Honors Biology

DNARNAProteins

REVIEW! What is DNA?Deoxyribonucleic Acid (DNA)

Monomers made up of nucleotides:Nucleotides consist of:

A five carbon sugar, deoxyriboseo Four in it’s ring, one extending above the ringo Missing one oxygen when compared to ribose

Phosphate groupo Is the source of the “acid” in nucleic acid

Nitrogenous base (Adenine, Guanine, Cytosine, Thymine)o A ring consisting of nitrogen and carbon atoms with

various functional groups attached o Double ring= purines (A and G)o Single ring= pyrimidines (T and C)

Double helix consists of:Sugar-phosphate backbone held by covalent bondsNitrogen bases are hydrogen bonded together; A pairs with T

and C pairs with G

REVIEW! Nucleotides

Protein synthesis: overviewDNA inherited by an organism specifies traits

by dictating the synthesis of proteins.However, a gene does not build a protein

directly; it dispatches instruction in the form of RNA, which in turn programs protein synthesis.

Message from DNA in the nucleus of the cell is sent on RNA to protein synthesis in the cytoplasm.

Two main stages: TranscriptionTranslation

Protein Synthesis: OverviewTwo main stages:

TranscriptionThe transfer of genetic information from DNA into an

RNA moleculeOccurs in the eukaryotic cell nucleusRNA is transcribed from a template DNA strand

TranslationTransfer of the information in RNA into a protein.

TranscriptionDetails:

1. Initiation- Promoter is the nucleotide sequence on DNA that

marks where transcription of a gene begins and ends; “start” signal

Promoter serves as a specific binding site for RNA polymerase and determines which of the two strands of the DNA double helix is used as the template.

Specific nucleotide sequence at promoter is TATAAACalled the “TATA box”; located 25-35 base pairs before

the transcription start site of a geneTATA box is able to define the direction of transcription

and also indicates the DNA strand to be readProteins called transcription factors can bind to the

TATA box and recruit RNA polymerase; it has a regulatory function

Note: TATA box is found upstream of start site and thus is NOT transcribed by RNA polymerase

TranscriptionElongation-

RNA elongates As RNA synthesis continues, the RNA strand peels

away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed.

Transcription3. Termination-

RNA polymerase reaches a sequence of bases in the DNA template called a terminator.

Signals the end of the gene; at that point, the polymerase molecule detaches from the RNA molecule and the gene.

mRNA (messenger RNA) or “transcript” exits the nucleus via the nuclear pores and enter the cytoplasm

Transcription animationhttp://www-class.unl.edu/biochem/gp2/

m_biology/animation/gene/gene_a2.html

RNA processingBefore mRNA leaves the nucleus, it is modified

or processed.1. addition of extra nucleotides to the ends of

the transcriptInclude addition of a small cap (a single G

nucleotide) at one end and a long tail (a chain of 50 to 250 A’s) at the other end

Cap and tail facilitate the export of the mRNA from the nucleus, protecting the transcript from attack by cellular enzymes, and help ribosomes bind to the mRNA

Cap and tail are NOT translated into protein.

http://vcell.ndsu.edu/animations/mrnaprocessing/movie.htm

RNA processing2. RNA splicing

Cutting-and-pasting process catalyzed by a complex of proteins and small RNA molecules, but sometime the RNA transcript itself catalyzes the process.

Introns“intervening sequences”; internal noncoding regionsGet removed from transcript before it leaves nucleus

ExonsCoding regions; parts of a gene that are expressed as amino

acidsJoined to produce an mRNA molecule with a continuous coding

sequenceCap and tail are considered parts of the first and last exons,

although are not translated into proteins.

http://student.ccbcmd.edu/biotutorials/protsyn/exon.html

RNA processing

More animationshttp://www.pbs.org/wgbh/aso/tryit/dna/prot

ein.htmlhttp://www.wisc-online.com/objects/

index_tj.asp?objID=AP1302

TranslationA typical gene consists or hundreds or thousands

of nucleotides in a specific sequence, which get transcribed onto mRNA.

Translation is the conversion of nucleic acid language into polypeptide language

There are 20 different amino acids. A cell has a supply of amino acids in cytoplasm,

either obtained by food or made from other chemicals.

Flow of information from gene to protein is based on a triplet code: genetic instructions for the a.a. sequence of a polypeptide chain are written in DNA and mRNA as a series of three-base pairs, or codons.

Translation- tRNATo convert the codons of nucleic acids on

mRNA to the amino acids of proteins, a cell employs a molecular interpreter, called transfer RNA (tRNA)

tRNA molecules are responsible for matching amino acids to the appropriate codons to form the new polypeptide.

tRNA’s unique structure enables it to be able to: 1. pick up the appropriate amino acids 2. recognize the appropriate codons in the mRNA

Translation- tRNAtRNA is made of a single strand of RNA

consisting of about 80 nucleotidesBy twisting and folding upon itself, it forms

several double-stranded regions in which short stretches of RNA base-pair with other stretches.

at one end of the folded molecule contains a special triplet of bases called an anticodon.Complementary to a codon triplet on mRNAAnticodon recognizes a particular codon triplet on

mRNAAt the other end of the tRNA molecule is a site

where an amino acid can attach.

Translation- tRNA

Translation- tRNAEach amino acid is joined to the correct

tRNA by a specific enzyme. Each enzyme specifically binds one type of

amino acid to all tRNA molecules that code for that amino acid, using a molecule of ATP as energy to drive the reaction.

The resulting amino acid-tRNA complex can furnish its amino acid to a growing polypeptide chain.

Translation- rRNA

Ribosomal RNA (rRNA)Organelle in the cytoplasm that coordinates the

functioning of mRNA and tRNA and actually makes polypeptides.

Consists of two subunits: large and smallEach ribosome has a binding site for mRNA, and three

binding sites for tRNA.E site

Removes tRNA from ribosomeP site

Holds the growing polypeptideA site

Obtains new amino-acid-tRNARibosome holds tRNA and mRNA molecules close

together, allowing the amino acids carried by the tRNA molecules to be connected into a polypeptide chain.

Translation- StepsCan be divided into same three phases:

initiation, elongation, and termination.1. Initiation

Brings together the mRNA, a tRNA bearing the first amino acid, and the two subunits of a ribosome.

Role is to establish exactly where translation will begin, ensuring the mRNA codons are translated into the correct sequence of amino acids.

Translation1. Initiation (continued…)Two steps:

1. an mRNA binds to a small ribosomal subunit. A special initiator tRNA binds to the specific codon, called the start codon, where translation begins on mRNA. Initiator tRNA carries the amino acid Methionine

(Met); its anticodon UAC binds to the start codon, AUG

2.A large ribosomal subunit binds to the smaller one, creating a function ribosome. The initiator tRNA fits into tRNA binding site (P site) on the ribosome. A site is vacant and ready for the next amino-acid carrying tRNA.

2. ElongationOnce initiation is complete, amino acids are added

one by one to the first amino acid. Each addition occurs in a three step process:1. codon recognition

The anticodon of an incoming tRNA carrying an amino acid, pairs with the mRNA codon in the A site of the ribosome

2. peptide bond formationPolypeptide separates from the tRNA to which it was

bound (P site) and attaches by a peptide bond to the amino acid carried by the tRNA in the A site.

The ribosome catalyzes formation of the bond.3. translocation

P site tRNA, moves to the E site and leaves the ribosome.

The ribosome then translocates (moves) the tRNA in the A site, with its attached polypeptide, to the P site.

Codon and anticodon remain bonded, and the mRNA and tRNA move as a unit

Movement brings into the A site the next mRNA codon to be translated, and the process begins again at step 1.

TerminationElongation continues until a stop codon

reaches the ribosome’s A site. Stop codons- UAA, UAG, and UGA, do not

code for amino acids but instead act as signal to stop translation.

The completed polypeptide is released from the last tRNA and exits the ribosome, which then splits into its separate subunits.

Translation Animationhttp://www-class.unl.edu/biochem/gp2/

m_biology/animation/gene/gene_a3.html

PolysomeSeveral ribosomes can translate an mRNA at the same time, forming what is called a polysome.

Peptide Bond Formation

Free ribosomes vs. bound ribosomesFree ribosomes

Found in cytoplasmSynthesize proteins for use primarily within

the cellBound ribosomes

Found on rough ERSynthesize proteins primarily for secretion or

for lysosomes

Free ribosomes vs. bound ribosomes

After protein synthesis…Each polypeptide coils and folds, assuming

a 3-D shape, its tertiary structure.Several polypeptides may come together,

forming a protein with quaternary structure.Overall significance:

Process whereby genes control the structures and activities of cells

The way genotypes determine phenotypes; proteins made from the original DNA nucleotides determine the appearance and capabilities of the cell and organism!

MutationsMutation is any change in the nucleotide

sequence of DNA.Can involve large regions of a chromosome

or just a single nucleotide pair, as in sickle cell diseaseIn one of the two kinds of polypeptides in the

hemoglobin protein, the sickle-cell individual has a single different amino acid.

This small difference is caused by a change of a single nucleotide in the coding strand of DNA. Only ONE base pair!

MutationsTwo general categories:

Base substitutionAlso known as a point mutationReplacement of one nucleotide with another.Depending on how the base substitution is translated, it can

result in no change in the protein (due to redundancy of genetic code), an insignficant change, or a change that significantly affects the individual.Occasionally, it leads to an improved protein that enhances

the success of the mutant organism and its descendants.More frequently, its harmful.

o May cause changes in protein that prevent it from functionally normally.

o If stop codon is a result of mutation and protein is shortened, it may not function at all.

MutationsBase insertions or deletions

Also known as frameshift mutationOften has a disastrous effectAdding or subtracting nucleotides may result

in an alteration of the reading frame of the messageall the nucleotides that are “downstream” of the

insertion or deletion will be regrouped into different codons.

Result will most likely by a nonfunctional polypeptide

MutationsWhat causes mutations?

Mutagenesis, or the production of mutations, can occur in a number of ways.

Errors that occur during DNA replication or recombination are called spontaneous mutations.

Mutagen, a physical or chemical agent that causes mutationsPhysical mutagen: high-energy radiation, such as X-

rays and UV lightChemical mutagen: consists of chemicals that are

similar to normal DNA bases pair incorrectly.

MutationsCan also be helpful both in nature and in

the laboratory.It is because of mutations that there is such

a rich diversity of genes in the living world, that make evolution by natural selection possible.

Also essential tools for geneticists.Whether naturally occurring or created in the

laboratory, mutations create the different alleles needed for genetic research.