- Oct 2023
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bio.libretexts.org bio.libretexts.org
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ribosome serves as the enzyme that mediates the dehydration synthesis reactions required to build protein molecules, whereas a class of enzymes called proteases is required for protein hydrolysis.
Ribosome removes the water molecule ( dehydration).
Proteases ( Adds water ) (Hydrolysis)
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ophile) in a nucleophilic substitution reaction. The activation reaction, which we will discuss in subsequent chapters involves the transfer of a phosphate from a phosphoanhydride, ATP, to the carboxylic acid group to
Nuclphile substation is adding a nucliphile then changing is location . 2 steps/
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Proteins are polymers of amino acids that fold into shapes that confer function on the proteins. In biological systems, the amino acids are linked together by a large ribonucleic acid/protein nanoparticle called the ribosome
Proteins are polymers of amino acids that fold into shapes that can have a different functions. The ribosome linked the nuclacic acids to make specific protein.
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bio.libretexts.org bio.libretexts.org
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some pH, then, the net charge will be 0. This pH is called the isoelectric point (pI). The pI can be determined by averaging the pKa values of the two groups which are closest to and straddle the pI. One of the online problems will address this in more detail
At some ph the overall charge of the protein becomes 0 net charge . That is called the isoelectric point (pI)
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A look at the titration curve for the carboxyl group of Gly (see above) shows that when the pH = pKa, the slope of the curve (i.e. the change in pH on addition of base or acid) is at a minimum. As a general rule of thumb, buffer solutions can be made for a weak acid/base in the range of +/- 1 pH unit from the pKa of the weak acids. At the pH = pKa, the buffer solution best resists the addition of either acid or base, and hence has its greatest buffering ability. The weak acid can react with the added strong base to form the weak conjugate base, and the conjugate base can react with added strong acid to form the weak acid (as shown below) so pH changes on the addition of strong acid and base are minimized. addition of a strong base produces a weak conjugate base: CH3CO2H + OH- ↔ CH3CO2- + H2O addition of strong acid produces weak acid: H3O+ + CH3CO2 → CH3CO2H + H2O
Buffer solution is made with +or-1 ph unit of the weak acid from the PH=PK . This allows for variations to occur and these can be motnitered. Which makes it the best resists to acid or base.
Weak acid + Strong base = weak conjugate base. That conjugated base + strong acid= weak acid.
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All naturally occurring amino acids in proteins are L, which corresponds to the S isomer
L correspond to S , D correspond to R.
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Again, the d- and l-designations are specific terms used for the way a molecule rotates plane-polarized light. It does not denote the absolute stereo configuration of a molecule. An absolute configuration refers to the spatial arrangement of the atoms of a chiral molecular entity (or group) and its modern stereochemical description e.g. R or S, referring to Rectus, or Sinister,
L and D for light reflection , Absolute configuration refers to the spatial arrangements of the atoms of a chiral molecule.
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All naturally occurring proteins from all living organisms consist of L amino acids, based on their structural similarities to L-glyceraldehyde.
All natural occurring proteins consist of L . Hmmm a lot of things in the universe are counter clock wise . Very interesting.
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The amino acids are all chiral, with the exception of glycine,
All amino acids are chiral except for glycine, whose side chain is H.
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a thioether functional group which generally cannot form a permanent dipole within the molecule and retains low solubility.
Look up a thither functional group. These can't make permanent dipole with the molecule and retains low solidity.
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present in tyrosine increase its reactivity and solubility compared to that of phenylalanine.
They have different rate of reaction and solubility.
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e aromatic amino acids (phenylalanine, tyrosine, and tryptophan
These contain aromatic functional groups
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aliphatic amino acids (glycine, alanine, valine, leucine, isoleucine, and proline) typically contain branched hydrocarbon chains with the simplest being glycine to the more complicated structures of leucine and valine.
Aliphatic amino acids contain branched hydrocarbons. This is important lol ... Glycin is the simplest one !!!!
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ers through a nucleophilic attack by the amino group of an amino acid at the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH-. The resulting link between the amino acids is an amide link which biochemists call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by water (hydrolysis). This is illustrated in Figure 3.1.33.1.3\PageIndex{3}.
Amino acids are linked through the peptide bond(When this happen the H2O is kicked out to make for space for connection. The oppitste happen in hyrdolysis.
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hey are not the result of selective cleavage of a larger protein into smaller peptide fragments.
smORFs are special , I think they are made with a process that is more of a closed system compared to the regular amino acids of adding water and removing water.
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These are encoded directly in the genome and are produced by the same processes that produce regular proteins
They are included int in the genome that's why they are in the DNA transcription process and RNA translation process. Same location. Can environment have an effect on creation?
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called smORFs
Produced in the same process DNA transcription and RNA translation.
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tructure is long enough
When the chain is long enough and can function we can call it a protein
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amide link
The carbonyl carbon-to-nitrogen bond
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nucleic acids are polymers of just 4 different monomeric nucleotides
Nucleotides are polymers which are made out of 4 different monomeric nucleotides.
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Proteins are polymers of twenty naturally occurring amino acids
amino acids make proteins. Different amino acids attached to each other equals different function which that equals different proteins.
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The R group side chains may be either nonpolar, polar and uncharged, or charged, depending on the functional group, the pH, and the pKa of any ionizable group in the side chain.
Depending on the R group the R group side chains can be either non polar, polar, uncharged or charged. This depends on the functional group , the ph and the pka of any ioniczable group in the side chain.
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The alpha designation is used to indicate that these two functional groups are separated from one another by one carbon group
the little a you see means that it is a carbon which is between the amino acid and the amine. Holds both of them . Figure 3.1.1
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he major building blocks of proteins are called alpha (α) amino acids. As their name implies they contain a carboxylic acid functional group and an amine functional group.
Alpha amino acid implies that they are made out of carboxylic acid functional group and amine functional group.
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Their structures, like their functions, vary greatly. They are all, however, polymers of alpha amino acids, arranged in a linear sequence and connected together by covalent bonds.
Proteins are polymers of alpha amino acids, arranged in a linear sequence and connected together by covalent bonds.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules.
Proteins are the most abundant molecule , it's organic . It has diverse functions which means diverse structures.
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