Module 5 - Protein structure, function, and synthesis

how many amino acids are there

20

what are the 3 models of proteins

ball and stick, ribbon, and space filling model

ball and stick model

3d model of individual atoms (ball) and bonds (stick)

ribbon model

shows secondary structure; alpha helix beta pleaded sheet and loops/turns in between

what are the 4 components of an amino acid bound to the alpha carbon

amino group, carboxyl group, hydrogen, r group

what happend to amino acids at physiological pH

carboxyl group gives H to amino group; becomes charged and a zwitterion

3 classifications of an amino acid

water interaction, polarity, basic/acidic

characteristics of hydrophobic amino acids

hide in interior of folded proteins, weak van der Waals forces stabilized them together

characteristics of hydrophilic amino acids

ionic or form hydrogen bonds from O/N in the r group (polar). found on outside of protein

characteristics of a basic amino acid

hydrophilic, positively charged (accepted a proton)

characteristics of an acidic amino acid

hydrophilic, negatively charged (donated a proton)

characteristics of a polar amino acid

amide (C(=O)-NH2), hydroxyl, thiol

what are the three special amino acids

glycine, proline, cysteine

glycine structure

R group is just H. smallest and nonpolar

glycine function as related to structure

free rotation around the C-N bond allows tight folding, and flexibility in the polypeptide backbone

proline structure

r group connects to amino group

proline function as related to structure

linkage restricts rotation of the C-N bond, limiting folding around proline

cysteine structure

contains a thiol (SH) group

cysteine function as related to structure

2 can form a disulfide bond (cross bridge) to connect different parts of the same protein OR different proteins together

n terminus

end of the peptide with free amino group

c terminus

end of the peptide with free carboxyl group

which structure levels of the protein are 3d

secondary, tertiary, and quaternary

primary protein structure

linear sequence of amino acids in the chain from amino end to carboxyl end. determines secondary tertiary and quaternary structure

what is the positioning of R groups in the primary protein structure

alternating sides of the chain, affecting folding and R group interaction

what are the 2 forms of writing protein primary structure

3 letter sequences or one letter abbreviations (Val-Gly-Ala-His or V-G-A-H) 

secondary protein structure

results from hydrogen bonding between neighboring functional groups. alpha helix and beta sheet

alpha helix secondary protein structure

very stable, right handed and let further amino acids interact. result from hydrogen bonds between 4th amino acid functional group above and below the spiral

beta sheet secondary protein structure

segments of the chain lying side by side bonded by h bonds between functional groups, can be parallel or antiparallel

in both secondary structures, bonding is between…

function groups (amide bonds to carbonyl)

what does secondary protein structure describe

conformation of PARTS of the polypeptide chain

tertiary protein structure

results from hydrogen bonds, hydrophobic interactions, ionic bonds and disulfide bonds

which amino acid forms disulfide bonds

cystine

what does tertiary protein structure describe

conformation of the ENTIRE protein

which protein structure stage can describe a protein in functional form

tertiary (unless protein has subunits) and quaternary

quaternary protein structure

spacial arrangement of protein subunits resulting from same bonding as tertiary (hydrogen, hydrophobic, ionic, and disulfide)

homodimer

protein containing 2 identical subunits

heterodimer

protein containing two non-identical subunits

how do eukaryotic and prokaryotic ribosomes compare

eukaryotic is bigger than prokaryotic

which direction does the ribosome read

5’ to 3’

large ribosome subunit sites

exit site, peptidyl site, aminoacyl site

what is the start codon

AUG, translation starts here

where on the ribosome is the aminoacyl tRNA accepted

aminoacyl site, A site

where does the peptide bond formation happen on the ribosome

peptidyl site, P site

where does the tRNA exit the ribosome

exit site, E site

what are tRNA

transfer rna, contain 70-90 nucleotides and are hairpin shaped

where does the amino acid attach to the tRNA

3’ hydroxyl site on 5’ CCA 3’ end of the tRNA

anticodon

3 bases within the anticodon loop of a tRNA

how are amino acids attached to tRNA

aminoacyl tRNA synthetases, 1 per amino acid

uncharged tRNA

tRNA without amino acid

charged tRNA

tRNA wihtin an amino acid

how many possible codons are there

64

why are codons sometimes described as redundant or degenerate

some amino acids specified by more than 1 codon

which direction are codons read

5’-3’

3 stages of translation

initiation, elongation, termination

translation: initiation in eukaryotes

initiation complex forms at the 5’ cap of the mRNA, small ribosomal unit and the initiation factors find AUG, then large ribosomal subunit is recruited and initiation factors release

translation: initiation in prokaryotes

initiation complex forms at one or more shine dalgarno sequences (since no 5’ cap) and starts translation at first AUG

how does translation initiation differ in practice between prokaryotes and eukaryotes

because prokaryotes have more than 1 shine-dalgarno sequence, 1 mRNA can code for several polypeptides unlike eukaryotes

translation: elongation

tRNA enters the a site, peptide bond forms, amino acid in P site moves to the A site (catalyzed by large subunit), ribosome shifts one codon, uncharged tRNA to the E site to leave and empty a site

translation: termination

stop codon reached, release factor binds to the A site, bond between tRNA and polypeptide breaks to create the c terminus of the polypeptide

which steps of translation are the same in both prokaryotes and eukaryotes

elongation and termination

how is gene expression regulated

DNA accessibility, transcription factors, RNA processing and post-translational modification

what do specific signal sequences within polypeptides indicate

indicates where the chain is headed for sorting

what does no sorting signal in a polypeptide mean

it is staying in the cytosol

what does an amino terminal signal mean for a polypeptide

it will be sent to the chloroplast or the mitochondria or the ER, can’t function in the cytosol

what does an internal signal mean for a polypeptide

it will be sent to the nucleus, can’t function in the cytosol

what case would a polypeptide be transported to the ER

special amino terminal signal is on the polypeptide, bound by signal recognition particle (SRP). ribosome and chain go to the ER

where can polypeptides made by ribosome on the rough ER be found

embedded within ER membrane, lumen of the endomembrane system or secreted out of the cell