protenes bio 205

what are the Levels of Protein Structure?

1. Primary: Amino acid sequence

2. Secondary: Local folding (α-helices, β-sheets)

3. Tertiary: 3D folding of a single chain

4. Quaternary: Assembly of multiple chains

Could you tell me the mRNA and DNA sequences corresponding to this polypeptide?

No, due to the degeneracy of the genetic code, as well as alternate splicing

How do we know that 3-D structure is determined by the primary a.a. sequence?

• Anfinsen (1960s) correctly predicted that the info necessary for correct folding is contained within the a.a. sequence

what is Genetic code?

•There are 20 amino acids to code for

•There are 4 possibilities at each nucleotide “position” of a codon

•the minimum # of nucleotides needed for a codon is 3

why is The genetic code is a non-overlapping triplet code?

• Based on simple mathematical probabilities, most people figured it was 3 per codon. Francis Crick and colleagues carried out elaborate experiments that involved creating viruses with specific mutations, checking viral functionality, etc. Eventually, they definitively demonstrated that the genetic code is triplet and non-overlapping

what does it mean “Charging” tRNA with their partner amino acid? and how?

• Aminoacyl tRNA synthetases recognize and attach the correct a.a. to tRNA (process requires ATP). Each amino acid has its own tRNA and Aminoacyl tRNA synthetase.

• attaching the correct amino acid to its matching tRNA via an ATP‑dependent, enzyme‑catalyzed two‑step process. This creates a high‑energy aminoacyl‑tRNA that the ribosome can use to build proteins accurately and efficiently

what did the Triplet binding assay (Nirenberg and Leder, 1964) say?

• Incubated specific trinucleotides with radioactively tagged charged amino-tRNAs

• 1 mixture with radioactive tRNA^Phe and 19 cold tRNAs, 1 mixture with radioactive tRNA^Lys and 19 cold tRNAs, etc.

• Added each mixture to test tubes containing a different trinucleotide (UUU, AAA, CCC, etc)

• 20 amino acids x 64 codons – 1,280 reactions!

• Ribosomes bind the tRNAs and trinucleotides

• Mixture is poured through a nitrocellulose filter

• Ribosomes are big and get trapped on the filter, while unbound tRNAs and trinucleotides flow through

• Filter is checked for radioactivity

• Only sample with UUU + radioactive tRNA^Phe would have a strongly radioactive filter

• Sample with UUU + radioactive tRNA^Lys (or any other tRNA) would not have a radioactive filter

• 3 of the codons matched none of the amino acids –>the stop codons

what happes if amino acid can be encoded by several codons?

the genetic code is said to be degenerate(revert to a simpler form as a result of losing a complex or adaptive structure present in the ancestral form.)

what is the stop codon?

• UAA

• UAG

• UGA

what is the start codon?

AUG

what is the Wobble?

• the ability of one tRNA to recognize 2+ different mRNA codons and still code for the same amino acid

• Proposed by Francis Crick in 1966:

Some tRNAs can tolerate a “mismatch” at the 3rd position of the codon. The binding is “looser”

• Wobble occur at the 5' nucleotide of the tRNA anticodon (which matches to the 3' nucleotide of the mRNA codon).

What’s the benefit of the woble?

•Buffering against mutations: reduces the chance of a harmful phenotype due to a point mutation

•Increases speed of translation

How many reading frames theoretically exist for a double-stranded DNA sequence?

6 total

How does the cell know which reading frame is correct?

by the presence of the first AUG (encodes Met)

what does The One “True” Open Reading Frame (ORF) mean?

• Random sequences hit stop codons often (3 of the 64 codons are stops), so long stretches without one are unlikely by chance. A long uninterrupted frame starting with AUG is strong evidence that it’s the real coding sequence. The other two frames are just “false” frames that happen to give gibberish peptides cut short by stop codons.

• The correct reading frame is set by the start codon (AUG), and it’s the one that stays open (no premature stop) through the coding region.

what are the characteristics of the genetic code?

1.Code is triplet.  Each 3 nucleotide codon in mRNA specifies 1 amino acid.

2.Code is “comma” free. mRNA is read continuously, 3 bases at a time without skipping bases

3.Code is non-overlapping.  Each nucleotide is part of only one codon and is read only once.

4.Code has start and stop signals.  AUG codes for Methionine and is the usual start signal.  UAA, UAG, and UGA are stop codons and specify the the end of translation of a polypeptide.

5.Code is almost universal.  Most codons have the same meaning in different organisms

6.Code is degenerate.  18 of 20 amino acids are coded by more than one codon.  Methionine and Tryptophan are the only exceptions.  Many amino acids are four-fold degenerate at the third position.

7.Wobble occurs in the tRNA anti-codon.  3rd base is less constrained and pairs less specifically. 

how is Translation is one of the most complex things the cell does?

• Translation machinery is 35% of dry weight of cell

• 21% of that is rRNAs

• 20,000 ribosomes

• 200,000 tRNAs

• 100,000 proteins and cofactors

what are the Ingredients in protein synthesis (translation)?

1)mRNA

2)Transfer RNA + amino acids (aminoacyl-tRNAs)

(actually these are many ingredients…

3) Ribosomes

4) Initiation, elongation and release factors

(actually these are many ingredients…)

5) energy (ATP + GTP)

what is a Summary of beginning protein synthesis: translation?

1.Protein synthesis occurs on ribosomes.

2.mRNA code is read from 5’ to 3’.

3.Protein is synthesized N-terminus to C-terminus.

4.Amino acids bound to tRNAs are transported to the ribosome.  Facilitated by:

• Specific binding of amino acids to their tRNAs.

• Complementary base-pairing between the mRNA codon and the tRNA anti-codon.

• mRNA recognizes the tRNA anti-codon (not the amino acid).

what does it mean for Prokaryotic mRNA to be polycistronic?

mRNA contains multiple open reading frames (ORFs) within a single transcript, each coding for a distinct protein. These ORFs are separated by intercistronic regions, which are non-coding sequences that can vary in length and may contain regulatory elements. This structure contrasts with monocistronic mRNA, which encodes only one protein per transcript and is typical of eukaryotes

how is tRNAs serveing as adaptor molecules between transcription and translation?

tRNA links the nucleotide language of mRNA to the amino acid language of proteins. Its anticodon pairs with an mRNA codon, while its 3' end carries the matching amino acid. Aminoacyl-tRNA synthetases load the correct amino acid onto each tRNA.

what does it mean Codon/ anti-codon interaction is via base-pairing?

The mRNA codon (3 nucleotides) and the tRNA anticodon (3 nucleotides) match each other through complementary hydrogen bonding, just like DNA strands do: A pairs with U, G pairs with C. The two strands run antiparallel, so mRNA 5'-AUG-3' pairs with anticodon 3'-UAC-5'. Because the tRNA is chosen by this pairing alone, no direct contact with the amino acid is needed

what is the Secondary structure fratures of tRNA

-small ~73-93 nucleotides

-distinct secondary structures with 4 double-stranded regions; “cloverleaf-shaped”

-unusual bases

what is Eukaryotic Ribosomes made up of?

• 1/3 proteins + 2/3 rRNAs

• Large subunit (60S)

  -catalyzes the formation of peptide bonds

• Small subunit (40S)

  -matches the correct tRNA to codon on mRNA

what are the 4 bining sites for Ribosomes?

•mRNA binding site: located in small subunit

•Aminoacyl site (A-site)

•Peptidyl site (P-site)

•Exit site (E-site)

what does the a site do?

“reads” the new codon in the mRNA

why is the fact that Ribosomes are Ribozymes!

 (RNA enzymes) imprtant?

• The ribosomal proteins are important for maintaining the stability and integrity of the ribosome but NOT for catalysis

• Peptidyl transferase activity is actually due to rRNA, not the protein part of the ribosome.

what is Peptidyl transferase activity (ribozyme)?

catalyzed reaction that forms peptide bonds between amino acids during protein synthesis, making the ribosome a ribozyme.

what is the mechanism of translation

1.Initiation: binding of initiator met-tRNA to Start site of mRNA together with the 2 ribosomal subunits

2.Elongation: formation of peptide bond by adding new amino acid as the ribosomal subunits move along the mRNA

3.Termination: ribosomal complex meets STOP signal on mRNA which newly-formed peptide is released from ribosome. 

How the translational machinery know which AUG to pay attention to?

• Prokaryotes: search for the Shine-Dalgarno sequence

• Eukaryotes: search for the Kozak consensus sequence (5’-GCCACCAUGG-3’)

• located both 5’ UTR

what do prokaryotic messenger RNAs do in prokaryotes?

there can be multiple ribosome-binding sites (Shine-Dalgarno sequences) in the interior of an mRNA chain, each resulting in the synthesis of a different protein. These are called polycistronic mRNAs.

how does translation begin in prokaryores?

• as the mRNA molecule is still be synthesized

• first making the shine dalgarno sequence

how does Initiation of protein synthesis in prokaryotes?

• Initiator tRNA itself is different, and is bound to a modified methionine called formylmethionine (tRNA^fmet). All other AUG use the “normal” (aka, elongating) tRNA^met

First methionin is modified

(fMet = formyl-methionine)

how does In eukaryotes: initiator tRNA^met work?

-A special type of tRNA called tRNA_i^Met is used for initiation.

-It is different from a regular tRNA^Met

-A different charging enzyme (synthetase) is responsible for attaching initiator Met to tRNA molecules

-the methionine on both are the exact same

larger explaion in eukaryotes inations for the making of protines

•Multiple protein factors called Eukaryotic translation initiation factors (eIFs) are interacting with both the ribosomal subunits and the mRNA sequence

•One complex binds to both the 5’ cap and the PABP of mRNA

•eIF-2 brings in that first tRNA_i^Met (GTP-bound)

•Scanning (100 nt/sec), looking for Kozak sequence

•Once that first AUG is found, GTP/ATP are hydrolyzed, and much of the complex falls away

•This provides the space for the 60S ribosomal unit to bind, and elongation can begin

the first Met-tRNA sits in the P-site

how are is the inations for the making of protines different from prokaryotes

•Less proteins involved

•first methionine is formylated

•No 5’ cap or PABP binding

•Different ribosomal sizes

•Shine-Delgarno sequence

What are the Elongation steps for protein sequences in Eukaryotic?

Each cycle adds one amino acid to the growing chain. The slides show it with a ribosome that has E, P, and A sites.

1. Aminoacyl-tRNA binds the A site. A charged tRNA whose anticodon matches the next mRNA codon enters the empty A site. The P site holds the tRNA carrying the growing polypeptide chain.

2. Peptide bond forms. The ribosome’s peptidyl transferase (an activity of the large subunit’s rRNA) transfers the whole chain from the P-site tRNA onto the amino acid on the A-site tRNA. The energy comes from the high-energy ester bond linking the chain to the P-site tRNA, which answers the “Energy from where?” box on your slide. The chain is now one amino acid longer and sits on the A-site tRNA.

3. Large subunit translocates. The large subunit shifts forward by one codon relative to the mRNA. The P-site tRNA (now uncharged) moves into the E site, and the tRNA holding the chain moves into the P site.

4. Small subunit translocates. The small subunit then moves forward by one codon along the mRNA, carrying the tRNAs with it. The A site is now empty and sits over the next codon, and the uncharged tRNA is ejected from the E site.

Then the cycle repeats: a new aminoacyl-tRNA binds the A site (the last slide).

how is Elongation steps for protein sequences in Eukaryotic more complicated?

•EF-Tu brings over an aminoacyl-tRNA

•Once correct codon-anticodon pairing is made, the bound GTP is “spent” (hydrolyzed), allowing the tRNA to fit into the A-site

•EF-Ts exchange GDP on EF-Tu for a new GTP

•Peptidyltransferase activity occurs

•EF-G forces the complex to slide over exactly 3 nucleotides (1 codon), “cost” of 1 GTP

GTP → GDP causes conformational changes in EF-Tu and EF-G (and other g-proteins throughout the cell), which affects how they interact with the translational machinery

“does elongation occur without other proteins?”)

No. Elongation does need help from proteins called elongation factors, just as initiation needs initiation factors. The simplified figures leave them out.

• eEF1A (EF-Tu in bacteria) escorts the aminoacyl-tRNA to the A site and uses GTP hydrolysis to check the codon-anticodon match.

• eEF2 (EF-G in bacteria) drives translocation, also powered by GTP hydrolysis.

The peptide bond itself is catalyzed by rRNA, but delivering tRNAs and moving the ribosome depend on these GTP-powered factors.

What are the four steps of the translation elongation cycle?

(1) Aminoacyl-tRNA binds the A site. (2) Peptidyl transferase forms the peptide bond, powered by the high-energy bond of the P-site tRNA. (3) Large subunit translocates. (4) Small subunit translocates and the uncharged tRNA leaves the E site. Elongation factors (eEF1A, eEF2) assist using GTP.

What are the steps of translation termination?

(1) A stop codon (UAG, UAA, UGA) enters the A site. (2) A release factor (eRF1) binds the A site, since no tRNA matches a stop codon. (3) Peptidyl transferase adds water instead of an amino acid, hydrolyzing the polypeptide from the P-site tRNA. (4) The ribosome subunits, mRNA, and tRNA dissociate

Termination?

• Termination stops Peptidyl Transferase activity: catalyzes the addition of -OH to the last a.a. in the chain and thus releasing it from the entire complex.

• Translocation of the ribosome such that the release factor is in the P-site causes the whole thing to fall apart

How does each antibiotic affect the ribosome (tRNA positions and polypeptide)?

• Tetracycline: Blocks aminoacyl-tRNA from binding the A site. P site has tRNA with the nascent chain, A site is empty.

• Streptomycin: Blocks the switch from initiation to elongation (also causes miscoding). P site has only the initiator tRNA (tRNAᵢ^Met), A site is empty, so almost no polypeptide is made.

• Chloramphenicol: Blocks peptidyl transferase (peptide bond formation). P site has tRNA with the nascent chain, A site has a new aminoacyl-tRNA, but the chain can’t lengthen.

• Cycloheximide: Blocks translocation. The chain has been transferred to the A-site tRNA, and the P site holds an uncharged tRNA, so the ribosome is stuck.

what are Polyribosomes (Polysomes)?

• Consists of an mRNA strand with two or more ribosomes attached, arranged like “beads on a string.”

• Each ribosome reads the mRNA at the same time, producing identical polypeptides in parallel

what are special cases of DNA to RNA to protein?

Lots of mRNA, little protein

•miRNAs repress mRNA

•General reduction in translation (unfavorable environmental conditions)

•mRNA/protein is unstable (↓ half-life)

Not much mRNA, lots of protein

•Many ribosomes

•mRNA has optimized 5’ UTR allowing for rapid and efficient translation

•mRNA/protein is very stable (↑ half-life)

what are the 2 major types of secondary structure?

• -α-helix is a right-handed spiral structure formed by a single polypeptide chain. It is stabilized by hydrogen bonds between the carbonyl oxygen (C=O) of one amino acid and the amide hydrogen (N-H) of an amino acid four residues ahead in the chain/hydrogen bonds are parallel to helical axis, forming “vertically”

  /Held by H-bonds between the hydrogen of one amino group and the oxygen of carbonyl of a different amino acid

  /side chains face outward

• 2^o structure: b-sheet•Polypeptide backbones are arranged side by side; almost completely extended./Hydrogen bonds form between pleated regions or sheets/• R groups of extend above and below the pleated sheet/Note the position of the R-groups on opposite sides (up and down) of the sheet./Anti-parallel: adjacent sheets lie in opposite orientations/Parallel: Adjacent sheets lie in same direction (N-term to C-term)

what is a TERTIARY STRUCTURE?

• 3-D arrangement of all secondary structures as well as R-groups

• comprise of Domains (regions that confer functional activities), leading to complex protein structures

• creates (sometimes multiple) binding sites for substrates

• interactions with both the polypeptide backbone and R-groups

how will Protein fold ?

so that polar sides face the cytosol

Disulfides bonds are an important covalent part of tertiary structure

what are 4 DNA-Binding Motifs ?

1)Homeodomain

(3 a-helices)

2)Zinc Finger (helix+sheet)

3)Helix-Turn-Helix(2 a-helices)

4)Leucine Zipper(2 a-helices)

What are Quaternary structures?

• interaction of 2+ polypeptides

• dimer

• tetramer

• can form in many different ways

what are some Examples of common protein functions?

• ENZYMES

What makes an enzyme special in terms of the reactions it carries out?

Each enzyme has a site to which substrate molecules bind, forming an enzyme–substrate complex. There, a covalent bond making and/or breaking reaction occurs, generating an enzyme–product complex. The product is then released, allowing the enzyme to bind additional substrate molecules and repeat the reaction. An enzyme thus serves as a catalyst, and it usually forms or breaks a single covalent bond in a substrate molecule.

ENZYMES: What is their function?

Catalyze covalent bond breakage or formation

Cells contain thousands of enzymes, each speeding up one particular reaction. Examples: alcohol dehydrogenase (breaks down alcohol in wine), pepsin (degrades dietary proteins in the stomach), ribulose bisphosphate carboxylase (converts CO2 to sugars in plants), DNA polymerase (copies DNA), protein kinase (adds a phosphate group to a protein).

STRUCTURAL PROTEINS: What is their function?

Provide mechanical support to cells and tissues

Outside cells: collagen and elastin (extracellular matrix, tendons, ligaments). Inside cells: tubulin (long, stiff microtubules) and actin (filaments supporting the plasma membrane). Keratin reinforces epithelial cells and is the major protein in hair and horn.

TRANSPORT PROTEINS: What is their function?

Carry small molecules or ions

In the blood: serum albumin carries lipids, hemoglobin carries oxygen, transferrin carries iron. In membranes: bacteriorhodopsin (light-activated H+ pump), glucose transporters (shuttle glucose in and out), and the Ca2+ pump (clears Ca2+ from muscle cytosol after contraction).

MOTOR PROTEINS: What is their function?

Generate movement in cells and tissues

Myosin in skeletal muscle provides the motive force for humans to move; kinesin interacts with microtubules to move organelles around the cell; dynein enables eukaryotic cilia and flagella to beat.

STORAGE PROTEINS: What is their function?

Store amino acids or ions

Iron is stored in the liver by binding to the small protein ferritin; ovalbumin in egg white is a source of amino acids for the developing bird embryo; casein in milk is a source of amino acids for baby mammals.

SIGNAL PROTEINS: What is their function?

Carry extracellular signals from cell to cell

Many hormones and growth factors are proteins. Insulin controls glucose levels in the blood; netrin attracts growing nerve cell axons to specific locations in the developing spinal cord; nerve growth factor (NGF) stimulates some nerve cells to grow axons; epidermal growth factor (EGF) stimulates growth and division of epithelial cells.

RECEPTOR PROTEINS: What is their function?

Detect signals and transmit them to the cell's response machinery

Rhodopsin in the retina detects light; the acetylcholine receptor in muscle cell membranes is activated by acetylcholine from a nerve ending; the insulin receptor lets a cell respond to insulin by taking up glucose; the adrenergic receptor on heart muscle increases heart rate when it binds epinephrine

TRANSCRIPTION REGULATORS: What is their function?

Bind to DNA to switch genes on or off

The Lac repressor in bacteria silences the genes for enzymes that degrade the sugar lactose. Many different DNA-binding proteins act as genetic switches controlling development in multicellular organisms, including humans.

SPECIAL-PURPOSE PROTEINS: What is their function?

Highly variable

Examples: antifreeze proteins of Arctic/Antarctic fishes (protect blood against freezing); green fluorescent protein from jellyfish (emits green light); monellin from an African plant (intensely sweet taste); glue proteins that mussels and other marine organisms use to attach firmly to rocks, even in seawater.

Which enzyme degrades dietary proteins in the stomach?

Pepsin

Pepsin is the stomach enzyme that breaks down dietary proteins. (Alcohol dehydrogenase = alcohol; DNA polymerase = copies DNA; protein kinase = adds phosphate to proteins.)

Hemoglobin, serum albumin, and transferrin belong to which class?

Transport proteins

Hemoglobin carries oxygen, serum albumin carries lipids, and transferrin carries iron in the bloodstream.

Myosin, kinesin, and dynein belong to which class?

Motor proteins

Myosin moves muscle, kinesin moves organelles along microtubules, and dynein powers cilia and flagella.

Ferritin, ovalbumin, and casein belong to which class?

Storage proteins

Ferritin stores iron in the liver; ovalbumin (egg white) and casein (milk) supply amino acids to developing birds and baby mammals.

Insulin, NGF, EGF, and netrin are examples of which class?

Signal proteins

These are hormones/growth factors that carry extracellular signals between cells. Don't confuse with the insulin receptor, which is a receptor protein.

Collagen, elastin, tubulin, actin, and keratin belong to which class?

Structural proteins

Collagen and elastin act outside cells; tubulin and actin inside cells; keratin reinforces epithelial cells and forms hair and horn.

what are Antibodies and their complex tertiary/quaternary structure?

• priten the bind tight to thier trafer atugens then produce i certberse and a defebce agenst infeftion

• - made up or 2 identical heave chains and 2 antige binding sies

• loter od disolfid bonse and riged body but the binding siet is not rigies

how do antiboy speicey ?

The typical human adult has 108 circulating antibody species! Most at low concentrations; when you get sick, certain clones will substantially increase in quantity

What happens after translation?

A newly synthesized polypeptide chain must undergo post-translational processing (chemical modification) to generate the final protein. • Though some Post-translational modifications (PTMs) occur on the nascent peptide (e.g., disulfide bridge formation and glycosylation), many happen later on in a protein’s life in transient or stable patterns

how does abtiboes defien agein infoetuo?

anpons cross ink to antifer to crat aggreation that sifle antios afes to injest it by phagocytic cells and to kill it with other proties

what is Phosphorylation?

happens to many proteins, both cytosolic and within organelles like the nucleus

How does histone phosphorylation affect gene expression?

• Phosphorylation is a very dynamic PTM, responsive to rapid differences in the extra- and intra-cellular environment. The same protein could get (de-)phosphorylated many many times during its life

• Protein (de-)phosphorylation can (de-)activate

what are some Post-translational modifications?

• Disulfide brige

• phospholayation

• glycolation

• methlaion /acteyion misoyation

what is Glycosylation?

• Occurs to 99% of ER proteins, to different extents

• Occurs to 20% of cytoplasmic proteins

• a preformed 14 carbon branching sugar is added to the newly formed protein

• Sugar side chains promote folding and stability of the glycoproteins; important for targeting and recognition; and sometimes function of the mature protein

what is Formation disulfide bonds?

• Happens right after or concurrently with glycosylation

• Oxidative reaction; reducing conditions (such as in the cytosol) causes the reverse reaction

• 20-30% of all proteins have disulfide bonds; ~60-80% of secreted proteins have them

what is the Proper folding and subunit assembly?

• Overlaps with the first 2

• The sugar residues, presence of disulfide bonds (if any), as well as the developing secondary structures of the emerging polypeptide contribute to proper folding of the protei

what are the Protein modification in the ER?

1.Glycosylation 2.Formation disulfide bonds 3.Proper folding and subunit assembly

hoe do Misfolded proteins get some chances to re-fold properly before they’re discarded?

• Unfolded Protein Response (UPR) program

what are Unfolded Protein Response (UPR) program?

• Misfolded proteins trigger the production of chaperones in the ER by activating a set of UPR receptors that are transmembrane proteins – parts of them exist in both the cytosol and ER lumen

• If misfolded proteins can’t be refolded, they are degraded. If the cell is filling up with misfolded proteins, cell death results

what are Molecular chaperones?

• complex protein machines that help re-fold misfolded proteins

• Chaperones often enclose the misfolded protein, provide isolation to prevent aggregation before fold completed

where do Fully folded proteins exit to

exit from the er to the Golgi

how are Proteins are carried in between compartments

properly folded into its biologically active 3-D shape before exiting ER in vesicles

how are Proteins exiting ER go into the Golgi apparatus to be further modified?

• Cis-Golgi receives COPII vesicles from ER containing newly synthesized proteins

• It also moves proves proteins backwards to the ER in COPI-coated vesicles. Why?

• These are mainly proteins that belong in the ER lumen

• Chemical modifications occur in the interior of the cis, medial and trans Golgi compartments

• Glycosylation, proteolytic cleavage, phosphorylation, disulfide bond formation (minor)

• The trans-Golgi packages the finalized proteins for shipping to their ultimate cellular locations

Where do protein have to be sorted?

lots of spots

how is the ER Unlike other organelles?

ER starts to acquire proteins before synthesis is complete; by associating ribosomes with the membrane – rough ER (RER) - or from COPI vesicle

where are Proteins destined for the ER are synthesized

by ribosomes attached to ER

How does the cell “know” where to send a protein?

Protein sorting sequences

How do we know the signal sequences are necessary and sufficient?

if she swich a signal sequenss on a protein it will also swich

whar are the 3 Mechanisms are used for the transport of proteins?

• Nuclear Pores

• Structure of nuclear pores

what is the Problem: for prote movment

Organelles are membrane bound; Membranes are generally impermeable to hydrophilic groups; either proteins would have to be hydrophobic or another mechanism is needed.

what are Nuclear Pores

Nucleus is a double membrane structure (nuclear envelope) -has many holes or pores -pores consist of over 30 proteins. -pores must allow 2-way traffic. -important for protein and mRNA transport. -allow water and small water-soluble substances to cross ; but larger molecules must be actively transported.

what is the Structure of nuclear pores

how are Proteins are actively and selectively transported into nuclear pores?

-Nuclear localization signal

- Directs a protein from the cytoplasm to nucleus. [Usually] a sequence of + charged Lys & Arg

-Nuclear import receptors - bind to proteins in cytoplasm and“guide” the protein to the pore by interacting with fibrils.

Final translocation is energy dependent - Uses GTP hydrolysis NOTE: Proteins going to the nucleus are transported structurally intact; don’t have to unfold

how does Protein sorting to the mitochondria work?

• Mitochondria are also double membrane structures, but they don’t have pores

• Can make some of their own proteins but also require protein import

• Do so by recognizing a specific N-terminal sequence; site on the outer membrane recognizes the sequence

• Protein is translocated through both membranes at same time

• In order to be translocated, proteins must be unraveled or unfold

how is Vesicular transport between membrane-bounded compartments is highly organized?

Each transport vesicle must take with it only the proteins and lipids appropriate to its destination and must fuse only with the appropriate target membrane.

what is the The functions of intracellular proteolysis-degradation?

the elimination of abnormal proteins, such as proteins that cannot be re-folded