Proteins

Question 1

Function of Proteins

Answer 1

Transport & Signalling

• Embedded in cell membrane
• Moving substances across

Enzymes

• Speeding up reactions (Synthesis of carb. in C.R.)

Structure and Movement

• Flagella, cilia
• Cell to cell signalling

Defense

• Antibodies

Question 2

TATA Box Binding Protein

Details, Structural Significance

Answer 2

• Transcription factor in eukaryotes
• Recognizes TATA box sequence near promoter region
• Has a groove-shaped structure that allows it to bind specifically to the TATA box in DNA

Question 3

Aquaporins

Details, structural significance

Answer 3

Membrane proteins that transports water.

Structural Features:

• Hydrophobic exterior: Allows for embedding in cell membrane
• Hydrophillic core: Allows passage of water across membrane

Quatinary Structure: Made of 4 protein subunits/monomers that form tetrameric aquaporin channel

• Each subunit contains alpha helices that form a pore, as well as a central pore from all 4 together
• Water is able to form H bonds with hydrophillic side groups that line the core in order to push through

Question 4

2 Ways Protein Structures are Represented

Answer 4

Space-filling Diagram:

• Actual relative size and location of each atom

Ribbon Diagram:

• Lines representing backbone of polymer
• Includes alpha helices and beta helices

Question 5

The Process of Transcription

Answer 5

DNA transcribed into mRNA by RNA polymerase II.

• Occurs in nucleus
• mRNA transported to cytoplasm

Question 6

The Process of Translation

Answer 6

• Ribosome reads mRNA codons (small subunit)
• tRNA w/ anticodon matches codon and brings the correct amino acid
• Large subunit forms peptide bonds, growing the polypeptide chain

Question 7

Nucleus in Protein Production

Answer 7

• Double membrane nuclear envelope protects chromosomes
• Nuceolus: Transcribes rRNA (ribosomal RNA)
  * Ribosomes used in protein production
• Information in gene (DNA) transcribed into mRNA

Question 8

Nuclear Pores

Answer 8

• Pores in the nuclear envelope that connect nucelus and cytosol

What goes OUT:

• rRNA bind to proteins to form ribosomal subunits
• Transcribed mRNA

What goes IN:

• DNA and RNA building blocks
• Enzymes requried for transcription

Question 9

Ribosomes

Structure, 2 types

Answer 9

• Subunits created in the nucleolus
• Large & small subunits that contain RNA and proteins
• Free: Soluble in cytoplasm
• Bound: Attached to endoplasmic reticulum
• Catalyzes the dehydration synthesis of polypeptide chains (more in TRANSLATION FC)

Question 10

Amino Acids

Answer 10

• 20 in total
• Central carbon, amino group, carboxyl group, hydrogen atom, variable side chain (R)
• R differs in size, shape, chemical properties (hydrophobic–may aggregate, hydrophillic– charged and form ionic bonds, H bonds)
• Synthesized to become Polymers / Polypeptides through condensation reactions

Question 11

Condensation Reaction

Answer 11

Dehydration synthesis involved in the polymerization of amino acids into polypeptides.

• Releases H2O
• Catalyzed within ribosome
• Creates a peptide bond: Bond between carboxylic acid of amino acid 1 and amine of amino acid 2

Question 12

Hydrolysis Reaction

Answer 12

Breaks amino acid polymers apart with the addition of H2O.

• Opposite of condensation
• Breaks peptide bonds

Question 13

Primary Structure of Protein

Answer 13

Unique sequences of amino acids in protein.
* Interaction of varying R groups in amino acids result in distinct 3d structure of protein

Question 14

Free vs. Bound ribosomes

Answer 14

Free Ribosomes: Found in Cytosol

• Creates proteins that stay inside the cell (cytosol, specific organelles)
• Cytosol: Enzymes in glycolysis, structure (actin, tubulin)
• Specific organelles: Histones or transcription factors (in Nucleus), membrane proteins (mitochondria, chloroplast), peroxisomes

  Special sequence on protein targets the protein to the specific organelle!

• Folding may occur BEFORE or AFTER transport to target organelle

Bound Ribosomes: Found on RER

• Creates proteins that are secreted or membrane-bound
• Or lysosomal!
• Proteins travel into lumen of ER where folding takes place, travels through endomembrane system

Question 15

Secondary Structure of Protein

Answer 15

Interactions between components of a proteins backbone forms alpha helices and beta sheets.

Alpha Helix:

• Polypeptide chain churned into coil by formation of non covalent hydrogen bonds
• H bond formed between carbonyl of one residue and amide of another residue 4 positions away
• R groups stick out, determining properties of whole structure

Beta Pleated Sheets:

• Broad adjacent strands running in parallel or antiparallel directions
• Hydrogen bonds between adjacent strands resulting in pleated like organization

Question 16

Tertiary Structure of Protein

Answer 16

Overall shape –Unique assembly of secondary structures to make a functional 3d protein.

Due to interaction of variable side chains (R) that bend and fold backbone. These interactions can be spontaneous or non-spontaneous.
* Hydrogen bonds
* Vander Walls interactions
* Covalent and Ionic bonds
* Disulfide bonds
* Hydrophobic interactions

Question 17

Cellular Mechanisms Assisting Protein Folding

Tertiary Structure

Answer 17

Molecular Chaperones proteins

• Bind to hydrophobic regions of new ppt
• Prevents incorrect folding until correct structure forms

Chaperonin complexes

• Forms isolation chambers for new proteins
• Allows folding without interference

Question 18

Quaternary Structure of Protein

Answer 18

Association of different polypeptide subunits to form fully functional protein.
* Multiple tertiary structures combined

Question 19

The Endomembrane System

order of organelles

Answer 19

(NERG-VP)

Nucleus/nuclear envelope → Rough ER → Golgi → Vesicles → Plasma membrane or lysosomes

• Modify, package, transport, and recycle proteins through a coordinated network of membranes.

Question 20

Signal Recognition Particle

Answer 20

Allows bound ribosomes on rough ER membrane to produce proteins that enter lumen for further processing (folding, etc.)

• mRNA has signal sequence that binds to signal recognition particle (SRP)
• SRP binds to SRP receptor (SRPR) on ER membrane before dissociating
• Polypeptide enters lumen through transmembrane channel and continues to grow
• Signal sequence cleaved
• Protein ends up in the lumen of ER for processing and maturation

Question 21

Destinations of Proteins post-ER Lumen

Answer 21

1. Remain in the ER
2. Journey to final destination through vesicles
3. Journey to the golgi apparatus for further processing

Question 22

Golgi Apparatus in EM system

Answer 22

Site of further protein modification.
* Vesicles carry proteins from ER –> Golgi
* Glycosylation, etc.

Question 23

Destinations of Proteins post-Golgi

Answer 23

1. Remain in the golgi
2. Cell membrane (Porins, receptors)
3. Secreted out of cell (Hormones, antibodies, enzymes)
4. Journey to other organelles (Peroxisome, lysosome, vacuole)

Determined by tags on protein!

Question 24

Peroxisomes

Answer 24

Membrane bound organelle required for fatty acid metabolism

Question 25

Mechanisms of Transport of Vesicles

Answer 25

* **Cytoskeleton:** Dense network of fibres that maintain and change cell shape * **Microtubule:** Protein polymers that form long fibres which stretch through the cell, functioning as "roadways" * **Kinesin & Dyenin** are motor proteins that attach to transport vesicle and "walk" along microtubules Uses energy from hydrolysis of ATP

Question 26

Bacterial Porin

Answer 26

* Prokaryotic * Beta sheets forms barrel with hydrophobic exterior and hydrophillic interior * Seen in mitochondria and chloroplast membrane... further evidence for prokaryotic ancestry

Question 27

Cystic Fibrosis

Answer 27

A consequences of a misfolded proteins due to mutation in **cystic fibrosis transmembrane conductance regulator (CFTR ion channel protein)** * Accumulation of thick mucus in lungs resulting in bacterial infections

Question 28

Residues in Polypeptides

Answer 28

**Amino acids** in peptide bonds in a polypeptide * Peptide bond polymer is **polypeptide**

Question 29

Peptide Bond

Answer 29

Bond berween **carboxyl** group of one amino acid and **amino** group of another (**C–N bond**) * Formed through dehydration synthesis * Creates polypeptides

Question 30

Modification of Proteins in the ER Lumen

Answer 30

**Glycosylation:** Addition of one or more carbohydrate chains * Occurs on most secreted and membrane bound proteins * Stability, folding, cell-cell recognition * *Note: Can occur in golgi as well...*

Question 31

How Are Proteins Sorted to Their Final Destination Post-Golgi?

Answer 31

* Each protein post-golgi has a TAG * Tag allows it to be packaged into particular type of transport vesicle * Transport vesicles have TAGs that allows it to be transported to final destination