Amino Acids and Protein Structure Summary PDF

**Amino acids** =molecules that combine to form proteins, consist of carboxyl- and amino group Alpha amino acids= amino group is linked to carbon atom next to -COOH carbon = zwitter ions: both + and -- charged All dissolvable in water *[Subtypes ]* - Aliphatic Amino Acids -\>Alanine (ala),...

**Amino acids** =molecules that combine to form proteins, consist of carboxyl- and amino group Alpha amino acids= amino group is linked to carbon atom next to -COOH carbon = zwitter ions: both + and -- charged All dissolvable in water *[Subtypes ]* - Aliphatic Amino Acids -\>Alanine (ala), isoleucine (ile), leucine(leu), proline(pro), valine(val), glycine(gly) - Aromatic Amino Acids -\>phenylalanine(phe), tryptophan(trp), and tyrosine(tyr) - Alcoholic Amino Acids -\>serine(ser), threonine (thr) - Basic Amino Acids -\>histidine(his), lysine(lys), arginine(arg) - Sulfur-Containing Amino Acids -\>methionine(meth), cysteine(cys) - Acidic Amino Acids -\>aspartate(asp), glutamate(glu) - Amide Amino Acids -\>asparagine(asn), glutamine(glu) *[Chemical structure]* Afbeelding met tekst, handschrift, Lettertype, diagram Automatisch gegenereerde beschrijving *[importance of the R-groups ]* Most important aspect= polarity =\> classification of amino acids in 4 groups: - Nonpolar: hydrophobic - Polar: hydrophilic - Acidic: hydrophilic - Neutral: hydrophilic  *[Basic amino acid structure]* Aa= Tetrahedral structures Afbeelding met Lettertype, diagram, schermopname, tekst Automatisch gegenereerde beschrijving *[Mirror amino acids]* Amino acids=\>chirality (2 forms: L and D) **L-amino acids**=\> mostly found in humans **D-amino acids**= \>mostly found in brain and nature. Converted from L-amino acids during post-translational modifications trough enzyme catalyzation. **Proteins** *[Peptides ]* =building block protein, chain of amino acids -\>peptide=small number of amino acids -\>polypeptides= large number of amino acids, bound to each other by peptide bond -\>peptide bond: covalent bond between carboxyl group (-charge) 1 amino acid and amino group (+charge) other amino acid. =\>formed by condensation reaction  =\>dipeptide= formed by reaction between alpha-carboxyl and alpha-amino groups of 2 amino acids =\>disulfide bonds between residues= oxidative reaction (hydrogen transferred to acceptor molecule) *[Function ]* *[Structure]* - Primary structure -\>chain of amino acids - Secondary structure -\>proteins can fold=\>repeating patterns occur, reactions in the backbone =\>2 most common secondary structures - Alpha helix 1 protein chain twists=\>shape resembles a right-handed coil =\>maintained by numerous hydrogen bonds (carboxyl- and nitrogen-groups) in the backbone - Beta pleated cheat Can occur when polypeptide chains run parallel =\>maintained by intermolecular and intramolecular hydrogen bonds - Extended helix of collagen Each strand of collagen = repetitive units (GLY-X-Y) - No repeated patterns= random coils - Tertiary structure 3D arrangement, interaction of side chains and not only the backbone =\>stabilized in 5 ways 1. Covalent bonds 2. Hydrogen bonding 3. Salt bridges 4. Hydrophobic interactions 5. Metal-ion coordination - Quaternary structure =\>for proteins with \>1 polypeptide chain =\>genes have specific binding sites and bind to each other =\>determines how the different sub-units fit into an organized whole =\>subunits-\>packed+ held together by.... - Hydrogen bonds - Salt bridges - Hydrophobic interactions Extra: conjugated proteins= proteins that contain non-amino acid portions Prosthetic group= name of the non-amino acid portion in a conjugated protein **Structure of tRNA** - All tRNA molecules have the following sequence at their ends: 5'-CCA-3' - They all have a few bases chemically modified=\> different the type of tRNA - Clover-leaf shape=\> because of complementary base-pairing between the nucleotides in the RNA-strand - Result = 4 loops (2^nd^ loop contains anti-codon sequence) - Loop 1 = D-arm and loop 3 = T-arm =\>bacterial tRNA: not found in a lot of copies in genome, transcribed by RNA polymerase, during transcription of tRNA genes=\> pre-t RNA is produced =\>eukaryotic tRNA: genes are repeated multiple times in the genome, transcribed by RNA polymerase III, during transcription of tRNA genes=\> pre-t RNA is produced, eukaryotic t RNA can contain introns =\>amino acid attaches to 3' side of the tRNA (covalent linkage between carboxy; group AA and 3/2 '-OH group of the ribose from the adenine in the 3' end tRNA  =\>coupling the amino acid to tRNA : aminoacyl-transferases *[Wobble pairing ]* Afbeelding met tekst, schermopname, Lettertype, ontwerp Automatisch gegenereerde beschrijving **Translation** -\>mRNA= translated in 5'-3' direction -\>polypeptide chain = made in N-terminal (amine-group) to C-terminal (carboxyl-group) direction  *[Ribosomes ]* -\>consists of 35% proteins and 65% ribosomal RNA =\>rRNA molecules : prokaryotic-3 types, eukaryotic-4 -\>RBS = -\>reads mRNA from 5'-3' -\> eukaryotic ribosomes: float around in cytoplasm, attached to endoplasmic reticulum, on outside of nuclear envelope. -\> structure : 2 subunits-\>come together to translate the mRNA - Prokaryotes: small subunit = 30S large subunit=50S - Eukaryotes: small subunit=40S large subunit=60S -\>structure has different sites-\>different actions - A-site (aminoacyl-tRNA site) =part of large- and small subunit Entry of tRNA molecule with amino acid attached - P-site (peptidyl-tRNA site) =part of large- and small subunit Holds growing protein chain and tRNA in place - E-site (EXIT-site) =only part of large subunit Exit for used tRNA and new protein chain. *[3 steps of translation in prokaryotes ]* 1. Initiation - Interaction of small ribosomal subunit (IF-1 and IF-3 are bound to this) with AUG initiation codon of mRNA - RBS =\>needed to find where the 30S subunit need to bind to the mRNA (shine-dalgarno sequence-\>towards 5') - Initiator tRNA (=tRNA.fMET) =\> carries the first amino acid fMET (formyl methiomine)=\>recognizes AUG 2. Elongation mRNA is read from 5'-3' -\>synthesizing the polypeptide chain from amino terminus (N-terminus) to carboxyl terminus (C-terminus) -\>elongation factors are bound to tRNA after correct amino acid is attached - Codon recognition: aminoacyl tRNA with specific amino acid enters the ribosome-\>A-site. Ribosome=\>correct base pairing between anti-codon tRNA and codon mRNA - Peptide bond formation: P-site=\>adjacent amino acids form peptide bonds The bond between t RNA and amino acid is broken down first, then the amino acid is attached to the adjacent amino acid (still in the A-site, connected to its tRNA ) by a peptide bond. (catalyzed by peptidyl transferase) - Translocation: ribosome moves 1 codon at a time. Shifts from P-\>A-site and the uncharged tRNA goes to EXIT-site. ! requires activity of OTHER protein elongation factor EF-G - EF-TU-GTP complex binds to ribosome, GTP is hydrolyzed, translocation occurs 3. Termination - RF1 (recognizes the stop codons: UAA, UAG) and RF2 (recognizes: UAA, UGA) bind to stop codon-\>triggers peptidyl transferase to split from the polypeptide in P-site. - RF3- GDP binds to ribosome =\>release of RF from stop codon and ribosome -\>GDP-\>GTP, RF3 hydrolyses the GTP-\>RF3 detaches from ribosome. - RRF (ribosome recycling factor)-\>mimics tRNA-\> binds to A-site, next EF-G binds -\>translocation of ribosome=\>RRF to P-site and last uncharged tRNA to the E-site-\>release of tRNA, EF-G-\>releases RRF=\> two subunits ribosome dissociate from mRNA =\>can bind to another mRNA *[3 steps of translation in eukaryotes]* 1. Initiation ! 2 main differences = NO Shine-Dalgarno sequences, 1^st^ amino acid is MET instead of fMET. - Eukaryotic initiator factor (eIF-4E) binds to 5'cap, end of mRNA - Scanning model for initiation (leaky scanning): 40S subunit + MET-tRNA + multiple eIF proteins + GTP binds and moves along the Mrna=\>scan to find start codon AUG (embedded in Kozak sequence) - 40S finds start codon=\>binds +60S binds (replaces eIF's, except for eIF-4F)=\>production of 80S initiation complex - Initiator MET-tRNA: bound to mRNA, in P-site ribosomes - Poly-A tail: PABPII (poly A binding protein II)=\>binds to eIF-4G in 5'cap=\>3' loops close to 5' 2. Elongation mRNA is read from 5'-3' -\>synthesizing the polypeptide chain from amino terminus (N-terminus) to carboxyl terminus (C-terminus) -\>elongation factors are bound to tRNA after correct amino acid is attached - Codon recognition: aminoacyl t RNA with specific amino acid enters the ribosome-\>A-site. Ribosome=\>correct base pairing between anti-codon tRNA and codon mRNA - Peptide bond formation: P-site=\>adjacent amino acids form peptide bonds The bond between t RNA and amino acid is broken down first, then the amino acid is attached to the adjacent amino acid (still in the A-site, connected to its tRNA ) by a peptide bond. (catalyzed by peptidyl transferase) - Translocation: ribosome moves 1 codon at a time. Shifts from P-\>A-site and the uncharged tRNA goes to EXIT-site. 3. Termination - STOP-codon is signaled (UAG, UAA, UGA) - Code for no amino acid-\> no tRNA has a anti-codon for them - Ribosome-\>recognizes stop-codon with help of RF (releasing factor) *[Polysomes ]* = multiple ribosomes translate 1 strand of m RNA at the same time =\>efficient protein synthesis (both in prokaryotes and eukaryotes)  *[Prokaryotic vs. Eukaryotic Translation: ]* - **Prokaryotes**: Translation can begin even before transcription is complete due to the lack of a nucleus.  - **Place of transcription** :  - In prokaryotes, transcription (DNA to RNA) and translation (RNA to protein) occur in the same compartment, the **cytoplasm**. Since there is no nucleus to separate these two processes, the ribosomes can immediately begin translating the newly synthesized mRNA, even before RNA polymerase finishes transcribing the full mRNA strand.  - **Coupled Transcription and Translation**:  - **Coupling** means that as the mRNA is being transcribed by RNA polymerase, ribosomes can bind to the 5\' end of the growing mRNA chain and begin translation almost simultaneously. This efficiency allows prokaryotic cells to quickly respond to environmental changes by synthesizing proteins as soon as their genes are transcribed.  - **Polysomes**:  - Prokaryotes often use **polysomes**, where multiple ribosomes simultaneously translate a single mRNA strand. This further speeds up the process of protein synthesis.  - **Eukaryotes**: Transcription occurs in the nucleus, and translation occurs in the cytoplasm. The mRNA undergoes processing (capping, splicing, polyadenylation) before translation Afbeelding met tekst, schermopname, Lettertype, nummer Automatisch gegenereerde beschrijving **Post-translational modifications** =\>increase the functional diversity of the proteosome (covalent adding functional groups, proteolytic cleavage of regulatory subunits or degradation of the entire protein) Sorts of modifications: - Phosphorylation - Glycosylation - Ubiquitination - Ubiquitin (polypeptide chain) = marker - Proteasome (the 'protein shredder') - 3 enzymes: E1 (activating ubiquitin), E2 (ubiquitin conjugating enzyme) , E3 (ubiquitin ligase) 1. Ubiquitin bind to E1 (use of ATP) 2. E3-\> binds to protein and E2 3. E1 and E2 bind 4. Ubiquitin is transferred from E1 to E2 5. Then, transferred to the target protein 6. E1 unbinds from E2 and binds to new ubiquitin 7. Ubiquitinated proteins are recognized by the proteasome and degraded (ATP needed) =.stability of many proteins is determined how strong they are ubiquitinated =\>ubiquitin is reusable - Nitrosylation =Ubiquitous PTM (adding a nitrosyl group to a protein= marking) =important part of cell-signaling - Methylation - Acetylation - Lipidation - Proteolysis **Protein synthesis regulation** =\>major protein synthesis regulators are: availability of mRNA, amount/activity ribosomes, initiation factors and elongation factors - **Transcriptional regulation**: Genes can be turned on or off based on signals from the environment or cell cycle.  - **Nonsense-mediated mRNA decay:** eliminating transcripts that contain early STOP-codons - **mRNA stability**: The lifespan of an mRNA molecule can affect how much protein is made.  - **Translation regulation**: Factors such as **microRNAs** can inhibit or promote translation.  - **Post-translational regulation**: Protein activity can be regulated by post-translational modifications like phosphorylation or ubiquitination.  - **Environmental changes :** basic environment = - charge, acidic environment = + charge