WEDNESDAY, FEBRUARY 14, 2007

AUG are always the start codons. Each codon is one amino acid and is made up of three bases. There are 20 amino acids, but there are multiple condons for each amino acid. Posted by Olivia & Carolat 5:52 PM42 comments Translation

What is it? DNA translation converts the mRNA sequence into amino acids that form protiens. This creates most of the protiens that make up cells. It creates the last step from DNA to a protien. Wher does it occur? Translation occurs outside the nucleas also known as in the cytoplasm. Eventhough this is true one article suggests that translation can occur inside the nucleas. Click here to see. When does it occur? Translation occurs right after transcription is done and the mRNA is transported out of the nucleas. How does it Happen? During DNA translation, messenger RNA, transfer RNA, and ribosomes work together to produce proteins. A ribosomal subunit attaches to a mRNA molecule. The Transfer-RNA transports the amino

acid from the cytoplasm to the ribosome. The start codon attaches to Met this starts making the protein. Posted by Olivia & Carolat 5:19 PM0 comments

What is it? The DNA Transcription is the process of building RNA copy of a DNA sequence. Where does it occur? It occurs in the nucleus of the cell. When does it happen? It occurs after DNA replication. How does it happen? 1. The gene sequence is copied into messenger RNA (mRNA) - The mRNA is single stranded and has 4 nucleotide like DNA, but instead of Thymine (T) it has Uracil (U). - Transcription continues until one entire gene has been converted to RNA. 2. After Transcription the whole mRNA strand is transported out of the nucleus to the cytoplasm. 3. In the cytoplasm, the mRNA strand is translated into an amino acid. Posted by Olivia & Carolat 5:09 PM0 comments TUESDAY, FEBRUARY 13, 2007 DNA Replication What is it? DNA Replication is a process used to copy chromosomes inside the nucleas of a cell before the cell divides. Where does it occur? This process occurs inside the cell's nucleas.

When does it Happen? The Replication of DNA occurs when before the cell can divide. How Does it Happen? 1.DNA Replication begins with one double strand of DNA. 2.The Double strand helix is partially unwound by SSB Protiens and helicases into what is known as a replication fork. 3.As the two DNA strands unzip the run in anti-parallel directions. 4. DNA polymerase moves into position at the point where synthesis will begin. But since the Polymerase can only move from 5' to 3' direction the strands will replicate differently. 5.In the leading strand the Primase lays down the RNA primer. 6.Now the the RNA primer had been laid down Polymerase III builds a second strand in the same direction that the double helix is being opened. 7. In the remaining gaps more RNA primers attach yeilding Okazki Fragments (lagging strands) 8. RNA Primer stripped away DNA polymerase replaces with DNA nucleotides. 9. Ligase "glues" the remaining gaps in the sugar-phosphate backbone.

What is protein synthesis? Inside the cell Protein synthesis is the transcription and translation of specific parts of DNA to form proteins. The following is a brief overview of how a gene (a section of the DNA molecule) serves as a template for the synthesis of a protein. The process can be split into two phases. Transcription occurs first, followed by translation. Heredity and reproduction

Image: K.G. Murti, Visuals Unlimited, Inc. DNA replication fork.

In this section: Animal cell organelles From cell to gene Proteins What is protein synthesis? We are all mutants

Transcription Transcription starts with an enzyme called polymerase copying the DNA sequence to a similar molecule called messenger RNA (mRNA). It replaces T with U (Uracil), a helper base, making it clear that the mRNA is a copy. The bases (A, T, G, C) on one strand of the DNA specify the order of bases on the new strand of mRNA (A, U, G, C). The DNA stays inside the nucleus, but the mRNA travels out into the cytoplasm. Translation Translation is the part of protein synthesis where the ribosomes in the cytoplasm use transfer RNA (tRNA) to attach to the mRNA and translate the bases into amino acids. tRNA molecules bring the specified amino acids that the ribosome links together to make a protein.

Can you synthesize a protein faster than a cell?

(1.6 Mb Shockwave)

The Genetic Code The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon. One codon, AUG serves two related functions:

Index to this page

The RNA Codons The DNA Codons Codon Bias Exceptions to the Code

it signals the start of translation it codes for the incorporation of the amino acid methionine (Met) into the growing polypeptide chain

The genetic code can be expressed as either RNA codons or DNA codons. RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation). But each mRNA molecule acquires its sequence of nucleotides by transcription from the corresponding gene. Because DNA sequencing has become so rapid and because most genes are now being discovered at the level of DNA before they are discovered as mRNA or as a protein product, it is extremely useful to have a table of codons expressed as DNA. So here are both. Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second nucleotide, and the last column gives the third nucleotide. The RNA Codons Second nucleotide U UUU Phenylalanine (Phe) UUC Phe U UUA Leucine (Leu) UUG Leu CUU Leucine (Leu) C CUC Leu CUA Leu UCA Ser UCG Ser CCU Proline (Pro) CCC Pro CCA Pro UAA STOP UAG STOP CAU Histidine (His) CAC His CAA Glutamine (Gln) UGA STOP A C UCU Serine (Ser) UCC Ser A UAU Tyrosine (Tyr) UAC Tyr G UGU Cysteine (Cys) UGC Cys U C

UGG Tryptophan (Trp) G CGU Arginine (Arg) CGC Arg CGA Arg U C A

CUG Leu AUU Isoleucine (Ile) AUC Ile A AUA Ile AUG Methionine (Met) or START GUU Valine Val GUC (Val) G GUA Val GUG Val

CCG Pro

CAG Gln

CGG Arg

G U C A G

ACU Threonine (Thr) AAU Asparagine (Asn) AGU Serine (Ser) ACC Thr ACA Thr ACG Thr AAC Asn AAA Lysine (Lys) AAG Lys GAU Aspartic acid (Asp) GAC Asp GAA Glutamic acid (Glu) GAG Glu AGC Ser AGA Arginine (Arg) AGG Arg

GCU Alanine (Ala) GCC Ala GCA Ala GCG Ala

GGU Glycine (Gly) GGC Gly GGA Gly GGG Gly

U C A G

The DNA Codons These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of DNA (3' to 5') as the template. [Discussion] This table could well be called the Rosetta Stone of life. The Genetic Code (DNA) TTT Phe TTC Phe TTA Leu TTG Leu CTT Leu TCT Ser TAT Tyr TCC Ser TAC Tyr TGT Cys TGC Cys

TCA Ser TAA STOP TGA STOP TCG Ser TAG STOP TGG Trp CCT Pro CAT His CGT Arg

CTC Leu CTA Leu CTG Leu ATT Ile ATC Ile ATA Ile

CCC Pro CAC His CCA Pro CAA Gln CCG Pro CAG Gln ACT Thr AAT Asn ACC Thr AAC Asn ACA Thr AAA Lys

CGC Arg CGA Arg CGG Arg AGT Ser AGC Ser AGA Arg AGG Arg GGT Gly GGC Gly GGA Gly GGG Gly

ATG Met* ACG Thr AAG Lys GTT Val GTC Val GTA Val GTG Val GCT Ala GAT Asp GCC Ala GAC Asp GCA Ala GAA Glu GCG Ala GAG Glu

*When within gene; at beginning of gene, ATG signals start of translation. Codon Bias All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different codons. However, the genome of most organisms reveals that certain codons are preferred over others. In humans, for example, alanine is encoded by GCC four times as often as by GCG. This probably reflects a greater translation efficiency by the translation apparatus (e.g., ribosomes) for certain codons over their synonyms. [More] Exceptions to the Code The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. However, some exceptions have been found. Most of these involve assigning one or two of the three STOP codons to an amino acid instead. Mitochondrial genes When mitochondrial mRNA from animals or microorganisms (but not from plants) is placed in a test tube with the cytosolic protein-synthesizing machinery (amino acids, enzymes, tRNAs, ribosomes) it fails to be translated into a protein.

The reason: these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic machinery, synthesis stops where Trp should have been inserted. In addition, most

animal mitochondria use AUA for methionine not isoleucine and all vertebrate mitochondria use AGA and AGG as chain terminators. Yeast mitochondria assign all codons beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).

Plant mitochondria use the universal code, and this has permitted angiosperms to transfer mitochondrial genes to their nucleus with great ease. Link to discussion of mitochondrial genes.

Nuclear genes Violations of the universal code are far rarer for nuclear genes. A few unicellular eukaryotes have been found that use one or two (of their three) STOP codons for amino acids instead. Nonstandard Amino Acids The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically altered, e.g. by phosphorylation, at a later time. However, two cases have been found where an amino acid that is not one of the standard 20 is inserted by a tRNA into the growing polypeptide.

selenocysteine. This amino acid is encoded by UGA. UGA is still used as a chain terminator, but the translation machinery is able to discriminate when a UGA codon should be used for selenocysteine rather than STOP. This codon usage has been found in certain Archaea, eubacteria, and animals (humans synthesize 25 different proteins containing selenium). pyrrolysine. In several species of Archaea and bacteria, this amino acid is encoded by UAG. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known.

Basics of Genetics

Genetics is the scientific study of how living organisms pass on their features from one generation to the next. This word was invented in 1906 by the British biologist William Bateson. Since the discovery of the genetic code in 1966, research into this view has broadened our understanding of the structure of life, and in controlling protein production in modern biology and biotechnology. Chromosomes, DNA and Genes Every one of us, except identical twins or clones, has a unique set of DNA, or a genome, which in part is what makes us separate individuals. Inside each of our cells nuclei, we have 23 pairs of chromosomes, and one in each pair is inherited from one of our parents. The threadlike chromosomes contain all our genetic information. DNA (deoxyribonucleic acid) molecules make up most of a chromosome and are the genetic material for all cellular organisms and most viruses. They act as the message carriers of chemical sequences governing the production of proteins. Such patterns are the genes, and all together they make up the blueprint of life. DNA has the spiral shape of the famous double helix. Like a ladder, it consists of two strands made up of sugars and phosphate groups, connected with base pairs (the rungs). There are four nucleotide bases, andadenine (A) will only combine with thymine (T); cytosine (C) always with guanine (G). Such base pairing means that the two strands are complementary. (e.g. the complementary strand of A-A-G would be T-T-C). DNA strands has a beginning and an end. One side has a phosphate, and is called the 5 end, while the other side without the phosphate is the 3 end. Each strand goes in opposite directions, i.e. they are antiparallel. These (the bases) letters of the DNA alphabet arrange themselves in DNA and RNA in three-letter-words, called codons. Codons instruct the cell into the production of specific amino acids, which form into proteins, the basic material of life. Click for a diagram of the DNA structure In a human cell, each DNA molecule contains about 3 billion base pairs, or genes, paving the way for countless genetic instruction groups. Scientists define a gene as the discrete instructions for making a single protein. In detail, a gene is the DNA sequence encoding a protein; starting with a start codon and ending with a stop codon. RNA and central dogma

RNA, another nucleic acid commonly found in the cytoplasm, is a ribonucleic acid sequence created from DNA, and is nearly identical to one of the strands of DNA. This is the strand of DNA that serves as a template to both its own replication and also the production of messenger RNA (mRNA), the process of which is known as transcription. The only difference between mRNA and the template DNA is that in kRibonucleic Acid, thymine is replace by uracil. RNA is produced from DNA by an enzyme called RNA polymerase. The mRNA moves from the nucleus to the ribosome of the cell. Translation, the synthesis of proteins from mRNA, will then occur in the ribosome. The transfer RNA (tRNA) binds the specific amino acids to the corresponding codons. The ribosome helps bind the amino acids into a chain and a protein is formed.