17-12-2021, 06:45 PM
(This post was last modified: 17-12-2021, 06:58 PM by MichelleL11.
Edit Reason: the inevitable typos
)
Before I begin review of the various articles out there in biocodicology it makes sense to establish some underlying biological information that is needed to understand each of the articles.
Each of the techniques that are going to be discussed measure and describe molecules present in living cells and in materials made from cells that were once living. The chemical structure details aren’t necessarily important, although a tiny bit of an introduction as to what these chemicals do in the cell will help clarify some of the techniques’ challenges.
The techniques measure and characterize either nucleic acids or proteins. All cells are basically protein factories. Proteins are the building blocks and machinery of the body. Proteins are made of strings of chemicals called amino acids. The amino acids determine how the protein "folds" and there by determines its shape and function in the cell. You are not allowed to view links. Register or Login to view. is some more high level information about proteins. Deoxyribonucleic acid (DNA) can be considered the blueprint for how to make the proteins because it encodes instructions as to what amino acids and in what order are needed to make the proteins. It is also called hereditary material because copies of the DNA are passed from cell to cell during growth (and from parent to child organism during reproduction). Importantly, DNA is found both inside the nucleus (relatively large, central membrane bound area) of the cell but also in mitochondria, which are smaller, also membrane bound areas within the cell, where energy is produced.
DNA is found in a double helix structure (twisted ladder -- also called "double stranded"). Down the ladder there are only 4 choices of information inputs (called “bases or nucleotides”) and it is this identity/order of these strings of nucleotides that provide the information for making the protein. The bases pair in a consistent way to form the rungs of the ladder. If you break the molecule down the middle of the “rungs” you have two copies of the same information, because the rung bases always pair with the same complementary base on the other side of the ladder (called a “base pair”). You are not allowed to view links. Register or Login to view. is a cartoon illustration of this.
One type of ribonucleic acid (RNA) found in the cell is an intermediary between the DNA and the protein production machinery. Unlike DNA, RNA has only one side of the ladder (also called "single stranded"). It is called messenger RNA because it provides a copy of the blueprint “message” from the DNA that is transported to the part of the cell where the protein production happens. Note that the RNA sequence is a copy of the DNA sequence because complementary base pairing “copy method” is used here. The DNA “unzips” and RNA bases are paired to form a single strand copy. You are not allowed to view links. Register or Login to view. is a cartoon illustration of this.
The primary characterization of DNA or RNA or protein is determining the precise order of the bases or amino acids. This process is called sequencing. The precise sequences found are what provide the unique signatures that allow DNA or RNA or protein to be identified as originating from a particular organism.
However, it is important to understand that for relatively close evolutionary relationships the vast, vast majority of DNA, RNA, and protein sequences are the same no matter what organism it comes from. This makes differentiating between relatively close relationships (such as any mammal from any other mammal – sheep from cow from goat from human) a relatively difficult task. This becomes even more difficult when trying to differentiate between even more closely related sources such as one sheep breed from another sheep breed. In many cases, the differentiating aspects between DNA or RNA or protein sequences of one breed from another are simply not known. Figuring out these “differentiation” hot spots (and separating these information carrying results from random noise errors that are an inevitable part of any sequencing process and may look like “differentiation”) is a very challenging part of the applicability of these tests.
Note that parchment contains all of these molecules in greatly varying amounts. It is mostly protein -- namely one kind of protein, collagen, a basic building block of skin. But DNA and RNA are present as well. Also note that time degrades all of these molecules making it progressly harder to determine the sequences. The rate of degradation depends heavily on (1) what is present in the sample, which involves how it was produced (e.g. processing contamination) and how it was handled (e.g. environmental contamination); and (2) the material storage conditions. I'll be discussing how this relates to parchment in future reviews.
Cheatsheet
Protein Building Block Amino Acids Variety of folded structures
RNA Messenger Nucleotide bases Single Strand
DNA Blueprint Nucleotide bases Double Helix
Each of the techniques that are going to be discussed measure and describe molecules present in living cells and in materials made from cells that were once living. The chemical structure details aren’t necessarily important, although a tiny bit of an introduction as to what these chemicals do in the cell will help clarify some of the techniques’ challenges.
The techniques measure and characterize either nucleic acids or proteins. All cells are basically protein factories. Proteins are the building blocks and machinery of the body. Proteins are made of strings of chemicals called amino acids. The amino acids determine how the protein "folds" and there by determines its shape and function in the cell. You are not allowed to view links. Register or Login to view. is some more high level information about proteins. Deoxyribonucleic acid (DNA) can be considered the blueprint for how to make the proteins because it encodes instructions as to what amino acids and in what order are needed to make the proteins. It is also called hereditary material because copies of the DNA are passed from cell to cell during growth (and from parent to child organism during reproduction). Importantly, DNA is found both inside the nucleus (relatively large, central membrane bound area) of the cell but also in mitochondria, which are smaller, also membrane bound areas within the cell, where energy is produced.
DNA is found in a double helix structure (twisted ladder -- also called "double stranded"). Down the ladder there are only 4 choices of information inputs (called “bases or nucleotides”) and it is this identity/order of these strings of nucleotides that provide the information for making the protein. The bases pair in a consistent way to form the rungs of the ladder. If you break the molecule down the middle of the “rungs” you have two copies of the same information, because the rung bases always pair with the same complementary base on the other side of the ladder (called a “base pair”). You are not allowed to view links. Register or Login to view. is a cartoon illustration of this.
One type of ribonucleic acid (RNA) found in the cell is an intermediary between the DNA and the protein production machinery. Unlike DNA, RNA has only one side of the ladder (also called "single stranded"). It is called messenger RNA because it provides a copy of the blueprint “message” from the DNA that is transported to the part of the cell where the protein production happens. Note that the RNA sequence is a copy of the DNA sequence because complementary base pairing “copy method” is used here. The DNA “unzips” and RNA bases are paired to form a single strand copy. You are not allowed to view links. Register or Login to view. is a cartoon illustration of this.
The primary characterization of DNA or RNA or protein is determining the precise order of the bases or amino acids. This process is called sequencing. The precise sequences found are what provide the unique signatures that allow DNA or RNA or protein to be identified as originating from a particular organism.
However, it is important to understand that for relatively close evolutionary relationships the vast, vast majority of DNA, RNA, and protein sequences are the same no matter what organism it comes from. This makes differentiating between relatively close relationships (such as any mammal from any other mammal – sheep from cow from goat from human) a relatively difficult task. This becomes even more difficult when trying to differentiate between even more closely related sources such as one sheep breed from another sheep breed. In many cases, the differentiating aspects between DNA or RNA or protein sequences of one breed from another are simply not known. Figuring out these “differentiation” hot spots (and separating these information carrying results from random noise errors that are an inevitable part of any sequencing process and may look like “differentiation”) is a very challenging part of the applicability of these tests.
Note that parchment contains all of these molecules in greatly varying amounts. It is mostly protein -- namely one kind of protein, collagen, a basic building block of skin. But DNA and RNA are present as well. Also note that time degrades all of these molecules making it progressly harder to determine the sequences. The rate of degradation depends heavily on (1) what is present in the sample, which involves how it was produced (e.g. processing contamination) and how it was handled (e.g. environmental contamination); and (2) the material storage conditions. I'll be discussing how this relates to parchment in future reviews.
Cheatsheet
Protein Building Block Amino Acids Variety of folded structures
RNA Messenger Nucleotide bases Single Strand
DNA Blueprint Nucleotide bases Double Helix
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