3 Enzymes DNA DNA replication PDF

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2.13 Opening Questions: Can chemical reactions be speeded up? Starches might eventually break down into sugars, but it goes much faster when the protein amylase is present.

•  How might amylase speed up the change from starch to sugar? •  What do you think is happening at the molecular level? If you still have your cracker, try another taste!

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Chemical Reactions •  Reaction –  Process of chemical change

•  Reactant –  Molecule that enters a reaction

•  Product –  A molecule remaining at the end of a reaction

•  Some reactions require a net input of energy – others end with a net release of energy –  Endergonic reaction: require a net input of energy –  Exergonic reaction: net release of energy

Chemical Reactions

Endergonic reaction!

Exergonic reaction!

2.13 Enzymes speed chemical reactions. •  The sum total of all the chemical reactions in an organism is called its metabolism. •  An enzyme is a protein that speeds up a chemical reaction without being changed itself. Almost every metabolic reaction occurs with the help of an enzyme.

2.13 Enzymes speed chemical reactions by lowering activation energy.

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Energy requirements without enzyme

Activation Energy

Enzyme lowers = Lower the energy required Activation for reaction to Energy proceed

Substrates Energy requirements with enzyme

Products Progress of the reaction

2.13 Each enzyme recognizes one specific target molecule called its substrate.

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2.13 Inhibitors are molecules that prevent enzymes from working.

Competitive inhibitors bind to the active site. © 2017 Pearson Education, Inc.

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2.13 Inhibitors are molecules that prevent enzymes from working.

Noncompetitive inhibitors bind to a distant site. © 2017 Pearson Education, Inc.

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2.13 Like all proteins, enzyme function depends on shape. •  Changes in shape can prevent function. •  Lactase is an enzyme that breaks down lactose (milk sugar). •  Gene mutations can change the shape of lactase and make it ineffective, leading to lactose intolerance.

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Chapter Table of Contents

Chapter 6 DNA: The Molecule of Life: Module Hyperlinks •  •  •  •  •  •  • 

6.1 DNA intro 6.2 DNA replication 6.3 DNA directs the production of proteins 6.4 Flow from DNA to RNA to protein 6.5 Transcription 6.6 Translation part one 6.7 Translation part two

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6.1 Opening Questions: What molecule holds the instructions for living things? Do these organisms all share the same genetic code? Explain.

Aquatic Algae

Caterpillar

Mushroom

Elephant Protist © 2017 Pearson Education, Inc.

Flower

Human Chapter Table of Contents

6.1 DNA is the molecule that holds the instructions for all living things. •  DNA is shorthand for

Deoxyribose Nucleic Acid •  A DNA molecule is a double helix with two strands made up of a long string of nucleotides.

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6.1 Each nucleotide consists of a sugar, a phosphate, and a base.

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Nucleic Acids •  Structure of nucleotide

Nucleic Acids •  There are 5 different types of nucleotides o  Adenosine o  Guanosine o  Cytidine o  Thymidine o  Uridine

•  Because there are 5 different types of bases o  Adenine o  Guanine o  Cytosine o  Thymine o  Uracil

6.1 In a DNA molecule there are four bases with specific pairing rules. •  Adenine (A) can only bond with thymine (T). •  Guanine (G) can only bond with cytosine (C). Each strand of DNA in a double helix is complementary. © 2017 Pearson Education, Inc.

A-T

C-G Chapter Table of Contents

6.2 Opening Questions: Can you build a DNA molecule? •  In a DNA double helix, adenine (A) can only bond with thymine (T) and guanine (G) can only bond with cytosine (C). •  Given a half strand of DNA, build the other strand.

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A• T T• A C•G A• T C•G G•C C•G Chapter Table of Contents

6.2 What makes DNA a great molecule for hereditary information? •  DNA strands are complementary! –  If you know ½ of the molecule, you can build the other.

•  To replicate, the DNA molecule unzips. •  Each strand serves as a template to build a new strand following the base-pairing rules. Genetic instructions are passed down via DNA replication. © 2017 Pearson Education, Inc.

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6.2 During DNA replication, a cell duplicates its chromosomes. •  New DNA molecules are made up of one of the original parental strands plus a new half. •  As a result, DNA replication is called semi-conservative.

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How the DNA Molecule Copies Itself •  The process of DNA replication involves several enzymes §฀  DNA polymerase •  adds the correct complementary nucleotide to the growing daughter strand •  but can only add to an existing strand or primer

§฀  Helicase •  unzips the DNA to expose the templates •  this creates a replication fork

§฀  DNA ligase •  seals fragments of DNA together

How nucleotides are added in DNA replication

How the DNA Molecule Copies Itself •  At the replication fork, a primer must first be added to give a place for DNA polymerase to start §฀  from one template, DNA polymerase adds nucleotides in a continuous fashion; this new daughter strand is called the leading strand §฀  because the other template is a mirror image, directionality becomes a problem because DNA can build a new strand in one direction only •  this second daughter strand is assembled is segments, each one beginning with a primer named Okazaki fragments •  the segments will be joined together by the DNA ligase to form the lagging strand

Building the leading and lagging strands

Okasaki fragments

The DNA polymerase can only lengthen DNA strand In 5’  3’ direction

How the DNA Molecule Copies Itself •  Before the newly formed DNA molecules wind back into the double helix shape, the primers are removed and the DNA fragments ligated together §฀  DNA ligase joins the ends of the fragments of DNA to form continuous strands

How DNA replication works

DNA replication movie

How the DNA Molecule Copies Itself •  Because so much DNA is being replicated in the many cells of the body, there is a potential for errors to occur §฀  DNA repair involves comparing the daughter strand to the parent DNA template to check for mistakes •  the proofreading is not perfect because mutations are still possible, although rare

Mutations •  Mutation is a change in the content of the genetic message •  Mutations occur due to: §฀  Mistakes during replication §฀  DNA alteration by chemicals (pollution, smoke…) §฀  DNA alteration by radiation (radioactivity, UV light…)

•  Mutations are rare

6.3 Opening Questions: True or false? •  True or false. DNA codes for all the information needed to make up an organism uses only four building blocks (A,T,C,G). •  True or false. All the DNA molecules in your body put end to end would reach from the Earth to the Sun and back over 600 times. •  True or false. Typing 60 words per minute, eight hours a day, it would take about 50 years to type the human genome. •  True or false. Humans and bananas share about 50% common DNA. All true! © 2017 Pearson Education, Inc.

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6.3 DNA directs the production of proteins via an intermediate molecule of RNA. •  RNA is also a nucleic acid (like DNA):

Ribonucleic Acid •  RNA has three major differences: 1.  It is single-stranded (not a helix) 2.  Sugar in RNA is ribose. 3.  Thymine (T) is replaced by uracil (U).

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•  RNA is similar to DNA except it has a ribose sugar instead of deoxyribose o  it uses uracil instead of thymine o  it is comprise of just one strand instead of two o 

DNA and RNA

•  Deoxyribonucleic acid (DNA) –  Two nucleotide chains twisted in a double helix –  Nucleic acid that carries heritable information about a cellʼs proteins and RNAs

•  Ribonucleic acid (RNA) –  Typically single-stranded nucleic acid –  Different RNAs interact with DNA and with one another to carry out protein synthesis

6.3 DNA holds information on how to produce proteins. •  DNA is able to act as the molecule of heredity because it can direct the production of proteins. •  DNA first directs the production of RNA, which in turn controls the manufacture of proteins. •  Proteins then perform the majority of cellular functions and control physical traits. © 2017 Pearson Education, Inc.

DNA RNA Proteins

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6.3 The flow of genetic information.

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6.4 Opening Questions: How does DNA make brown eyes? •  What color are your eyes? •  What color are your neighbor’s eyes? •  How might your DNA instructions for eye color vary from your neighbor’s? •  How are the instructions in DNA turned into the physical pigment in your eye?

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6.4 Genetic information flows from DNA to RNA to protein in two steps.

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6.4 Transcription rewrites the DNA code into RNA, which then leaves the nucleus. •  Transcription follows the DNA base-pairing rules with one exception: –  Uracil (U) is used instead of thymine (T).

•  The molecule that results from transcription is called messenger RNA (mRNA). © 2017 Pearson Education, Inc.

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6.4 In translation, the RNA molecule serves as instructions for making a protein.

•  At the ribosomes in the cytoplasm, each mRNA codon is translated into an amino acid to build a protein. © 2017 Pearson Education, Inc.

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6.5 Opening Questions: What is a gene? •  How would you define a gene? •  Write your answer down and then share it with your neighbor. •  Are your answers the same?

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6.5 Transcription creates a molecule of RNA from a molecule of DNA. •  During transcription, the DNA double helix separates. •  One strand of DNA is used to generate a molecule of RNA. •  The RNA is processed to become messenger RNA, which then exits the nucleus via a nuclear pore. © 2017 Pearson Education, Inc.

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Transcription •  The enzyme that produces the mRNA is the RNA polymerase §฀  it binds to a sequence of DNA called promoter then moves down the DNA molecule adding matching RNA nucleotides that are paired with DNA bases, creating a complementary RNA copy of the sequence of DNA §฀  Guanine pairs with cytosine Adenine pairs with uracile §฀  RNA polymerase elongate the RNA chain in the 5’ to 3’ direction §฀  Transcription ends when RNA polymerase reaches a sequence that signals it to stop

Transcription

Transcription movie

6.5 Review Question: What is a gene? •  There is no simple, agreed-upon definition that accurately describes all known genes. –  Is it a stretch of DNA? –  Does it produce a protein? –  What if a protein is made from two different genes?

•  As we study the genome, it actually becomes harder to find one definition. •  For now, we can define a gene as a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA. © 2017 Pearson Education, Inc.

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6.6 Opening Questions: DNA and you. •  Would you get a personal DNA test if you could? –  Why or why not?

•  Would you get a personal DNA test before you had a baby? –  Why or why not?

•  Should we run personal DNA tests on newborn babies? –  Why or why not? © 2017 Pearson Education, Inc.

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6.6 Translation involves three kinds of RNA: rRNA, mRNA, and tRNA. •  Translation of the mRNA takes place in the cytoplasm within ribosomes.

•  Ribosomes are made from proteins and ribosomal RNA (rRNA). •  Transfer RNA (tRNA) molecules carry amino acids to the ribosome. © 2017 Pearson Education, Inc.

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6.6 Within each ribosomes are binding sites for the mRNA and for tRNA. •  One end of a tRNA has an anticodon that matches up with the mRNA. •  The other end holds an amino acid.

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6.6 The genetic code uses triplet codons.

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6.7 Opening Questions: Can you translate the genetic code? •  What amino acid would be produced from an mRNA with the sequence:

AUG-ACU-GAG-UCA-UAA

Hint: Use your genetic code table!

Met-Thr-Glu-Ser-Stop © 2017 Pearson Education, Inc.

Chapter Table of Contents

6.7 Translation creates a molecule of protein via the genetic code. •  Translation is divided into three phases: –  Initiation –  Elongation –  Termination

•  Translation begins when two subunits of a ribosome assemble on an mRNA. •  A tRNA then brings in amino acids that match the codon in the mRNA. © 2017 Pearson Education, Inc.

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6.7 Translation results in a polypeptide. •  Elongation continues until the ribosome reaches a stop codon on the mRNA. •  The ribosome machinery then disassembles. •  The completed polypeptide is now available to be used or modified by the cell into a functioning protein. © 2017 Pearson Education, Inc.

Polypeptide

Amino acid

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Translation •  Ribosomes are the protein making factory where the translation occurs §฀  A ribosome is a complex of several proteins and three chains or ribosomal RNA (rRNA) §฀  Ribosomes are composed of 2 subunits (2 parts) o  A small subunit o  A large subunit

§฀  The small subunit has a short sequence of its rRNA exposed that is complementary to a sequence in the mRNA. This sequence help the mRNA to recruit the ribosome. o  The mRNA binds to the small subunit

Translation •  The ribosome large subunit has three pockets that are binding sites for transfer RNA (tRNA) §฀  These binding sites are called A, P and E §฀  The tRNA molecules bring the amino acids to the ribosome to make proteins

A ribosome

Translation •  Transfer RNA (tRNA) molecules are chains of about 80 nucleotides. The chain form hydrogen bonds between its nucleotides. As a result the tRNA molecule form a 3-looped structure that is crucial for its function

The structure of tRNA. Tertiary structure of tRNA

Translation •  The structure of tRNA is important for its function §฀  On one end there is the amino acid attachment site §฀  On the other end there is the anticodon, a three nucleotide sequence complementary to one of the codons of the genetic code §฀  Activating enzymes bind amino acids to the proper tRNA

Translation •  The process of translation starts by binding of the mRNA to the small ribosomal subunit. Then the large ribosomal subunit binds and form the complete ribosome §฀  The mRNA passes through the ribosome three nucleotides at a time §฀  A new tRNA with the complementary codon, and carrying an amino acid to be added to the polypeptide chain enters the ribosome at the A site (accepting site) §฀  Before the new tRNA can bind to the A site, the previous tRNA has to shift to the P site (peptide site)

Translation §฀  The P site holds the tRNA with the elongating polypeptide chain §฀  After a new tRNA enters the ribosome at the A site a peptide bond form between the amino acid carried by that new tRNA and the last amino acid of the tRNA in the P site that is charged with the polypeptide. The growing polypeptide is transferred to the amino acid of the tRNA in the A site §฀  The ribosome moves down the mRNA shifting the now emtpy tRNA from the P site to the E site (where it will be released) and shifting the tRNA with the polypeptide from the A site to the P site, clearing the A site for the next tRNA

How translation works

Translation •  Translation continue until the ribosome find a stop codon •  The stop codon signal the end of the protein, the ribosome is dissociated

Movie on translation

Ribosomes guide the translation process...