Chapter 11: DNA Biology

The Three Phases of Translation

1. Initiation 2. Elongation Cycle 3. Termination

Chargaff's Rules

1. The amount of A, T, G, and C in DNA varies from species to species. 2. In each species, the amounts of A and T are equal (A=T), as are the amounts of G and C (G=C)

Initiation

1. The small ribosomal subunit attaches to the mRNA molecule in the vicinity of the start codon (AUG/methionine). 2. The anticodon of the initiator tRNA-methionine complex pairs with this codon. 3. The large ribosomal subunit joins to the small subunit.

Elongation Cycle

1. The tRNA molecule at the P site contains the growing polypeptide chain. 2. This tRNA passes its peptide to tRNA-amino acid at the A site. The tRNA at the P site enters the E site. 3. During translocation, the tRNA-peptide moves to the P site, the empty tRNA in the E site exits the ribosome, and the codon at the A site is ready for the next tRNA-amino acid. This is repeated at a very fast rate and the outgoing tRNA is recycled to pick up another amino acid in the cytoplasm to take to the ribosome.

P Binding Site

A binding site in ribosomes for a tRNA molecule attached to a peptide. P for peptide

A Binding Site

A binding site in ribosomes for a tRNA molecule attached to an amino acid. A for amino acid

Stop Codons

A codon that signals the end of a polypeptide. See the card above.

What is an anticodon?

A group of three bases found in tRNA that is complementary to a specific codon of mRNA.

Guanine

A purine with a double ring, binds to cytosine.

Adenine

A purine with a double ring. It binds to thymine in DNA, and binds to uracil in RNA.

Thymine

A pyrimidine with a single ring, binds to adenine and is only present in the DNA molecule.

Cytosine

A pyrimidine with a single ring, binds to guanine.

What is a DNA promoter

A region of DNA with a special nucleotide sequence that marks the beginning of a gene. See term 31.

Triplet Code

A sequence of three bases in an RNA molecule (the four available being adenine, cytosine, guanine, and uracil), codes for one amino acid. There are 64 different combinations but only 22 different amino acids.

E site

A site in ribosomes where tRNA molecules exit. E for exit.

Transcription

A strand of RNA forms that is complementary to a portion of DNA. All three classes of RNA are formed in this step.

Hydrogen Bonds (reminder)

A weak bond between two molecules resulting from an electrostatic attraction between the proton in one molecule and an electronegative atom in another. Since the bond is so weak, this is ideal for DNA replication and RNA synthesis.

What makes up a nucleotide?

All nucleotides contain phosphate, a five-carbon sugar, and a nitrogen containing base.

mRNA is processed

Before the new primary mRNA molecule can leave the nucleus, it must be processed so that it can be properly used. There are three steps: 1. Capping- the cap is composed of an altered guanine nucleotide. 2.The addition of a poly-A tail- on the 3' end, enzymes add a poly-A tail, a series of adenosine nucleotides. Only mRNA molecules that have a cap and a tail are considered stabilized and remain active in the cell. 3. Splicing- Introns are removed and exons are spliced together. The mRNA molecule is now called a mature mRNA molecule. See numbers 34 and 35

DNA Structure

DNA is a double stranded molecule that wraps around itself to form a double helix. The two strands are anti-parallel and run in opposite directions. Each strand has a 5' end where a free phosphate group appears and a 3' end where where a free OH group appears.

The flow of genetic information

DNA to RNA to protein

DNA

Deoxyribonucleic Acid. A molecule that appears as a double helix with a repeating pattern. It is made up of two sugar-phosphate backbones and nitrogenous bases bonded together by hydrogen bonds. Provides genetic instructions.

tRNA takes amino acids to the ribosomes

Each tRNA is a single-stranded nucleic acid that doubles back on itself to form complementary base pairing. There is at least one tRNA molecule for each amino acid. The amino acid binds to one end of the molecule. The opposite end of the molecule contains an anticodon. When a tRNA amino acid comes to a ribosome, its anticodon pairs with an mRNA codon. Afterward translation is done, a protein contains the sequence of amino acids originally specified by DNA.

What are codons?

Each three-base unit of an mRNA molecule is called a codon, and codes for a single amino acid. Sixty-one codons correspond to a particular amino acid while the remaining three code are stop codons that signal the end of a polypeptide.

Amino acids have one codon.

False. Most amino acids have more than one codon, this protects against mutation in the event that a single base changes. That single base may not make a difference if the codon still codes for that particular amino acid.

Gene Expression

Genes specify proteins and gene expression has occurred when the protein it specifies is functioning in the cell.

Complementary Base Pairing

The nitrogenous bases that make up the "rungs" of the DNA ladder (adenine to thymine, guanine to cytosine) are bonded together via hydrogen bonds.

Messenger RNA (mRNA)

Produced in the nucleus of a eukaryotic cell, DNA serves as the template for this molecule during a process called transcription. Once formed, mRNA carries genetic information from DNA to the ribosomes in the cytoplasm, where protein synthesis occurs through a process called translation.

What is a polypeptide?

Protein. Peptide bonds bond amino acids to make proteins. "Poly"-Many "Peptides"-Peptide bonds.

Uracil

Replaces the thymine found in DNA, present in RNA

RNA

Ribonucleic Acid. The four nucleotides that make up the RNA molecule are Adenine, Guanine, Cytosine, and Uracil. Unlike DNA, RNA is single-stranded and sometimes doubles back on itself, allowing complementary base pairing to occur. Allows protein synthesis to occur according to the instructions DNA provides.

Ribosomal RNA

Ribosomal RNA is produced in the nucleolus of the cell, where a portion of DNA serves as a template. Ribosomal RNA joins with proteins made in the cytoplasm to form the subunits of ribosomes, one large and one small (remember that they are subunits rather than the whole ribosome). The subunits then leave the nucleus and come together in the cytoplasm when protein synthesis is about to begin.

Ribosomes are the site of protein synthesis

Ribosomes have a binding site for mRNA as well as binding sites for two tRNA molecules at a time. These binding sites facilitate complementary base pairing between tRNA anticodons and mRNA codons. The P binding site is for a tRNA molecule attached to a peptide, the A binding site is for a newly arrived tRNA molecule attached to an amino acid, and the E site is for tRNA molecules exiting the ribosome.

What is an intron?

Segments of DNA in a gene that do not code for a protein. See number 32

Termination

Termination occurs when a stop codon appears at the A site. The polypeptide and the assembled components that carried out protein synthesis are separated from each other. 1. A protein called a release factor binds to the stop codon and cleaves the polypeptide from the last tRNA. 2. The mRNA, ribosomes, and tRNA molecules can then be used in another round of translation.

What is a peptide bond?

The carboxyl group of one molecule interacts with the amino group of another molecule. This releases an H2O molecule and is known as a dehydration reaction. Usually occurs between amino acids to synthesize a protein molecule.

Start Codon

The codon that stands for the amino acid methionine signals the initiation of translation and is written in triplet code as AUG.

DNA Ligase

The enzyme that seals together any breaks in the sugar phosphate backbone of the DNA molecule that occurred during replication.

DNA Polymerase

The enzyme that synthesizes the new DNA strand. The complementary base pairs pair together and "zip shut" the DNA molecule.

Helicase

The enzyme that unwinds the DNA helix and breaks the hydrogen bonds holding the complementary base pairs together, to prepare for DNA replication.

DNA Replication (step 1)

The hydrogen bonds between the nucleotides are broken, and the helix begins to unwind thanks to an enzyme called helicase. New nucleotides, ever present in the nucleus, pair to the now single stranded DNA molecule. DNA polymerase (an enzyme) is responsible for synthesizing the new DNA strand and runs in a 5'-3' direction. Breaks in the sugar-phosphate ladder are sealed by DNA ligase.

What is an exon?

The other portions of a gene contain the protein coding regions of the gene. See number 32

DNA Replication

The process of making an identical copy of a DNA molecule. Occurs during the "S" phase of the cell. Two DNA strands are separated and each old strand of the original molecule serves as a template for a new strand

Overview of Translation

The second step by which gene expression leads to protein synthesis. Requires several enzymes and all three types of RNA.

What are the two processes of gene expression?

Transcription and Translation

mRNA Formation

Transcription begins when the enzyme RNA polymerase (not to be confused with DNA polymerase) binds tightly to a promoter, a region of DNA with a special nucleotide sequence that marks the beginning of a gene. RNA polymerase opens up the DNA helix so that complementary base pairing can occur. Then the enzyme adds new RNA nucleotides that are complementary to those is the DNA strand. A new mRNA molecule has been made.

Transfer RNA (tRNA)

Transfer RNA is produced in the nucleus of a eukaryotic cell. It transfers amino acids present in the cytoplasm to the ribosomes. There are 22 (although 2 are fairly new, and it should be noted that some teachers may want you to answer 20 on their tests) different amino acids, and each has its own tRNA molecule. At the ribosome, a process called translation joins the amino acids to form a polypeptide chain.

Genes specify all proteins, not just enzymes.

True

In eukaryotes, transcription takes place in the nucleus, and translation takes place in the cytoplasm.

True