Folding (Disulfide bond formation)

∙ Formation of multimeric proteins

∙ Cleavage

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∙ Characteristic of native state? Position least energy

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∙ What is the oil drop model? All hydrophobic amino acids close together  and inside protein

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∙ What do chaperons do? Provide temporary shelter for hydrophobic  amino acids before more proteins can be made. Proteins tend to  immediately fold, chaperons halt this folding.

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∙ Amino acid Disulfide bond formation? Cystein due to sulfhydryl group ∙

∙ Disulfide bonds Form inside ER NEVER Cytoplasm

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∙ What do Disulfide Isomerases do? Break down SS bonds, rearrange SS  bonds, cysteine engagement

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∙ What is an easy way to deactivate a protein? Breaking disulfide bonds  to deactivate or reduce This Inactivates enzymeschange in shape ∙

∙ Checkpoint past knowledge: What happens when 2 alpha helix are next to one another. Motif forms wrap around to form coil-coil domain. This  bond forms in ER NEVER Cytoplasm

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∙ Fun Fact: Folding and formation of disulfide bonds can happen at the  same time. Amino acids are really sticky.

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∙ Why Protein Glycosylation? Amino acids are sticky and tend to blob.  Glycosylation reduces aggregation and influences folding. It adds  oligosaccharide sugars to increase protein stability. Participates in cell cell adhesion of leukocyte extravasation and part of cell surfaces like  antigens of blood groups

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∙ Examples of Sugar? Mannose, Fucose, Xylose, N-Acetyl galactosamine,  N-Acetyl glucosamine, galactose, glucose, Neuramininc Acid ∙

∙ What are the 2 types of glycosylation? N-linked happens mostly in ER  on Asparagine—this adds a large preformed oligosaccharide which  differentiates it from O-linked glycosylation

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∙ What us Dolichol? It’s a lipid that flips in membrane and brings sugar to ER Lumen

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∙ Where does O-linked glycosylation take place? Happens mainly in  Golgi. Examples includes ABO blood types. 1 added sugar, 1 enzyme ∙

∙ Other examples of glycosylation include cartilage in joints and  connective tissue

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∙ Easy way to inactive protein? Make longer

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∙ What happens right before entering Golgi/or secreting cell? Proteolytic  cleavage happens. Prohormone convertases remove part of  polypeptide to activate a molecule

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∙ Bond Formation CAN NOT happen in cytoplasm, cleavage can occur in  golgi or outside of cell

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∙ Where does phosphorylation happen? Cytosol (reversible attachment  of phosphate group)

∙ What adds phosphates? Kinases  

∙ What removes phosphates? Phosphatases  

∙ Serine, Threonine, and Tyrosine can be phosphorylated  ∙

∙ Other ways to change shape of protein? Binding of calcium to  calmodulin activity proteins that are calcium dependent. Example  muscle contraction and exocytosis including secretion of  neurotransmitter at pre-synaptic ending

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∙ Why does non-human insulin have different lifetime? Change in shape  affects receptor binding

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∙ Which is the ONLY enzyme that does NOT have a go signal? Every ER  enzyme

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∙ What causes delivery of lysosomal enzymes to lysosomes? Acidic pH in endosomes causes protein to detach from receptor and become  lysosomal enzyme

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∙ What is exocytosis? Protein secretion to surface in secretory vesicles ∙

∙ How does transfer to Golgi happen? Vesicles

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∙ Sorting? Trans Golgi Network

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∙ Coat proteins specific for different destinations

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∙ Energy Small GTPases

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∙ What transports into nucleus?

∙ Histones

∙ Ribosomal proteins

∙ DNA& RNA polymerase

∙ Transcription factors

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∙ Delivery sequence to go to nucleus? Nuclear localization sequence.  Transport occurs through nuclear pores.  

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∙ Transport to into nucleaus: Importin binds to the protein to be  transported. Translocated through nuclear membrane

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∙ Mitochondra: Finished in cytosol. Not allowed to mature/fold ∙

∙ What is the proteasome? Chamber of death. Cuts into pieces  ∙ E1 Activates ubiquitin

∙ E2 Conjugation

∙ E3 Transfer (stamping)

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∙ In Alzheimer’s disease, cross linking of tau is defective which means  lower ubiquitin and higher amyloid

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∙ Hemoglobin is not glycosylated because it never see the ER ∙

∙ What is an organelle? Space in cell membrane bound and optimized for function

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∙ Vesicle docking: Arginines and glutamines

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∙ Endosome means more sorting needed. Vesicles responsible for  bringing and sorting stuff between trans golgi network

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∙ Aggregation: similar stuff sort together

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∙ Regulated secretion: For proteins that are not needed all the time ∙ EX. Hormones, transmitters, and cytokins

∙ Vesicles wait for signal  

∙ Selectogranins in trans golgi cause elective protein aggregation