Signal Sequences

• Direct proteins to correct cell adress
• sequence at N-term. (5-10) transfer to ER and usually to golgi 
• mitochondria have sequences of positivly charged AA alternating with hydrophobic
• Peroxisoms have sequence of 3 on C-terminus
• complementary sorting receptors 
• Nuclear localizing signals 
• mutation cases altered signal sequence, protein remains in cytosol.

Ran GTPase

Cytosolic Pathway 

• involves sorting of all nuclear, cytosolic, peroxisom, mitochondria and chloroplast
• post translational transport
• transported via diffusion (simple and facilitated) 

Mitochondrial n terminal sequence

• sequence for protein to move into mitochondrial matrix. removed after import by a signal peptidase

TOM Complex

• transferes proteins across the outer membrane of mitochondria
• SAM complexes helps proteins in the outer membrane to fold properly, found after TOM

TIM Complexes

• transport proteins across the inner membrane
• OXA complex mediates insertion of the inner membrane proteins that arent synthesized with in the mitochondria

Chaperone Proteins (HSP70)

• help keep protein unfolded for transportation through a membrane 
• ATP dependent process 
• outside the mitochondria and bound in the matrix side of TIM23

Inner Membrane Pathways

• path A has stop transfer sequence after MTS which blocks translocation of C-term end
• Path B hydrophobic domain termed Oxa 1. MTS cleaved and Oxa1 causes inner membrane insertion 
• Path C lacks MTS have has multiple internal mitochondrial targeting sequences that are recognized by TOM and TIM. TIM responsible for incorporating its hydrophobic regions into membrane

Intermembrane Pathways

• MST sequence and then secong hydrophobic targeting sequence. Blocks complete translocation of protein, which is cleaved after it moves away from TIM
• Path B no n terminal MTS. delivered directly to the intermembrane space via the general import pore

Peroxisomes

• single membrane
• specific sequence (ser-lys-Leu) loacated at the c terminus is import signal 
• peroxins (pex5) acts as transport protein that binds with pex14 receptor to make multimeric complex

Three types of weak bonds

• hydrogen bonds: holds double helix together
• electrostatic interactions: positive and negative
• van der Waals attractions: hydrophobic interactions. allow for lipid bilayers. weakest bond

Protein Structure

Coiled-coil

• forms when two alpha helices have most of their nonpolar(hydrophobic) on one side so that they can twist around each other with these side chains facing inward 

Protein Structure

Zinc Finger motif

• constructed with an alpha helix and a two beta strand sheet. 

Primary Protein Structure

• amino acid sequence defines interactions
• sequences controlled by genes
• straight
• define chemistry that goes on at every point of polypeptide

Secondary Protein Structure

• alpha helix: peptide backbone spirals, R groups on outside, 3.6 residues per turn, proline breaks helix, hydrogen bonds between every 4 amino acids to stabalize
• Beta strand: stretched out polypeptide, zig-zag backbone, R group alt. up donw up down but not on sides
• Beta sheet: parallel or antiparallel sheets have mix of the too.
• altering a  gene may alter secondary structure

Tertiary Structure

• globular domain
• fibrous domain: long alpha helical regions
• 3/D structure

Quaternary Structure

• a particular protein molecule is formed of a complex withmore than one polypeptide chian
• Dimer 2 polypeptides needed to form structure
• trimer. tetramer, octomer ect
• homo same hetero different

Protein Phosphorylation

• phosopoamino acids: tyrosine, serine, threonine
• protein kinases promote phosphorylation
• protein phosphotases remove phosphate group

Special Amino Acids: Cysteine

• can form disulfide bridges because of terminal sulfhydryl group
• helps to stabilize protein

Km

• the concentration of substrate that allow the reaction to proceed at one half its max rate

competitive inhibition

• has same Vmax but lower Km

Non-competitor inhibition

• lower Vmax and same Km

Thermodynamics

^G=^H-T^S

• G<0 exergonic spontaneous reaction
  
• G>0 endergonic, non-spontaneous 

Translational motion

• one place to another
• diffusion is accounted for by this
• diffusion is a function of mass and size