Nucleotides and Nucleic Acid 2.3

Transcription Stage 1

-RNA polymerase attaches to the DNA double helix at the start of a gene. -The h bonds between the two strands in the gene break separating them and the DNA molecule uncoils at this point. -One of these strands is used as a template strand to make an RNA copy.

Transcription Stage 3

-The RNA polymerase moves along the DNA separating strands and assembling the mRNA strand. -The h bonds between the uncoiled strands of DNA reform and coil back into a double helix.

Translation Stage 1

-The mRNA attaches itself to a ribosome and transfer RNA (tRNA) molecules carry amino acids to the ribosomes. -A tRNA molecule with an anticodon that's complementary to the start codon on the mRNA attaches itself to the mRNA by complementary base pairing. -A second tRNA molecule attaches itself to the next codon on the mRNA in the same way.

Transcription Stage 2

-The polymerase lines up free RNA nucleotides alongside the template strand. Complementary base pairs means the mRNA is a complementary copy of the template strand. T is replaced by U. -When they have paired up, they join together forming an mRNA molecule.

Translation Stage 3

-The process continues producing a chain of linked amino acids (polypeptide chain) until there's a stop codon on the mRNA molecule. -The polypeptide chain moves away from the ribosome and translation is complete.

Transcription Stage 4

-When RNA polymerase reaches a stop codon, it stops making mRNA and detaches from DNA. -mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm.

Translation Stage 2

-rRNA in the ribosome catalyses the formation of a peptide bond between the two amino acids attached to the tRNA molecules. -The first tRNA moves away moves away leaving its amino acid behind. -A 3rd tRNA molecules binds to the next codon on the mRNA . Its amino acid binds to the first two and the second tRNA molecules moves away.

Purifying DNA

1) Break up cells in sample e.g. blending 2) Make up solution of detergent, salt and distilled water. 3) Add cells to a beaker containing solution. Heat it in a water bath at 60° for 15 mins. 4) Put in an ice bath to cools and filter the mixture. Transfer to a boiling tube. 5) Add protease enzyme and RNase enzyme to filtered mixture. 6) Slowly add cold ethanol down the side of the tube so it forms a layer on top of the mixture. 7) DNA will form a white precipitate that can be removed with a glass rod.

Self-Replication

1. DNA helicase breaks the H bonds between the two polynucleotides. The helix unzips. 2. Each single strand acts as a template for a new strand. Free-floating nucleotides join to the exposed bases by complementary base pairing. 3. The nucleotides of the new strand are joined together by DNA Polymerase forming the sugar-phosphate backbone. H-bonds form between bases on the new and original strand. They twist to form a double helix. 4. Each new molecule of DNA contains a strand from the original DNA molecule and one new strand

Replication Fork

A Y-shaped point that results when the two strands of a DNA double helix separate so that the DNA molecule can be replicated

Nucleotide bonding

A phosphate group is linked to either the C5 (carbon atom 5) or C3 (carbon atom 3) of the sugar by covalent bonds formed by condensation reactions. (Phosphodiester Bond).

Codon

A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid

Purine Bases

Adenine and Guanine. Contain two two carbon-nitrogen rings.(double ring)

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

ATP and ADP

Both ADP and ATP are phosphorylated nucleotides. Phosphorylate=add phosphate groups to it. ADP-contains adenine, a sugar ribose and two phosphate groups. ATP-adenine, ribose and three phosphate groups. ATP provides energy for chemical reactions in the cell. It's synthesised from ADP and inorganic phosphate (P) using the energy from an energy releasing reaction. The ADP is phosphorylated into ATP and a phosphate bond is formed. Energy's stored in the phosphate bond and when it's needed the ATP is broken back down into ADP and inorganic phosphate. This releases the energy for the cell to use.

Pyrimidine Bases

Cytosine and Thymine. Only has one carbon-nitrogen ring so is smaller (single ring).

The sugar in DNA

DEOXYRIBOSE Each nucleotide has the same sugar and a phosphate group but the base can vary. Four bases are Adenine, Thymine, Cytosine, Guanine A molecule of DNA contains two polynucleotide chains.

Purifying DNA - Why are these conditions used?

Detergent-Breaks down cell membranes Salt-Binds to DNA and makes it clump together 60°-Stops enzymes in cells from breaking down DNA Protease enzymes-Break down protein. E.g. proteins bound to the DNA. RNase enzymes-Breaks down any RNA in the mixture.

Phosphodiester bonds

Form between the phosphate group of one nucleotide and the sugar of another. In a condensation reaction.

Ribosomal RNA (rRNA)

Forms the two subunits in a ribosome. The ribosomes move along the mRNA strand during protein synthesis and helps it to catalyse the formation of peptide bonds between the amino acids.

Transfer RNA (tRNA)

Found in the cytoplasm Has an amino acid biding site at one end and a sequence of three bases at the other called an anticodon. Carried the amino acids that are used to make protein to the ribosomes during translation.

Anticodon

Group of three bases on a tRNA molecule that are complementary to the three bases of a codon of mRNA

Semi-conservative replication

Half of the strands in each new DNA molecule are from the original piece of DNA.

Molecular Structure of Nucleotides

Made from: -A pentose sugar -A nitrogenous base -A phosphate group All contain the elements C, H, O, N and P They are the monomers that make up DNA and RNA. ATP and ADP are special types of nucleotides

Messenger RNA (mRNA)

Made in nucleus 3 adjacent bases are called a codon Carries the genetic code from the DNA in the nucleus to the cytoplasm where it's used to make a protein during translation. Used because RNA is too large to leave the nucleus.

Polynucleotides

Nucleotides join up between the phosphate of one nucleotide and the sugar of another by phosphodiester bond. They can be broken down again by breaking the phosphodiester bond.

DNA Polymerase

Only works in the 3' to 5' direction.

Okazaki Fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

The lagging strand

The strand which runs in the 5' to 3' direction toward the fork Replicated discontinuously in Okazaki fragments

Antiparallel

The 5' end of the molecule is where the phosphate group is attached to the fifth carbon atom of the deoxyribose sugar. The 3' end is where the phosphate group is attached to the third carbon atom of the deoxyribose sugar.

Sugar-phosphate backbone

The chain of sugars and phosphates in a polynucleotide.

Transcription

The process of making RNA from a DNA template. Takes place in the nucleus The first stage of protein synthesis.

Translation

The second stage of protein synthesis Occurs at the ribosomes in the cytoplasm. Amino acids are joined together to forma polypeptide chain, following the sequencing of codons carried by the mRNA.

The leading strand

The strand of DNA which runs in the 3' to 5' direction toward the fork Able to be replicated continuously by DNA polymerase

The sugar in RNA

The sugar is RIBOSE Also has a phosphate group and four different bases. But has uracil instead of thymine. A RNA molecule is made up of a single polynucleotide chain.

DNA ligase

This enzyme is in charge of "gluing" together Okazaki fragments

The genetic code

Triplet code-3 bases=1amino acid. Universal-used in all organisms. Degenerate-More than one code for some amino acid. 64 options and only 20 amino acids. Non overlapping-reads 3 then the next 3. Has start and stop codes to finish a polypeptide.

Double Helix

Two polynucleotides joined together by hydrogen bonding between the bases. Each base bonds with the corresponding complementary base pair. 2 Hydrogen Bonds with A & T 3 Hydrogen Bonds with C & G Antiparallel.