Unit 1 - Nuclei acids, the genetic code and protein synthesis

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Evidence for the structure of DNA

Many observations contributed to the evidence from which the structure of DNA was eventually deduced

1. Chemical Analysis, 2. Chargaff’s work on base equivalence, 3. Franklin and Wilkins’ work on X-ray crystallography

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The structure of RNA

->Ribonucleic acid >is also a polynucleotide. The chain of nucleotides is formed in exactly the same way as in DNA, but the molecule has some very important differences:1. It is a single stranded molecule, 2. The pyrimidine Thymine never occurs

2. but is always replaced by Uracil, another pyrimidine. (Think "No cup of T for U!"), 3. It is much smaller than DNA., 4. It comes in three different forms, ribosomal, transfer and messenger.

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The Strucure of DNA

->is a polymer of nucleotides or in more detail of deoxyribonucleotides.

DNA is a macromolecule polymer made of subunits called nucleotides. The nucleotides are arranged in two chains which are coiled into a spiral shape called a double helix.

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Nucleotides are made up of:

1. a phosphate. 2. a sugar - deoxyribose., 3. a base - either adenine, guanine, thymine or cytosine.

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Double Helix

2 chains which are coiled into a spiral shape (part of DNA).->held together by hydrogen bonds between complementary bases (base pairs->ie. Purine<->Pyrimidine)

=>(In DNA adenine can only pair with thymine=>adenine<->thymine and guanine<->cytosine)->chains are anti-parallel (10 base pairs in complete turn of helix)

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DNA Replication

Since DNA forms the genetic code and that it is known that genes may be inherited, it follows that DNA must be copied exactly before being incorporated into gametes at meiosis.

It also follows that all new cells in an organism must gain a copy of the genes at mitosis, because they are able to continue the characteristic biochemical behaviour of that organism.

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DNA and Protein Synthesis

DNA is the molecule which controls the synthesis of proteins. Proteins are used for growth and repair and also as enzymes, in which form they catalyse all other cellular activities.

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DNA

=>blueprint->a macromolecule polymer made of subunits called nucleotides. The nucleotides are arranged in two chains which are coiled into a spiral shape called a double helix

->is the molecule which controls the synthesis of proteins.->DNA is able to exert a controlling influence over the whole cell and ultimately, the whole organism. The segments of DNA which hold the key to this control are the genes

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Proteins

=>machines made from blueprint (DNA) instructions (RNA)->are used for growth and repair and also as enzymes, in which form they catalyse all other cellular activities.

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enzymes

form they catalyse all other cellular activities.

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ein Synthesis

relies on the effective communication of the coded information held in the genes to the sites of protein manufacture, the ribosomes in the cytoplasm.

Since DNA is part of larger structures (chromosomes), which are unable to move from the nucleus, intermediate messenger molecules are needed. These are messenger RNA molecules.

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Ribosomal RNA

is 80% of the total RNA in a cell. It is involved with the formation of ribosomes and is therefore important as the site of protein synthesis in a cell.

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Messenger RNA

is 3-5% of the total RNA in a cell, depending on the protein synthesis activity at the time. It forms in the nucleus and is used to communicate the genetic code in the allele to the ribosome during protein synthesis

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Transfer RNA is

is a clover leaf shaped molecule and is up to 15% of the total RNA in the cell. It is involved in carrying the amino acids through the cytoplasm to their correct places in a growing polypeptide chain

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phosphodiester bond.

a sugar-phosphate-sugar bond is called a

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polynucleotide

Each time the sugar joins to a phosphate, a molecule of water is eliminated in a condensation reaction.->This sugar-phosphate-sugar bond is called a phosphodiester bond.

The process repeats so that a very long chain of nucleotides is made, a

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antiparallel

In DNA a second polynucleotide chain forms next to the first, but this runs in the opposite direction. The chains are therefore described as antiparallel

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What were the 3 theories for the mechanism for this exact copying or replication of the DNA?

1.fragmentation theory->parent DNA molecule breaks into segments & new nucleotides fill gaps precisely 2.Conservative hypothesis->Complete parent DNA M. acts as a template for new daughter M. which is assembled from new nucleotides->parent M.->unchanged

3. Semi-conservative hypothesis->The parent DNA molecule separates into its two component strands, each of which acts as a template for the formation of a new complementary strand. The two daughter molecules therefore contain half the parent DNA and half

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The semi conservative hypothesis

The semi conservative hypothesis was shown to be the true mechanism by the work of Meselsohn and Stahl->

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cistron

A cistron is the shortest length of DNA that can code for a whole polypeptide.

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Nucleic Acids

are macromolecule involved in the storage /transfer of genetic information. ->they are built up of mononucleotide->Any of the organic compounds making up the genetic material of living cells.->

Nucleic acids direct the course of protein synthesis, thereby regulating all cell activities. ->The two main types are, DNA and RNA->Both are long chains of repeating nucleotides.

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Mononucleotide is made up of

1. a pentose (5-carbon sugar), 2. an organic nitrogenous base, 3. 3. phosphoric acid

-> a further condensation reaction between the nucleoside and phosphoric acid produces a mononucleotide

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Nucleotide

Any of a class of organic compounds, including the structural units of nucleic acids.->Each consists of a nucleoside and one or more phosphate groups. In nucleic acids, the phosphate of one nucleotide joins to the sugar of the next to form the backbone.

Important nucleotides that are not part of nucleic acids include ATP, cyclic AMP (needed in glycogen breakdown), and certain coenzymes

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Sugars

Sugars (whose names end in -ose) are the simplest carbohydrates. The most common is sucrose, a disaccharide; there are numerous others, including glucose and fructose (both monosaccharides);

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carbohydrate

Any member of a very abundant and widespread class of natural organic compounds that includes sugars, starch, and cellulose->

They are commonly classified as monosaccharides (simple sugars; e.g., glucose, fructose), disaccharides (2-unit sugars; e.g., sucrose, lactose), oligosaccharides (3–10 or so sugars), and polysaccharides (large molecules with up to 10,000 monosaccharide un

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monosaccharide

Any of the simple sugars that serve as building blocks for carbohydrates.->They are classified based on their backbone of carbon (C) atoms: Trioses have three carbon atoms, tetroses four, pentoses five, hexoses six, and heptoses seven.

Monosaccharides combine with each other and other groups to form a variety of disaccharides, polysaccharides, and other carbohydrates.

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hydroxyl groups

(-OH)

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carbonyl group

(-C=O)

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isomer

One of two or more substances with identical molecular formulas but different configurations, differing only in the arrangement of their component atoms.

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Important hexoses include

glucose, galactose, and fructose.

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Nucleoside

Each consists) and a nitrogen-containing base->

Nucleosides usually have a phosphate group attached, forming nucleotides.->Usually obtained by decomposition of nucleic acids, nucleosides are important in physiological an of a molecule of a five-carbon sugar (ribose in RNA, deoxyribosed medical research

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Ester

Any of a class of organic compounds that can react with water (see hydrolysis) to produce an alcohol and an organic or inorganic acid.

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DNA Polymerase

is an enzyme which catalyses polymerisation of the polynucleotide chains, but it can work only whe the chain is built up in the 5' to 3' direction. (not in the 3' to 5' direction)

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DNA ligase

is another enzyme which joins together short replicated sections of the original polynucleotide chains. -> if this process is completed along hte lenght of the molecule->2 identical 'daugher' molecules are formed.(each being an exact copy of orig double h

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Polymer

Each strand is a long chain

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Purine

Any of a class of heterocyclic compounds with a DOUBLE-RING (two-ring) structure composed of carbon and nitrogen atoms.->The simplest member, purine itself (C5H4N4), is not common, but its derivatives with the structure are

ie. two of the nucleotides in nucleic acids, GUANINE and ADENNE=>are presented in both types of nucleotides (RNA & DNA)

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heterocyclic compound

Any of a class of organic compounds whose molecules contain one or more rings of atoms with at least one atom (the heteroatom) being an element other than carbon-> it may include single, double, or triple bonds and contain one or more single ring

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Pyrimidines

Any of a class of heterocyclic compounds with a ring structure of four carbon and two nitrogen atoms->The simplest member, pyrimidine itself (C4H4N2), is not common, but derivatives with the structure are

ie. 3 of the bases in nucleic acids->CYTOSINE (present in both nucleotides DNA & RNA), THYMINE(->DNA)and URACIL(->RNA).

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How is a dinucleotide formed?

when a condensation reaction occurs between the phosphate group of one nucleotide and the pentose of another.

(->more nucleotides can be added ->building a long polynucleotides chain.

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Phosphodieseter bonds

link the nucleotides togehter (those bonds are covalent and contribute to the stability of the polynucleotide)

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DNA Replication

->is called 'semi-conservative replication' bcs each newly formed double helix contains one of the polynucleotide chains of the original double helix.

->observations have shown that double helix opens up at a number of different sites->known as replication forks->to speed up the process as it would take to long otherwise.

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Gene

is a small section of the DNA->and each chromosome contains 1000ds of genes. ->the only parts of the nucleotides that vary are the BASES->info must be coded by their types/sequences along polynucleotides.

DEFINITION: as the sequence of nucleotide pairs along a DNA molecule that codes for an RNA of polypeptide product.

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Chromosome

Microscopic, threadlike part of a cell that carries hereditary information in the form of genes.->Every species has a characteristic number of chromosomes; humans have 23 pairs

Human chromosomes consist primarily of DNA

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Codon

is a sequence of 3 nucleotide bases (a base triplet) on the messenger RNA (mRNA) which codes for a specific amino acid.

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Why is the genetic code described as degenerate?

because the number of amino acids is less than the number of codons, ie. a specific amino acid may be coded for by more than one codon

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Protein synthesis

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How does Ribonucleid acid (RNA) differ from DNA?

1. it is a single stranded molecule, 2. it contains the pentose ribose instead of deoxyribose, 3. the base thymine is replaced by uracil (thymine<->uracil)

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Ribose

Five-carbon sugar found in RNA

The ribose of one nucleotide joins with the phosphate of the next to form the RNA backbone.

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There are 3 different types of RNA present in cells:

1. messenger RNA (mRNA), 2. Ribosomal RNA (rRNA), 3. Transfer RNA (tRNA)

they are all involved in some way with the synthesis of proteins

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Synthesis

The artificial building up of a chemical compound, by the union of its elements or from other suitable starting materials.

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mRNA

->Messenger RNA->is formed in the nucleus during the process of transcription and carries the instructions from the DNA to the ribosomes

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rRNA

->Ribosomal RNA-> is a component of the ribosomes on which the polypeptide chains are built up

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tRNA

->Transfer RNA->is present in the cytoplasm adn picks up amino acids and transports them to the ribosomes for assembly into polypeptides

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Transcription

Synthesis of RNA by RNA polymerases using a DNA template.->.->the process in which mRNA is synthesised from the info carried on the DNA template->the codes is copied

the organic process whereby the DNA sequence in a gene is copied into mRNA; the process whereby a base sequence of messenger RNA is synthesized on a template of complementary DNA.->The formation of RNA from a DNA template

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Coding strand

only 1 of the DNA strand (of the double helix) acts as a coding strand (template) and is copied by base pairing of nucleotides

(->Base pairing leads to the formation of a DNA double helix from two complementary single strands)

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Base pairing

->leads to the formation of a DNA double helix from two complementary single strands.

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RNA

A nucleic acid found in all living cells. Plays a role in transferring information from DNA to the protein-forming system of the cell.

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exons

coding regions->Coding regions of messenger RNA included in the genetic transcript which survive the processing of RNA in cell nuclei to become part of a spliced messenger of structural RNA in the cytoplasm.

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Introns

Non-coding, intervening sequences of DNA that are transcribed, but are removed from within the primary gene transcript and rapidly degraded during maturation of messenger RNA. most genes in the nuclei of eukaryotes contain introns

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Translation

the process in which the information carried on thmRNA is used on the synthesis of a polypeptide chain. The base sequence of hte mRNA determines the sequence of amino acids in the polypeptide

the process whereby the genetic code carried by mRNA is read and used to construct proteins->carried out by ribosomes

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Anticodon

a triplet of 3 exposed nucleotides on a tRNA molecule. These nucleotides are complementary to those of a spedific codon on the mRNA.

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Transcription

-> information from DNA passed to RNA->(part of protein synthesis) involves the transfer of the coded info from the nucleus to the cytoplasm.Occurs in Nucleus

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Cytoplasm

Portion of a eukaryotic cell outside the nucleus.->

(it contains all the organelles, including mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, lysosomes, and peroxisomes.

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Translation

->information from RNA used to make protein->the converstion of teh coded inromation into polypeptides on the ribosomes.

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Ribosomes

Small cellular components composed of specialised ribosomal RNA and ribonucleic acid (RNA).

the cellular organelle responsible for translating mRNA into protein. Eukaryotic ribosomes are complexes of specialized RNA species and numerous proteins

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Amino Acids

Organic compounds that generally contain an amino (-nh2) and a carboxyl (-cooh) group. Twenty alpha-amino acids are the subunits which are polymerised to form proteins.

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Protein Synthesis

involves the transfer of coded info from nucleus to cytoplasm & the conversion of info into polypeptides on the ribosomes.

A process where information is taken from DNA to acts as a blue print for creating a particular protein that is in demand by the body. This blueprint will allow the construction of the protein with the various materials required in its production.

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How do cells make proteins?

For a cell to make protein, the information from a gene is copied, base by base, from DNA into new strands of messenger RNA (mRNA). Then mRNA travels out of the nucleus into the cytoplasm, to cell organelles called ribosomes. There, mRNA directs the assem

of amino acids that fold into completed protein molecule.-> pic see->www.accessexcellence.org/AE/AEPC/NIH/gene03.html &h=250&w=492&sz=33&tbnid=GQNC6G0OR3kJ:&tbnh=64&tb nw=127&hl=de&start=8&prev=/images%3Fq%3Drna%2B% 26svnum%3D10%26hl%3Dde%26lr%3D

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Introns

Genes that contain regions that do not code for amino acids. These regions are called introns.

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Exons

are the coding regions inside genes. (during transcription)

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RNA

->carries instructions from the blueprint (DNA)->- Nucleic acid (like DNA), -Single stranded (not like DNA), -Ribose instead of deoxyribose (not like DNA), -Adenine, Guanine, and Cytosine bases (like DNA), -Uracil instead of Thymine (not like DNA)

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So when the cell needs a job done it:

-Gets instructions from DNA, 2. -Sends instructions through dispatcher (RNA), 3. -Machinery makes the right protein for the job, 4. -Protein performs its function inside or outside of cell

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What is the Genetic Code?

1.-Each gene contains a specific sequence of nucleotides, 2. -Every three nucleotides (a codon) code for one amino acid, 3. -Code is unambiguous, 4. -Code is degenerate , 5. -Code is (almost) universal, - The code is based on the messenger RNA, NOT DNA

1. - DNA gene sequence is transcribed to form messenger RNA, 2. -Complementary base pairing means RNA sequence = DNA sequence, 3. - Protein-making machine (ribosome) reads messenger RNA sequence, 4, -Carriers bring the amino acids to the ribosome by base

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A Codon

Every three nucleotides

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The Human Genom

the genome consists of all teh genes in teh chromosomes of an individual

The Human Genom Project has the aim to identify all genes in Human DNA , mapping positions of genes on chr. & determ. sequence of base pairs along rDNA.

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Chromosomes

The self-replicating genetic structures of cells containing the cellular DNA that bears in its proteins.

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Gene

Unit of heredity that occupies a fixed position on a chromosome.

Each gene has a specific position and sequence on the chromosome.

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Errant Genes

cause diseases-> ie. Alzheimer was discovered on chromosome 1, 14 and 21.

->medical implications are that diagnosis of cert. diseases cld be easier as well as prediction of disease onset, as well as treatment by gene therapy (replacing def. genes or supplement with other genes for prevention

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What are some of the ethical, legal and social issues arising from the human genom project?

1. ownership of personal genetic info , who should have access to it are concerns, 2. advantage of knowledge of gene. desieases are possib. of treatment but if info is used wrongly or without permission ->c oncern,

3. some genetic tests are reliable but what about newer techniques? how reliable? what about interpretation?

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*Analysis of a molecule of DNA showed that cytosine accounted for 42% of the content of the nitrogenous bases. Calculate the % of bases in the molecule which would be thymine. Show your working.

Total % of C + G = 84% therefore T will be (100 - 84) / 2=> 8%

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* During the processes of transcription, one of the DNA strands os used as a template for the formation of a complementary strand of messenger RNA (mRNA). See diagram in book, p. 93, write the letters of the complementar bases in the boxes of the mRNA str

CGA / AGU / ACG

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* Describe the role of messenger RNA (mRNA) in the folowing processes. -> Transcription:

(mRNA) is a copy of DNA->(Copy of) part of DNA/eq->(Copy of) one strand->mRNA is complementary (to DNA)->mRNA made up of complementary bases->

mRNA strand, built/formed (looking for idea that mRNA strand is put together during the process)/ref to enzyme->Carries genetic code to cytoplasm/out of nucleus/to ribosome

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* Describe the role of messenger RNA (mRNA) in the folowing processes. -> Translation:

Genetic info/base sequence/code->in mRNA determines amino acid sequence->Codons/base triplet on mRNA ->determines amino acid->

(Codons) pair with COMPLEMENTARY triplet/anticodon->on tRNA-> ref to start/stop codons/sequences/binding sequences->occurs on ribosomes

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*Is Cytosine present in DNA / mRNA?

is present in DNA as well as mRNA

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*Is Uracil present in DNA / mRNA?

is only present in mRNA

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*Is Pentose sugar present in DNA / mRNA?

is present in DNA as well as mRNA

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*Is single stranded present in DNA / mRNA?

is only present in mRNA

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* Describe how Enzyme A separates the 2 DNA strands in a double strand of DNA to form 2 separated strands in a semi-conservative replication of DNA .

It breaks the hydrogen bonds between the 2 strands.

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* Give the phase of the cell cycle during which DNA replication occurs.

Interphase/S phase/synthesis phase

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