Chapter 12

Triplet

A sequence of 3 bases

Anticodon

A sequence of three nucleotides on tRNA complementary to the codon in mRNA *********************************** ▪ let's start with the drawings at the right hand side that depicts a messenger RNA structure ▪ let's take a look at the circled area called a codon... within the circled area there are three nucleotides - PSC is one nucleotide, then - PSG and PSA ▪ P = phosphate, S = sugar, and the varying C,G,A in orange represent those varying bases ▪ P and S do not change, they just serve as the backbone structure for messenger RNA ▪ In that one codon there are three bases.. so one codon contains one triplet ▪ if messenger RNA contains any information, that info must be hidden in that base sequence bc P and S do not change ▪ so the varying sequence of bases must represent the hidden info that the mRNA brings into the kitchen area/ribosome

Bases

Adenine (A) , Guanine (G) Cytosine (C), Thymine (T) → only for DNA, Uracil (U) → only for RNA DNA has A, G, C, & T ← no U RNA ha A, G, C & U ← no T

The Chemistry of Heredity - What are we made of? (3)

All genetic information is stored in the nucleus of the millions of cells in the body. Each nucleus contains chromosomes, 46 compact structures of intertwined molecules of DNA, and about 30,000 genes, components that convey one or more hereditary traits. DNA is a special template written in a molecular code on a tightly coiled thread that carries all genetic information.

DNA analogy

DNA is analogous to a cookbook that contains many recipes to make meals. DNA makes not meals (of course!) but proteins.

What makes up DNA? (3)

DNA is made of fundamental chemical units, repeated over and over. Each unit is composed of three parts: nitrogen-containing bases, the sugar deoxyribose, and phosphate groups. Adenine (A), Guanine (G), Cytosine (C), and Thymine (T) are the bases.

Complementary Base Pairs

DNA to DNA (Replication) A -- T, G -- C, T -- A, C -- G DNA to RNA (Transcription) A -- U, G -- C, T -- A, C -- G NOT A -- T! Because RNA does not have T! ********************************* ▪ we learned the copying of DNA/cookbook during replication, or the copying of DNA to RNA during transcription ▪ all these copying processes are a little different from copying something using xerox machine ▪ when copying of DNA molecule is taking place, a base copies onto another base, it doesn't copy onto the same base - so if you look at the top portion , base A copies to base T, G to C, T to A, and C to G - these are called complementary base pairs - they have to follow that complementary pairing role ▪ now if you look at the bottom, when we copy DNA to RNA during transcription, the base A copies to U, and so on

Nucleotide (2)

Each nucleotide consists of the three components: base, phosphate, and sugar. A sequence of three nucleotides thus contains the sequence of three bases.

Alpha helix and beta conformation - secondary structure

Most proteins contain one or more stretches of amino acids that give rise to a characteristic three dimensional structure. The most common of these are the alpha helix and the beta conformation. The telephone cord illustrates the nature of the secondary structure of the protein.

Proteins

Proteins are made of amino acids. The general formula for an amino acid includes four groups attached to a carbon atom: (1) a carboxylic acid group, -COOH; (2) an amine group, -NH2; (3) a hydrogen atom, -H; and (4) a side chain designated as R:

Tertiary structure

Tertiary structure refers to the three-dimensional structure of the entire polypeptide.

Cracking the Chemical Code

The 3 billion base pairs in each human cell provide the blueprint for producing a human being. The specific sequence of base pairing is important in conveying the mechanism of how genetic information is expressed. The expression is seen through proteins. Through directing the synthesis of proteins, DNA can control the characteristics of an individual, including inherited illnesses

Human Genome Project

The Human Genome Project is the effort to map all the genes in the human organism. On June 26, 2000, scientists announced that a rough draft of the project to decode the genetic makeup of humans had been completed. The goal, to determine the sequence of all 3 billion base pairs in the entire genome, was completed for the approximately 30,000 genes found on the 46 human chromosomes. This information might one day help to diagnose and cure diseases, understand human development, and trace our evolutionary roots. This was a unique collaboration between government, private sector, and a philanthropic organization.

tRNA

The RNA that transports amino acids to the site of protein synthesis in ribosomes.

Function od a protein

The function of a protein is dependent on its shape or three-dimensional structure. Small changes in the primary structure can have dramatic effects on its properties. Sickle cell anemia is an example of a condition that develops when red blood cells take on distorted shapes due to an error in the amino acid sequence. Because these cells lose their normal shape, they cannot pass through tiny openings in the spleen and other organs. Some of the sickled cells are destroyed and anemia results. Other sickled cells can clog organs so badly that the blood supply to them is reduced.

Chimera

The mythical creature chimera represents a combination of a lion, a goat, and a serpent. Recombinant DNA is sometimes referred to as a chimera.

Codons: How are they relevant in genetic expression?

The order of bases in DNA determines the order of amino acids in a protein. Because there are 20 amino acids present in the proteins, the DNA code must contain 20 code "words"; each word represents a different amino acid. The genetic code is written in groupings of three DNA bases, called codons. The diagram shows possible codons, determined according to the base sequence of the nucleic acid strand. The expression of the genetic information is then seen through the specific proteins assigned.

Primary Structure (2)

The primary structure of a protein is its linear sequence of amino acids and the location of any disulfide (-S-S-) bridges. The sequence is characterized by the amino terminal or "N-terminal" (NH3+) at one end; and the carboxyl terminal or "C-terminal" (COO-) at the other.

Transcription

The process in which information encoded in a DNA molecule is copied into a (mRNA) molecule.

The Double Helix of DNA

X-Ray Diffraction pattern of a hydrated DNA molecule taken in 1952. This technique uses the fact that a molecule's electrons diffract X-Rays at particular angles and the resulting pattern, like the one above, can be used to solve the structure of a crystal Using Rosalind Franklin's X-ray diffraction data, Watson and Crick proposed a molecular model for DNA. This model had a double strand of repeating nucleotides. Complementary base pairing (AT, CG) is held in place by hydrogen bonds (shown in red). The nature of the base pairing required that the two strands be coiled in the shape of a double helix..

DNA analogy

express = cook amino acid = food ingredient mRNA = messenger

Gene analogy (3)

▪ A gene, a segment of DNA, is analogous to a specific recipe in the cookbook. ▪ Thus each gene makes a specific protein. ▪ Each gene is made of building blocks called nucleotides.

What does a segment of DNA look like? (3)

▪ A typical DNA molecule consists of thousands of nucleotides covalently bonded in a long chain. ▪ The phosphate groups are responsible for linking each nucleotide. ▪ A phosphate group of one nucleotide reacts with an -OH group present on the deoxyribose ring of another nucleotide, forming and eliminating a H2O molecule.

Chargaff's Rules (4)

▪ Erwin Chargaff's research showed that for all humans, the percentage of adenine in DNA is almost identical to the percentage of thymine. ▪ Similarly, the percentages of guanine and cytosine are almost equal. ▪ From this, Chargaff concluded that the bases always come in pairs; adenine is always associated with thymine and guanine is always associated with cytosine. *Thus, Chargaff's rule states: %A = %T and %G = %C*

Learning Objectives

▪ How does genetics work? ▪ What are the basic features of DNA and the DNA double helix? ▪ What are the primary, secondary, and tertiary structures of proteins? ▪ How are the processes of genetic engineering? ▪ What is genetic modification and can we and/or should we control the chemistry of life through genetic engineering?

DNA Replication (3)

▪ The original DNA double helix partially unwinds and the two complementary portions separate. ▪ Each of the strands serves as a template for the synthesis of a complementary strand. ▪ The result is two complete and identical DNA molecules.

Nucleotide P + S + B

▪ here we have a structure of a DNA molecule consisting of the sequence of nucleotides ▪ at the top, the circle is one nucleotide ▪ with your imagination you can circle three more, so in this picture there is a total of four nucleotides in this molecule ▪ each nucleotide has three subcomponents ▪ P = phosphate(yellow), connected to sugar in pentagon shape, connected to base in hexagon shape ▪ among those subcomponents, phosphate and sugar, you cannot tell any difference, those are all the same in each nucleotide ▪ so those two , phosphate in yellow and sugar in hexagon constitute the backbone structure in DNA molecule, that backbone is shaded in blue ▪ so the only difference you can see among the nucleotides is the sequence of those bases ▪ at the top you have Thymine (T), then Adenine (A), Cytosine (C), and Guanine (G) ▪ SO the sequence of those bases determines specific DNA molecule ▪ if you look at the sugar in pentoagon shape again, that sugar is deoxyribose , and you can find number two and number 3... ▪ if you compare 2 and 3 at the bottom most, at number 2, at the bottom, there's no oxygen , just H, whereas at #3 you have OH ▪ since that #2 does not have oxygen, they call this sugar deoxy, meaning not having oxygen ▪ so the sugar in this pentagon shape is deoxyribose, that tells apart DNA from the structure of RNA

Structure for P S B

▪ here we have the structure for those three components of a nucleotide ▪ first column, phosphate, second column, sugars ▪ the first sugar on the top is deoxyribose, and the bottom one is ribose - if we compare those two, the only difference occurs at #2 (the above one) just has H, no O - the bottom one has OH - we call the top one deoxy, bc it has no oxygen ▪ now at the last column on the right hand side, there you have structures of the 5 bases ▪ A,G,C you can find in both ▪ T you can only find in DNA ▪ U you can only find in RNA

Genetic Code

▪ let's take a look at the column on the far right hand side, where you have a sketch of mRNA ▪ that contains 3 codons as we saw in the previous slide ▪ so if you look at the first codon at the top, there's a triplet, a sequence of 3 bases, CGA, that specific base sequence, is identified to that specific matching amino acid by this table as you can see on the left hand side ▪ so if you look at the CGA in that table, it says arginine , so that codon carries the info for amino acid arginine ▪ this table is called the genetic code ▪ so in this table, each sequence of a triplet is identified to a specific amino acid ▪ so you can identify the next codon triplet AUA, by looking it up

DNA or RNA are nucleic acids which are polymers

▪ since DNA and RNA are polymers, each must consist of a building block called a monomer ▪ in this case, the monomer is called nucleotide ▪ each nucleotide has 3 subcomponents ▪ B = base , S = sugar, P = phosphate ▪ if you look at the DNA structure in the middle, again since it's a polymer, it has a sequence of building blocks (the nucleotide) ▪ same manner for RNA, building blocks are nucleotides, B+S+P and so on - how can we tell those two molecules apart? - bc DNA has different sugar than RNA - DNA has deoxyribose whereas RNA has just ribose

Protein Synthesis

▪ so at ribosome proteins are synthesized, just like in the kitchen, meals are cooked ▪ so tRNA brings those amino acids identified by the codons ▪ so here you put down the amino acids ... if all of those amino acids are connected, then that makes a protein ▪ a protein is a sequence of amino acids, which means that is a polymer

Replication DNA and double helix

▪ this slide shows the structure of DNA, what they call the double helix ▪ if you look at the left hand side, there you can see the double strands of the DNA molecule, this is the structure you can see during replication, or the copying of DNA/cookbook to another cookbook ▪ if we take a look at the magnified version of the middle portion to the right, there you see one DNA molecule copies to another DNA molecule ▪ if you compare those rectangular areas shaded blue, those are the backbones of DNA molecules, that contain phosphate in yellow, and sugar in pentagon shape ▪ the backbones are exactly copied, however, if you look at the bases in between those two rectangles, they're not exactly the same, starting from the top base G copies to base C and so on

Intro to molecular genetics

▪ we often hear terms like DNA , genes, or gene, but we don't often know their exact meanings ▪ Analogies to help explain: - DNA is a cookbook that contains recipes - gene = a recipe in that cookbook - genes = recipes ▪ we use a cookbook and recipes to make a meal in the same manner that our body uses a gene and we express that gene ▪ express = cooking ▪ using genes we make proteins

Nucleotides

A combination of a base, phosphate group, and a deoxyribose sugar is a nucleotide.

Replication

A process by which copies of DNA are made during cell division.

Genetic Terminology - gene

Gene The unit of heredity; a DNA segment that codes for one protein A segment of a DNA molecules carries the sequence of bases that directs the synthesis of one particular protein. ***************************** gene = recipe within a cookbook that sequence of bases contains all the information to synthesize one specific protein

mRNA

The RNA that carries genetic information from DNA to the ribosome and acts as a template for protein synthesis

Translation

The process in which information encoded in an mRNA is used to assemble a specific protein *************************** ▪ replication = the copies of the cookbook ▪ the cookbook gets delivered by the mRNA , and after it's delivered it needs to be translated bc ribosome cannot understand that cookbook ▪ after the translation we are ready to make proteins

Two amino acids can link together via a peptide bond:

The process may repeat itself over and over, creating a peptide chain. Once incorporated into the peptide chain, the amino acids are known as amino acid residues.

What codes amino acids? (3)

The sequence of three bases codes one amino acid. The sequence of, say, 30 bases then can code 10 amino acids. From the combination of the 10 amino acids can then be synthesized a protein molecule.

Codon

The sequence of three nucleotides in messenger RNA (mRNA) that codes for a specific amino acid