Today is Thursday,November 19th, 2015

Pre-Class:Today we start DNA. Tell me everything you know about it. You must write this down (the more scientific, the better).

(But write down everything you can)

What are the names of all the DNA bases we’ve learned so far?

Also, today is our Strawberry Lab. It’s in the turn-in box – go get a copy! Also get a small paper towel. www.savagechickens.com

In This Lesson:Unit 5

DNA Structure and Replication(Lesson 1 of 3)

Today’s Agenda

• Strawberry DNA Extraction• Where we are and where we’ve been• Challenge Questions• DNA Structure• DNA Replication

– As in, what happened in S phase.• DNA Pickup Line?

• Where is this (all) in my book?– Pages 182 and following…

By the end of this lesson…

• You should be able to identify the detailed structures of DNA.

• You should be able to describe the process by which DNA copies itself.

Orientation

• First, we studied atoms.• Atoms make up all matter.• Some of this matter is considered organic,

and is organized into four major groups.• Life-supporting organic matter has non-

living functions, like diffusion and osmosis.

Orientation

• Diffusion and osmosis help living things carry on life and undergo respiration.

• Life’s smallest unit is the cell.• There are prokaryotes and eukaryotes, and

they all have different organelles.• Even among eukaryotes, there are plant

cells and there are animal cells.

Orientation

• All cells, however, need to grow and reproduce.

• For body cells (also known as somatic cells), growth occurs through mitosis.

• Mitosis is a process in which the genetic material (DNA) is copied and the nucleus (and right after, the cell) divides.

Orientation

• Sex cells (or gametes), use the process of meiosis.

• The chromosomes in your cells are made of DNA, which makes you who you are.

• Today we will begin learning about how DNA copies and how it “codes” for proteins, which is the molecular basis for genetics.

Challenge Questions

• To the whiteboards!

Introducing DNA

• Video: DNA Introduction• Video: TED – Judith Hauck – The Twisting

Tale of DNA

DNA’s Discovery

• Discovered by Friedrich Miescher in 1869.– Noticed something in

pus in discarded surgical bandages.

– Called it “nuclein,” but other than a guess didn’t know it had any role in heredity.

http://upload.wikimedia.org/wikipedia/commons/b/bc/Friedrich_Miescher.jpg

Johann Friedrich Miescher

DNA’s Discovery• DNA’s structure was discovered in 1953 by:

http://www.nobelprize.org/nobel_prizes/medicine/laureates/1962/watson.jpghttp://sciencecomm.wikispaces.com/file/view/3441067.jpg/96607078/3441067.jpg

http://www.floridahumanist.org/images/FrancisHarryComptonCrick.jpg

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DNA Overview Video

• Video: DNA Overview

DNA• The big important statement:

– DNA in a long strand and wrapped around proteins is called chromatin. When condensed, a piece of chromatin is called a chromosome.

– Segments of the DNA strand are called genes. These genes tell the cell what proteins to make, which determine your traits.• Genes are like chapters in the book of DNA.• Each cell has the whole book, but depending on their

jobs, the cells read different chapters.

DNA and Review

• DNA is a nucleic acid, a long string of nucleotides.

• DNA takes the shape of a double-helix.

• There are four kinds of nucleotides:– Adenine– Cytosine– Guanine– Thyminehttp://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg

Nucleotide Review

• Each nucleotide has a:– Sugar molecule with 5-carbons (pentose)

• Deoxyribose in DNA• Ribose in RNA

– Phosphate group• Phosphorous-based molecule

– Nitrogenous base (makes the nucleotide unique)• Adenine• Thymine• Cytosine• Guanine

Nucleotide Structure Review

http://www.biologyjunction.com/images/nucleotide1.jpg

AdenineThymineCytosineGuanine

SKETCH ME! I’m useful!SKETCH ME! I’m useful!

Nucleotide Structure Review• More “scientific”

Nucleotides and Nucleosides

• Just so you know, you’ll occasionally hear of a nucleoside.

• The only difference between a nucleoside and a nucleotide is that a nucleoside is just a sugar and nitrogenous base – no phosphate group.

DNA• Surrounding the base pairs and

forming the sides of the “ladder” is a sugar-phosphate backbone.

• The backbone is made of a sugar (deoxyribose) and a phosphate group, alternating and in reverse order from the other strand.– Backbone is linked by

phosphodiester bonds.– The end of DNA with the phosphate

on top is the 5’ (“five prime”) end.– The other end of the backbone is the

3’ (“three prime”) end.

http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg

3’ and 5’? Huh?

• 3’ and 5’ get their names from the pentose sugar’s carbon atoms.

• Each carbon in pentose is numbered and has a specific job in the formation of DNA.– Carbon 1 = base attachment– Carbon 2 = oxygen (ribose) or not

(deoxyribose)?– Carbon 3 = another nucleotide

attachment– Carbon 4 = completes ring– Carbon 5 = phosphate attachment

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Pentose.gif http://www.synapses.co.uk/genetics/pentose1.gif

DNA• DNA stands for

Deoxyribonucleic Acid.• By hydrogen bonds,

cytosine bonds to guanine and adenine to thymine.

• A ↔ T• C ↔ G

http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg

Base Pairs

• (Held together by hydrogen bonds)

• How can we remember this?

DNA Unwound (Basic)

Deoxy-ribose

P

Thymine

Deoxy-ribose

P

Cytosine

---H---

---H---

---H---

Deoxy-ribose

Adenine

Adenine

Deoxy-ribose

P

Guanine

Thymine Deoxy-ribose

Deoxy-ribose

P

DNA Unwound(Advanced)

Deoxy-ribose

P

Thymine

Deoxy-ribose

P

Cytosine

---H---

---H---

---H---

5’

5’

3’

3’Thymine

Deoxy-ribose

P

Guanine

Adenine Deoxy-ribose

P

Deoxy-ribose

P

Deoxy-ribose

Adenine

PD Bond

PD Bond

PD Bond

PD Bond

Complementary Base Pairs

• Video: Complementary Base Pairs

DNA Worksheet

• Try problems 1 and 2 on your DNA worksheet.1: A C1: T G

2: G A A G G C G T T

DNA

• Adenine and guanine are purines and have a double-ring structure.

• Cytosine and thymine are pyrimidines and have a single-ring structure.

• A purine always bonds to a pyrimidine.

• How can we remember this one?

Chargaff’s Rule

• Little side note here:– Austrian chemist Erwin Chargaff proposed that

the amount of purines in a cell equal the amount of pyrimidines.

– Makes sense!– Video!– Exclamation point?

Chargaff’s Rule Sample Question

• A DNA molecule is 40% guanine. By percent, how much thymine is in the molecule?

• 10%• If it’s 40% guanine, it’s 40% cytosine.• That’s 80% total, so 20% is left to be split

between adenine and thymine.• The molecule thus must be 10% adenine and 10%

thymine.

DNA Worksheet

• Try problems 3, 4, and 5 on your worksheet.3: T T G C A A G T C

4:

5. Always three rings (keeps the same width).

DNA Worksheet

• Try problems 6 and 7 on your worksheet.6: Sugar/Phosphate Backbone

7: A ↔ T, C ↔ G7: Purines – 2 rings, Pyrimidines – 1 ring

DNA Replication

• There comes a time in (almost) every DNA molecule’s life when it needs to be replicated (copied).– That time would be S phase.

• Here’s the general process:– Unwind the double-helix.– Break the hydrogen bonds (“unzip” the DNA).– Use enzymes to replace base pairs on each side.

Looks like this… [IMPORTANT]

Note that even though there

are two strands

forming down here, each is only “half”

new.

The “old” strand is

sometimes known as the

template strand

because it’s a model for the

new one.

Looks like this… [IMPORTANT]

http://online.santarosa.edu/homepage/cgalt/BIO10-Stuff/Ch10-Protein_Synthesis/DNA-Replication-Animation.gif

DNA Replication - Schematic

• Video: DNA Replication – Schematic

Time for a Game!

• In this game, you will be practicing the process of replication.

• Don’t mess up the base pairs!• You’ll also use the DNA you make to figure

out which organism it comes from.

• http://nobelprize.org/educational/medicine/dna_double_helix/dnahelix.html

Adding some names…

• In that activity, we matched DNA bases to one another. Ts were with As, Gs with Cs.

• Because they go together, we call these pairings complementary.– “The complementary base of G is C.”

Enzymes• The role we played – breaking the DNA “ladder”

and replaced missing base pairs – is a role played by enzymes in the human body.

• There are four main enzymes – here are the first two:1. DNA Helicase

• Unzips the DNA double-helix (breaks H-bonds).• The points at which Helicase has opened the DNA strand are

called replication forks.

2. DNA Polymerase• Adds complementary base pairs.

DNA Helicase Animation

http://gifsoup.com/view/1504259/dna-helicase.html

DNA Replication – Molecular

• Video: DNA Replication – Molecular

Replication

---H---

---H---

---H---Deoxy-ribose

P

Thymine

Deoxy-ribose

P

Cytosine

Deoxy-ribose

Adenine

Adenine

Deoxy-ribose

P

Guanine

Thymine Deoxy-ribose

P

Deoxy-ribose

P

DNA Helicase breaks H-bondsStrands move apart

P

Deoxy-riboseThymine

Deoxy-riboseGuanine

P

Deoxy-riboseAdenine

P

Deoxy-ribose

P

Cytosine

Deoxy-ribose

Adenine

Deoxy-ribose

P

Thymine

P

DNA Polymerase makes new DNA

H H

H H

H H

The Replication Caveat

• As it turns out, DNA Polymerase can only work from the 5’ end to the 3’ end.

• This means that one side of the DNA strand can be made continuously.– The leading strand.

• The other side of the DNA must be made in pieces.– The lagging strand.

Replication Bubble

http://www.svusd.org/hp_images/1752/D23456-Replication%20Bubble.jpg

Notice that though Helicase can move in

both directions, Polymerase can only read from 3’ to 5’ on the template strand.

As a result, one new strand is built

continuously from 5’ to 3’, but one is built

from 3’ to 5’ in pieces.

Replication Videos

• Video: Honors – DNA Replication• Video: Honors – DNA Replication 2

Additional Replication Vocabulary

• The pieces of the new strand are called Okazaki Fragments.

• Okazaki Fragments are started by RNA Primase, an enzyme that lays the foundation for them to be built.

• At the end, Okazaki Fragments are linked (annealed) by DNA Ligase, another enzyme.

• While all this is happening, the cell has placed single-stranded binding proteins (or SSBs or SSBPs) onto the exposed nitrogenous bases to prevent the DNA from “re-zipping-up.”

Putting It All Together

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit6/genetics/DNA/DNArep/images/lag.gif

What We Know About DNA

• We always hear that DNA is the genetic material of the cell, or the command center, or what is responsible for you. Whatever. What exactly does that mean?

• DNA helps the cell “decide” which proteins to make.– The proteins are different for everyone.– That’s why your DNA makes you unique

• And why we can use DNA to test potential criminals.

Time for a Flowchart

• Find some room in your notebooks.

Guiding Question

• How can one person have two different eye colors?

• Your questions? What do you want to know?

Time for a Gizmo

• It’s called Building DNA, and that’s just what you’ll be doing.

• As usual, you’ll need a second window open for Quia:– Building DNA Gizmo

• [Log-in Instructions]

Exit Ticket (Part One)

• What are the full names of the four nitrogenous bases in DNA?

• Which are purines, which are pyrimidines?• Which bases pair to which?

Exit Ticket (Part Deux)

• Which enzyme “unzips” the DNA double helix?

• Which enzyme places new nucleotides to complete the base pairs?