Thursday 2217 AIM How can we transcribe the

Thursday 2/2/17 • AIM: How can we transcribe the DNA code? • DO NOW: 1 - Explain the role of enzymes in DNA replication. • 2 - Describe DNA Replication • 3 - How does DNA Replication create a semi-conservative model?

Replicate the following • GATTACA • CTAATGT GATTACA CTAATCT GATTACA CTAATGT

DNA and RNA are polymers of nucleotides • DNA is a nucleic acid, made of long chains of nucleotides Phosphate group Nitrogenous base Sugar Phosphate group Nitrogenous base (A, G, C, or T) Nucleotide Thymine (T) Sugar (deoxyribose) DNA nucleotide Polynucleotide Sugar-phosphate backbone Figure 10. 2 A

• Hydrogen bonds between bases hold the strands together: A and T, C and G Hydrogen bond Ribbon model Partial chemical structure Computer model Figure 10. 3 D

Untwisting and replication of DNA • each strand is a template for a new strand helicase DNA polymerase Figure 10. 4 B

DNA replication - Genes - the units of inheritance (6/10) - You. Tube

• DNA replication begins at many specific sites Origin of replication Parental strand Daughter strand Bubble Two daughter DNA molecules Figure 10. 5 A

3 end P P P P • Each strand of the double helix is oriented in the opposite direction 5 end P Figure 10. 5 B 3 end 5 end

• DNA polymeras e works in only one direction • Telomere sequences are lost with each replication. • Cancer, aging DNA polymerase molecule 5 end Daughter strand synthesized continuously Parental DNA 5 3 Daughter strand synthesized in pieces 3 5 P 5 3 3 5 P telomeres DNA ligase Overall direction of replication Figure 10. 5 C

TRANSCRITION - You. Tube

• The information constituting an organism’s genotype is carried in its sequence of bases – The DNA is transcribed into RNA, which is translated into the polypeptide DNA TRANSCRIPTION RNA TRANSLATION Protein Figure 10. 6 A

• DNA replicaation: both strands of the double helix act as templates to make new DNA • In transcription only one strand of DNA is the template (the gene)

Transcription produces genetic messages in the form of m. RNA polymerase RNA nucleotide Direction of transcription Template strand of DNA Figure 10. 9 A Newly made RNA

Transcription • The process that builds an RNA molecule from a DNA template • Why does the cell want to build RNA? • To get the genetic code out of the nucleus to the ribosome • WHY? • To build a protein and lead to a physical trait

Transcription cont. • We want to transcribe the gene • Only one strand of the DNA double helix acts as a template and is transcribed • Base Pair Rules • A-U • C-G • Adenine on DNA attracts a Uracil of RNA

Transcribe the following • DNA: AACGGTAGTACGTA • RNA: UUGCCAUCAUGCAU

RNA: ribonucleic acid • Large nucleic acid built from many nucleotides bonded together • Remember a nucleotide consists of a phosphate group, 5 carbon sugar and nitrogen containing base

RNA nucleotide • The 5 -Carbon sugar is ribose • The 4 nitrogen containing bases: – Adenine – Uracil – Cytosine – Guanine

3 types of RNA • m. RNA: messenger RNA: carries the genetic code from the nucleus to the ribosome • r. RNA: ribosomal RNA: builds ribosomes • t. RNA: transfer RNA: carries amino acids to the synthesizing polypeptide

Assessment • DNA: TTGCAATCG • transcribe

FRIDAY 2/3/17 • AIM: How is RNA modified before it leaves the nucleus? • DO NOW: Transcribe the following

Modification of RNA • The rough draft is called the primary transcript • Before it leaves the nucleus it gets modified • Addition of 5’cap and Poly-A tail • The most important is RNA splicing

RNA modification • 5’ cap and Poly A tail protect the RNA from being broken down by cellular enzymes • They also help the ribosome recognize the RNA

RNA splicing • Introns: junk DNA that does not code for proteins • Exons: good DNA codes for protein • Splicesome: enzymes that catalyze the removal of introns and the connection of exons • Allows the human genome to produce a variety of polypeptides • One gene codes for one polypeptide

• How do your cells know which amino acids it wants or needs? • ANSWER: the genetic code determines the polypeptide (sequence of amino acids)

Now the m. RNA is ready to leave the nucleus and enter the cytoplasm

Quick Review • What are the 3 major events that occur during transcription? • Why is it important to modify the primary RNA before leaving the nucleus?

Monday 2/6/17 • AIM: How is m. RNA translated? • DO NOW: 1 -How does a cell know which proteins to synthesize? • 2 - Why do our cells make proteins? • 3 -Explain the importance of messenger RNA. • HOMEWORK: Text read pages 337 -338 and page 341 • EXAM THURSDAY

DO NOW ANSWER • 1 - The chromosomes which carry genes determine which proteins to make • 2 - Our cells make proteins so that they can express physical traits • 3 - m. RNA: messenger RNA carries the genetic code out of the nucleus into the cytoplasm

The Genetic code • Codon: sequence of 3 nucleotides that specify an amino acid • There are 20 amino acids that build ALL polypeptides • It is the unique sequence of amino acids that build polypeptide chains • It is the unique folding of polypeptides that build proteins • Proteins then lead to physical traits

Codons to know • AUG: start codon. All m. RNA start with this codon. It translates to Methionine (Met) • UAA Stop codons • UAG tells translation • UGA to end

An initiation codon marks the start of an m. RNA message AUG = methionine Start of genetic message End Figure 10. 13 A

Translation • There is a specific start AUG codon • There are 3 possible stop codons that terminate UAA, UAG or UGA

3 types of RNA • m. RNA: messenger RNA: carries the genetic code from the nucleus to the ribosome • r. RNA: ribosomal RNA: builds ribosomes • t. RNA: transfer RNA: carries amino acids to the synthesizing polypeptide

Translation: RNA to amino acid sequence • Involves m. RNA, t. RNA, r. RNA and ribosomes • Before m. RNA leaves the nucleus, proteins called splicesomes cut out and paste together coding regions of the primary m. RNA transcript • Plays a major role in polypeptide diversity • Now it is ready for translation

m. RNA: carries codon message out of the nucleus

t. RNA: Transfer RNA carries amino acids to the m. RNA-ribosome complex

t. RNA anticodon • 3 base pair sequence complementary to the m. RNA codon • Anticodon-codon complex allows amino acids to bond in proper sequence

Tuesday 2/7/17 • • AIM: How are proteins synthesized? DO NOW: DNA: TACGGCCAAGCACGA c. DNA m. RNA aa t. RNA HOMEWORK: review book read 114 -116. q 1 -12 pgs 116 -118

Ribosomal RNA builds ribosomes

Translation- m. RNA and t. RNA interact at a ribosome

Translation continued

Remember • The gene is part of the DNA that has the actual instructions for building the protein • It is transcribed into m. RNA which is what gets translated

Remember • • • 20 amino acids 4 Nitrogen bases 3 Nitrogen bases make up a codon 64 codons in total for 20 amino acids This means some codons code for the same amino acid

Reading frame • Each codon specifies an amino acid • The reading frame is the sequence of codons in a gene • If the reading frame is changed, the amino acid sequence may be changed • Possibly resulting in a dis-functional protein

Sickle cell anemia

How many amino acids build all of the human proteins? 20

How many nitrogen bases build RNA? 4 How many nitrogen bases make up a codon? 3

How many codons are there? 64

Therefore more than one codon can specify an amino acid

Lets build a protein DNA : m. RNA: t. RNA: aa: TACCCTCAACT AUGGGAGUUGA UACCCUCAACU met - gly- val- glu- ser

Amino acid sequence • MET-GLY-VAL-GLU-SER • We got a polypeptide but is this a functional protein? • NO! Remember it is the unique shape of a protein that gives it a specific function

What I want you to know about translation • Gene expression, protein synthesis • Process that builds a polypeptide chain from a m. RNA molecule • The original message comes from the DNA template • t. RNA anticodon bonds to m. RNA codon bringing an amino acid into its proper place • Translation occurs in the ribosome

Translation Stage of Protein Synthesis • Rectangles = amino acids • Crooked Cross = transfer RNA with an amino acid on top and anticodon at bottom • X = messenger RNA molecule with codons • Double oval = ribosome

• AIM: How are codons translated into polypeptides? • DO NOW: Handout. Label 1 -10 • Homework: Handout

RNA: ribonucleic acid • Polymer made up of small subunits called nucleotides • Each nucleotide has a 5 C sugar, nitrogenous base and phosphate group • The 5 carbon sugar in RNA is ribose • The four possible nitrogenous bases are • Adenine, uracil, cytosine and guanine

• Instead of thymine, adenine attracts a uracil nitrogenous base

m. RNA: messenger RNA

Assessment • Handout 1 -5 and A-E

• AIM: How is the reading frame effected if the base pair sequence changed? • DO NOW: Transcribe and translate the following: • DNA: TACCCTCAACT • Homework: Read 267 -269. Reading Check pages 267 and 269

• How would m. RNA and amino acid sequence change if the following DNA template changed? Original DNA: TACCCTCAACT Changed DNA: TACCCTCATTCTCAAC

DO NOW ANSWER • If the gene sequence is changed and causes a change in the amino acid sequence (polypeptide), the physical characteristic changes

Are all genes in each cell expressed in every cell? NO! All of the 30, 000 genes are in each body cell but only specific genes are expressed in specific cells

Differentiation • AKA Protein synthesis AKA gene expression • The regulation of gene expression • Different genes are expressed in different cells • Different cells build different proteins

1 - How many base pairs make up a single codon? 2 - How many amino acids build all human proteins?

• 3 nitrogen bases=codon • 64 codons in total • 20 amino acids build all proteins • More than one codon for a single amino acid • This is why some mutations have NO effect on the polypeptide chain

How do you make a polypeptide? Gene-m. RNA-ribosomecodon/anticodon bonding which makes a long chain of amino acids

How are polypeptides related to physical characteristics? Polypeptides build proteins which lead to chemical reactions that cause physical traits

Functional protein • Polypeptide: Long chain of amino acids – Combine with other polypeptides – Folds into a unique shape – This makes a functional protein – The shape of a protein is unique to its function – If you change the shape, you change the function

Denaturing a protein • Changes the shape of the protein • If the shape of the protein changes the function changes or it does not function at all. • How would a protein get denatured? – Gene mutation – Mistake in m. RNA modification – Mistake in translation – Mistake in polypeptide folding

• If my DNA makes a mistake, how will the protein behave? – The protein will have a different shape, and without its shape, it cannot function properly – Proteins are shape specific – Denature: changes the shape of a protein

GENE Mutations • Change in nucleotide sequence of bases in a DNA molecule (gene) • May or may not change the amino acid sequence • Nonsense mutation: gene sequence changes but amino acid does not • EX: normal DNA CTT mutated DNA: CTC

Gene Mutations • Nucleotide substitutions: single base pair is replaced with a different incorrect pair • Insertion: addition of 1 or more base pairs • Deletion: removal of one or more base pairs

Sources of mutations • Mutagen: any chemical that causes a change is nucleotide sequence of a gene – Chemicals – Medication – Vaccine – Radiation – carcinogens

How are mutations inherited? • If a mutation is in a gamete (sperm or egg), it will be inherited by the zygote

Mutations • How is the polypeptide changed if the reading frame of an m. RNA molecule is changes from GGC to AGC? • amino acid in the polypeptide chain is changed from SER to GLY • Mutation in reading frame of a gene could result in protein dysfunction