DNA DNA

The Code of LifeThe Code of Life

What is DNA?

Composed of 3 three parts: Sugar called

deoxyribose Phosphate molecule

(PO4) Nitrogen base (four

types) Adenine Guanine Thymine Cytosine

When a sugar, phosphate, and nitrogen base are bonded together, they are called nucleotides. (Note that the n. base is connected to the sugar)

Structure of DNAStructure of DNA

DNA is made up of DNA is made up of a long chain of a long chain of nucleotidesnucleotides The sugar and The sugar and

phosphate make phosphate make up the up the backbone of the backbone of the DNA.DNA.

The nitrogen The nitrogen bases extend bases extend outward and outward and attach to a attach to a second strand second strand of DNAof DNA

DNA is a two-DNA is a two-stranded stranded molecule that molecule that spirals around spirals around itself forming itself forming what is called a what is called a doubledouble helixhelix

Deoxyribose?Deoxyribose? Deoxyribose is the Deoxyribose is the

sugar that forms sugar that forms the backbone of the backbone of DNADNA

Deoxy- means that Deoxy- means that the sugar has an the sugar has an oxygen missing oxygen missing from itfrom it

Regular ribose Regular ribose sugar have all sugar have all their oxygen their oxygen atomsatoms

Chargraff’sBase-Pairing Chargraff’sBase-Pairing RulesRules

IN DNA: IN DNA: Adenine always binds to ThymineAdenine always binds to Thymine Guanine always binds to CytosineGuanine always binds to Cytosine

Complete the complementary strand:Complete the complementary strand:ATTGCCATAATTGCCATA

IN RNA:IN RNA: Adenine always binds to URACILAdenine always binds to URACIL Guanine always binds to CytosineGuanine always binds to Cytosine

DNA Space-SaversDNA Space-Savers

DNA is coiled like a DNA is coiled like a telephone and telephone and wrapped around a wrapped around a protein spool called a protein spool called a histone. histone. Each histone wrapped Each histone wrapped

with DNA is called a with DNA is called a nucleosomenucleosome

Histones are also Histones are also coiled and formed into coiled and formed into chromosomeschromosomes

DNA ReplicationThe Steps of DNA Replication STEP 1: The two parent strands are unwound with the help of

DNA helicases (enzymes) – it unzips the lead strand from the complementary strand

STEP 2: Single stranded DNA binding proteins attach to the unwound strands, preventing them from winding back together.

STEP 3: The strands then bind to DNA polymerase, an enzyme which catalyzes the addition of new nucleotides to each side of the original strands. (DNA polymerase also checks the accuracy of its own work!).

STEP 4: While the DNA polymerase on the leading strand can operate in a continuous fashion, DNA primer is needed repeatedly on the lagging strand to facilitate synthesis of Okazaki fragments. DNA primase, helps to build the primer.

Finally, each new Okazaki fragment is attached to the completed portion of the lagging strand in a reaction catalyzed by DNA ligase.

Okazak-a –WHAT? OK…One strand of DNA can

be replicated smoothly (no stops and starts – straight through) it is called the leading strand.

Each side of DNA has an end called the 5` and the 3`

When making DNA one always links nucleotides in the 5`-3` direction

When unraveled, DNA has one strand that is going one direction 3`-5` and another going 5`-3`

To assemble a new DNA, the added nucleotides must be going 5`-3`, this works for the leading strand but not the lagging strand.

Solving the Problem. Short strands

of DNA are added to the 5`-3` section of DNA.

These strands are called Okazaki fragments.

When the fragments have all been added, an enzyme called DNA ligase stitches the fragments together to make one cohesive DNA strand

Protein Synthesis

RNA = ribonucleic acid

• RNA contains a ribose sugar, a phosphate and a nitrogenous base

• RNA does not use thymine, it uses uracil

• RNA is a single-strand molecule that can leave the nucleus

• RNA’s job is to take instructions from the DNA in the nucleus and delivery them to the ribosome for protein synthesis

Three Types of RNA

mRNA: Carries the “message” or code for protein synthesis to the Ribosome

rRNA: RNA and proteins combine to make the Ribosome

tRNA: 3-base sequences that bind to specific amino acids (which were digested and absorbed by the cell) in the cytoplasm

1. Messenger RNA

2. Ribosomal RNA

3. Transfer RNA

Two Steps to Protein Synthesis

1. Transcription: (copying down the message from DNA format into RNA format)

a) Occurs in the Nucleusb) DNA splits open at the location of the desired

genec) RNA makes a complementary copy of gened) RNA is edited (introns are cut out and are

reabsorbed and exons are pasted together making mRNA)

Protein Synthesis Continued

2. Translation: (“translating” from the language of DNA into the language of Proteins)

a) Occurs in the cytoplasm and the Ribosome

b) mRNA enters the ribosome and each 3-base sequence (codon) is read.

c) The ribosome attaches the tRNA molecule with correct anticodon to the mRNA

d) The tRNA’s amino acid is detached and added to a growing protein chain.

Transcription

To transcribe means to copy down (a court stenographer copies down what is being said, a secretary takes his boss’s recordings and copies them down on his computer)

Transcription is the process in which DNA is unraveled and RNA is made.

The Process of Transcription

The Steps of Transcription:

1. The enzyme RNA polymerase opens up the DNA helix for short stretch (~ 15 base pairs) at the desired gene

2. RNA synthesis begins at promoters: sites on DNA that are recognized as "start" signals for RNA synthesis.

3. RNA is synthesized in 5' to 3' direction. Complementary RNA bases are added to the lead DNA strand (substituting Uracil for all thymines)

4. RNA is synthesized until the polymerase reaches the site on the DNA strand called a terminator. Terminators are regions where RNA synthesis stops and RNA is released from DNA.

Transcription Practice

DNA Sequence:

TAC CCC GGC ATC CGC ACT

What is the complementary DNA Strand?

What is the mRNA strand?

Which two strands are almost identical?

ANSWERS:

DNA Sequence:

TAC CCC GGC ATC CGC ACT

What is the complementary DNA Strand?

ATG GGG CCG TAG GCG TGA

What is the mRNA strand?

AUG GGG CCG UAG GCG UGA

Which two strands are almost identical?

The mRNA and the Complementary DNA strand are almost identical except that Uracil is used instead of Thymine in the mRNA

Pre-mRNA: Editing the RNA

Before messenger RNA can leave the nucleus, it needs to be edited (just like you edit your research paper before you turn it).

DNA strands have more nucleotides than are needed to code for all proteins. Introns are sections of DNA not needed for a protein (it

stays IN the nucleus) Exons are sections of DNA needed for a protein (when

converted into RNA these exons EXIT the nucleus) Enzymes such as RNA Polymerase edit out the introns

and splice together the exons. Once this is done a mRNA strand is formed and ready to

leave the nucleus

Editing Practice

What would you edit out of the following sentence?

The the cat ate the fat mat sat rat.

Which words would be the introns?

Which words would be the exons?

Vocabulary for TranslationVocabulary for Translation

1.1. Codon-Codon- 3 nucleotides located on RNA that code for a 3 nucleotides located on RNA that code for a specific amino acid (note: 64 possible codons, but only specific amino acid (note: 64 possible codons, but only 20 amino acids)20 amino acids)

2.2. tRNAtRNA = transfer RNA, floats around in cytoplasm of cell = transfer RNA, floats around in cytoplasm of cell carrying a specific amino acid. When mRNA codes for carrying a specific amino acid. When mRNA codes for a specific amino acid, tRNA binds to the mRNA and a specific amino acid, tRNA binds to the mRNA and drops off the amino acid.drops off the amino acid.

3.3. Ribosomal unitRibosomal unit: lower attaches to mRNA, upper unit : lower attaches to mRNA, upper unit attaches to tRNA and the amino acid/polypeptide chain attaches to tRNA and the amino acid/polypeptide chain that forms.that forms.

4.4. Start codonStart codon: AUG –tells the ribosome where to begin : AUG –tells the ribosome where to begin translatingtranslating

5.5. Stop codon:Stop codon: varies – tells the ribosome where to stop varies – tells the ribosome where to stop translatingtranslating

The Process of Translation:

1. mRNA leaves the nucleus and enters the ribosome

2. The start signal for translation is the codon AUG. This codon codes for the amino acid methionine. A complementary tRNA (UAC) charged with methionine binds to the translation start signal on the mRNA strand and leaves its methionine behind.

3. After the first charged tRNA appears in the A site (active site), the ribosome shifts so that the old tRNA is now in the P site (polypeptide site). The ribosome also moves along the mRNA to a new codon.

Simulation:

Translation Continued4. A new tRNA molecule whose anticodon corresponds to the

next codon on the mRNA, enters the A site. The tRNA molecule drop off its amino acids which binds to the first amino acid – this is the beginning of the polypeptide.

5. The first tRNA is now released and the ribosome shifts again so that a tRNA carrying two amino acids is now in the P site, and a new charged tRNA can bind to the A site. This process of elongation continues until the ribosome reaches a stop codon.

6. When the ribosome reaches a stop codon, no tRNA binds to the empty A site. This is the ribosome’s signal to break into its large and small subunits, releasing the new protein and the mRNA.

Simulation:

Translation practice

mRNA Sequence

AUG GGG CCG UAG GCG UGA

How many codons are in the above sequence?

What is the anticodon (tRNA) sequence for the above mRNA sequence?

What is the order of the amino acids for the above sequence?