1. 2 AIM: How do organisms build/break macromolecules? Chapter 5 – The Structure and Function of...

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AIM: How do organisms build/break macromolecules?

Chapter 5 – The Structure and Function of Macromolecules

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Cells make most macromolecules (carbs, proteins and nucleic acids) by linking smaller, similar molecules called monomers to each other.

This paperclip will represent a monomerWhat do we get if we attach many similar

paperclips to each other in series?



Chapter 3 - The Molecules of Cells

AIM: How do organisms build/break macromolecules? You get a long chain of “paperclips” called a polymer.

This molecule is called a polymer (poly- means many). It is a molecule with many monomers = polymer.



Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers

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How do organisms build (synthesize) biological macromolecules?


AIM: How do organisms build/break macromolecules? Building macromolecules (synthesis):

We want to take these two small molecules (monomers) and attach them together by covalent bonds


Chapter 5 - The Structure and Function of MacromoleculesAIM: How do organisms build/break macromolecules?



AIM: How do organisms build/break macromolecules? Building macromolecules (synthesis):

This is done by removing OH from one and H from the other. These will combine to form water… a process known as dehydration synthesis or condensation reaction






Dehydration Synthesis

+ H2O






H H H H H H HH

monomermonomermonomer

Polymer






Dehydration (condensation) synthesis:




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How do organisms break down biological macromolecules?

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Review Slide - Two types of chemical reactions to synthesize and break

1. Dehydration (Condensation) Synthesis

-Reaction used to build -macromolecules

- Remove a water

2. Hydrolysis

- Reaction used to break down macromolecules

- Add water




NEW AIM: Describe the structure and function of carbohydrates.

We will now begin to look at the structure and function of the biological macromolecules…

Chapter 5 - The Structure and Function of MacromoleculesAIM: Describe the structure and function of carbohydrates?



1. Carbohydrates

AIM: Describe the structure and function of carbohydrates?



?AIM: Describe the structure and function of carbohydrates.

This is asking…what is the monomer of carbohydrates?

AIM: Describe the structure and function of carbohydrates.

Chapter 5 - The Structure and Function of MacromoleculesAIM: Describe the structure and function of carbohydrates?


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Notice their names…They both end in –ose.

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Triose sugars(C3H6O3)

Pentose sugars(C5H10O5)

Hexose sugars(C6H12O6)

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

HO C H

H C OH

H C OH

H C OH

H C OH

HO C H

HO C H

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

H C OH

C OC O

H C OH

H C OH

H C OH

HO C H

H C OH

C O

H

H

H

H H H

H

H H H H

H

H H

C C C COOOO

Ald

oses

Glyceraldehyde

RiboseGlucose Galactose

Dihydroxyacetone

Ribulose

Keto

ses

FructoseFigure 5.3



The carbonyl is at the end of the carbon skeleton making them all aldehydes or what we call aldoses (there is the –ose again)

The carbonyl is in the middle of the carbon skeleton making them all ketones or ketoses.

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(CH2O)These monomers have the empirical formula:

The element ratio in a monosaccharide is 1C : 2H : 1O

Monosaccharides are also just carbon and water, hence carbohydrate (carbon hydrated with water).

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H

H C OH

HO C H

H C OH

H C OH

H C

O

C

H

1

2

3

4

5

6

H

OH

4C

6CH2OH 6CH2OH

5C

HOH

C

H OH

H

2 C

1C

H

O

H

OH

4C

5C

3 C

H

HOH

OH

H

2C

1 C

OH

H

CH2OH

H

H

OHHO

H

OH

OH

H5

3 2

4

(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.

OH3

O H OO

6

1

Figure 5.4



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Organisms connect them to each other by dehydration (condensation) synthesis to make polymers…

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Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.

Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.

(a)

(b)

H

HO

H

HOH H

OH

O H

OH

CH2OH

H

HO

H

HOH

H

OH

O H

OH

CH2OH

H

O

H

HOH H

OH

O H

OH

CH2OH

H

H2O

H2O

H

H

O

H

HOH

OH

O H

CH2OH

CH2OH HO

OHH

CH2OH

HOH

H

H

HO

OHH

CH2OH

HOH H

O

O H

OHH

CH2OH

HOH H

O

HOH

CH2OH

H HO

O

CH2OH

H

H

OH

O

O

1 2

1 41– 4

glycosidiclinkage

1–2glycosidic

linkage

Glucose

Glucose Glucose

Fructose

Maltose

Sucrose

OH

H

H

Figure 5.5





Monosaccharides Disaccharide

Glucose (Glu) + Glucose (Glu)

Glucose (Glu) + Fructose (Fru)

Glucose (Glu) + Galactose (Gal)

maltose

sucrose

lactose

These are the disaccharides you need to know at the moment. There are many, many others in biology as there are many different monosaccharides.




sugars


By definition, sugars are the monosaccharides and disaccharides. Their names typically end in –ose like glucose, maltose, lactose, etc…



It is time to continue adding monomers to make a polymer…

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What will plants do with all this glucose stored as starch in the future…what is the function of starch?1. Energy Source: transfer the energy to ATP to do work in the cell

2. Biosynthesis: Plants can use the molecules of glucose directly to build other molecules needed in the cell such as amino acids, fatty acids, to build proteins, plasma membranes, etc…

Chloroplast Starch

Amylose Amylopectin

1 m

(a) Starch: a plant polysaccharideFigure 5.6

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Glycogen chains

What is the difference major difference b/w starch and glycogen?

It is HIGHLY branched.

The same thing plants do…energy source for moving molecules in cells or moving yourself around etc… and for biosynthesis.

What will animals do with all this glucose stored as glycogen?

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Compare the structure of cellulose to that of starch and

glycogen.

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Function?

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Figure 5.9



How do herbivores digest cellulose?These mammals contain bacteria in part of their digestive system

called the rumen that can break down the cellulose (mutualism – bacteria get a place to live and food, cow gets to use cellulose in usable fatty acid form secreted by the bacteria)

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Digesting Polysaccharides

If you cannot digest it, you cannot absorb it and it ends up being egested, which is why cellulose = fiber or roughage.

Why is fiber beneficial then?

It scrapes the walls of your digestive track, which stimulates mucous secretion and smooth passage of material amongst many other benefits….

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(a) The structure of the chitin monomer.

O

CH2OH

OHHH OH

H

NH

CCH3

O

H

H

(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.

(c) Chitin is used to make a strong and flexible surgical

thread that decomposes after the wound or incision heals.

OH

Figure 5.10 A–C




2. Lipids

AIM: Describe the structure and function of lipids?


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AIM: Describe the structure/function of lipids.

Major subclasses of LIPIDS:

1. Triglycerides (a.k.a – fat)

2. Phospholipids

3. Steroids



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Tri- means three

-glyceride means glycerol

The tri- implies that the triglyceride (fat molecule) has three fatty acids.

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fattyCarboxylic acid

Above in yellow is a fatty acid. It is called this because the molecule is fatty (hydrophobic/non-polar – all the CH2’s) and has one carboxylic acid and hence fatty acid.

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fattyCarboxylic acid

The fatty acid links to the glycerol by…Dehydration synthesis between the glycerol’s hydroxyl and the carboxylic acid of the fatty acid (see picture). Functional groups are at it again!

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One of the three ester linkages

A complete triglycerideJoined together by ester linkages!!

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46(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12



Stacking like bricks

This allows them to act like “bricks” and stack upon each other forming a SOLID NEAR ROOM TEMPERATURE

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Kinked structures do not stack well and therefore tend to be liquid at room or near room temperature.

Ex. All of your plant oils: vegetable oil, canola oil, peanut oil, walnut oil, olive oil, etc…



Vegetable oil

Vegetable oil that has been partially hydrogenated. See how it is starting to become a solid

Hydrogenation



hydrogenation

Typical NATURAL Cis-unsaturated fatty acid

Trans UNATURAL form of the same fatty acid after only partial hydrogenation of the oil.

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Triglyceride functions?

1. Energy Storage

2. Insulation – subcutaneous fat, just below our skin

3. Protect organs (padding) – visceral fat below your muscles





2. Phospholipids

3. Steroids

Now let’s look at the second sub-class…phosphlipids



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AIM: Describe the structure/function of lipids. Therefore the molecule is

broken into two parts:

1. The hydrophilic head

2. The hydrophobic tails

Phospholipid Structure

- Negatively charged phosphate- Charged R group

Hydrocarbon fatty acid tails

- Ester linkages




AIM: Describe the structure/function of lipids. Phospholipid function

Let’s try and figure out the function. Imagine you took millions upon millions of phospholipids and dissolved them in an aqueous solution. What would they do?





Identify the structure in the above picture. Where do we find this in nature?It’s a phospholipid bilayer silly and this is the general structure of plasma (cellular)

membranes!!





PLASMA MEMBRANES!!

Therefore, phospholipids make up the majority of what?



They will form the bulk of ALL the cell membranes in the cell from the cell membrane itself, the nuclear membrane, ER membrane, mitochondrial membrane, etc…


AIM: Describe the structure/function of lipids. What is the role of the unsaturated (kinked) fatty acid tail?

The kinked tail keeps the plasma membranes fluid so that proteins and phospholipids can move and therefore do their jobs (fluid mosaic model of the membrane).







2. Phospholipids

3. Steroids

On to the third sub-class…steroids




AIM: Describe the structure/function of lipids. When people say “steroid” they usually think muscle and testosterone. This is only one of many, many different steroids used in the body as hormones and in cell membranes.

Remember that a hormone is a molecule released by one cell into the blood, which will talk to another cell and tell it what to do like insulin.

What is a steroid?

In fact, perhaps the most important and talked about steroid of all time is…

Cholesterol



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cholesterol

Different steroids have different attachements to the rings.

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(you don’t have to eat it)Function?


3. Proteins

AIM: Describe the structure and function of proteins?


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63

Table 5.1



Remember that proteins are the workers, the machines, the scaffolding. They do almost all the work…

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Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH H2O

Fructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

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4 Products are released.Figure 5.16




?AIM: Describe the structure and function of proteins.

What is the monomer of proteins?



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Therefore, how many different amino acids are there?

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20There are twenty different amino acids encoded for by the genome and used to make (synthesize) proteins.

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O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3CH3

CH2

CH

C

H

H3N+

C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–



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O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+

C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O–

NH2 O

C

CH2

CH2

C CH3N

+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N

+

H

O

O–

O– O

C

CH2

C CH3N

+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N

+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N

+

H

O

O–

CH2

NH+

NHCH2

C CH3N

+

H

O

O–

Serine (Ser) Threonine (Thr)Cysteine

(Cys)Tyrosine

(Tyr)Asparagine

(Asn)Glutamine

(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)



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C-terminus N-

terminus


polypeptide

AIM: Describe the structure and function of proteins.

A polypeptide is simply a long chain (typically greater than five) of amino acids linked by peptides bonds.

Is this the N or C terminus?

It’s the C-terminus



AIM: So what are the macromolecules?


Consists of 4 polypeptide subunits

& the heme is shown in detail with bound iron.



What is the function of hemoglobin?Hemoglobin is a protein

that binds to (carries) oxygen (O2) – each protein binds four O2 molecules.

They are found inside the red blood cells of your blood.

The amino acid sequence determines the protein structure



structure determinesand

function





What if the aa sequencechanges ?Since the structure of the polypeptide is SOLELY determined by the sequence, if you change the sequence, you may change the structure and therefore the function might change.



1 vhltpEeks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg keftppvqaa yqkvvagvan alahkyh 147

The Amino Acid Sequence of Human Hemoglobin β chain:

This is the sequence of the hemoglobin β chain.

1 vhltpVeks avtalwgkvn vdevggealg rllvvypwtq rffesfgdls tpdavmgnpk vkahgkkvlg afsdglahld nlkgtfatls elhcdklhvd penfrllgnv lvcvlahhfg keftppvqaa yqkvvagvan alahkyh 147

A single mutation in the DNA can cause E (glutamate) to be V (valine) resulting in the disease known as...

SICKLE-CELL ANEMIA



Sickle Cell Anemia- Caused by a change in a single amino acid (E6V) in the β chain of hemoglobin…

-Results in abnormal, sickled shape red blood cells, which block the flow of blood resulting in extreme pain, organ damage and possible heart failure / death.





Sickle Cell AnemiaFig. 5.21




AIM: Describe the structure and function of proteins. The structure of a protein is divided into four parts: 1. Primary structure

2. Secondary structure3. Tertiary structure4. Quaternary structure (not all proteins have this level)



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Figure 5.20

–

Amino acid subunits

+H3NAmino end

o

Carboxyl end

oc

Gly Pro Thr Gly

Thr

Gly

GluSeuLysCysProLeu

Met

Val

Lys

Val

LeuAsp

AlaVal ArgGlySer

Pro

Ala

Gly

lle

SerPro PheHis Glu His

Ala

Glu

ValValPheThrAla

Asn

Asp

SerGly Pro

ArgArg

TyrThr

lleAla

Ala

Leu

Leu

SerProTyrSer

TyrSerThr

Thr

Ala

ValVal

ThrAsn Pro

LysGlu

Thr

Lys

SerTyrTrpLysAlaLeu

Glu Lle Asp



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O C helix

pleated sheet

Amino acidsubunits NC

H

C

O

C N

H

C

O H

R

C N

H

C

O H

C

R

N

HH

RC

O

R

C

H

N

H

C

O H

NC

O

R

C

H

N

H

H

C

R

C

O

C

O

C

N

HH

R

C

C

O

N

HH

C

R

C

O

N

H

R

C

H C

ON

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N H

O C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

R

N

H

C

OC

N

H

R

C

H C

O

N

H

C



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()

An alpha helix forms when the chain of amino acids spirals around and hydrogen bonds to itself These hydrogen bonds stabilize the helix (keep it from falling apart).

Alpha helices are ALWAYS right handed

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Beta ()

The Beta sheet forms when two or more linear chains of amino acids run parallel to each other and form H-bonds as points of attachment.

These hydrogen bonds stabilize the beta sheet (keep it from falling apart).

Side chains are not involved in gluing in the sheets together

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1. Hydrogen bonds –Form between polar side chains 2. Ionic bonds – Form between charged / ionic side chains

3. Covalent bonds –Form between the side chains of two cysteine amino acids = disulfide bridge. 4. Hydrophobic interactions / van der WaalsNon-polar side chains group up away from water and stick to each other

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Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme



Peptide bonds (covalent)

Backbone H-bonds

Side chain / backbone H-bonds, ionic bonds, covalent bonds and hydrophobic/van der Waals interactionsSide chain/backbone H-bonds, ionic bonds, covalent bonds and hydrophobic/van der Waals ineractions

Held together by…

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Remember that secondary, tertiary and quaternary structure are all held together by a large number of hydrogen and ionic bonds. If these bonds are disrupted, the protein will unfold down to its primary structure (denature)

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Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded polypeptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

2

1

3

Figure 5.23



91Figure 5.24




4. Nucleic Acids

AIM: Describe the structure and function of nucleic acids?



A nucleotide

AIM: Describe the structure of DNA and RNA?




A nucleotide (the monomer)


Three parts to a nucleotide:

1. Phosphate

2. A 5-Carbon Sugar

3. Nitrogenous Base





There are five different nitrogenous bases



Purines vs Pyrimidines

A, C, G and T are found in DNAA, C, G and U are found in RNA


AIM: Describe the structure of DNA and RNA? In addition to there being five different bases, there are also two different sugars…





1

23

4

5

The first is ribose:- Ribose is found in RNA

- Ribonucleic Acid (RNA)

- Keep your eye on carbon 2





The other is Deoxyribose (Deoxy- means without

oxygen).- Deoxyribose is found in DNA- Hence Deoxyribonucleic Acid (DNA)- Look at carbon 2, it is without oxygen compared to carbon 2 on ribose



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AIM: Describe the structure of DNA and RNA? The hydroxyl on carbon 3 of the top

nucleotide and the hydrogen on the phosphate attached to carbon 5 on the bottom nucleotide will combine to form water…(dehydration synthesis).





This forms a phosphodiester bond between them

Resulting in repeating sugar phosphate units .

Will this be DNA or RNA? Explain.




The 5’ and 3’ ends…


The end with the phosphate is called the ________ end because

The end with the hydroxyl is called the ________ end because

the phosphate is attached to the 5’ carbon.

the phosphate is attached to the 3’ carbon.

5’

3’

5’

3’



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105



5’

3’ 5’

3’

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Base Pairing

In a DNA molecule, A base pairs with T (they form two H-bonds with each other)...

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…and C base pairs with G (they form THREE H-bonds with each other).

Base Pairing

What else can we say about these base pairs in terms of the type of base?



Draw the the Anti-Parallel Complementary Strand

What is meant by antiparallel?

What is meant by complementary?

A

G

C

C

T

T

T

A

A

G

G

C




How about the structureof RNA?AIM: Describe the structure of DNA and RNA?



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Structure of RNA

-RNA is single stranded

- It can fold up (purposely) and base-pair with itself and therefore it can form many different structures depending on its _______________.sequence of nucleotides




Where is DNA found in the cell ?AIM: What are some of the functions of nucleic acids?

- The vast majority of DNA is found of course in the nucleus

What do you know about the nucleus?




AIM: What are some of the functions of nucleic acids? Where in the cell are polypeptides (proteins) synthesized

?



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PROBLEM: the “books” are stuck inside the nucleus, while the protein building machinery (ribosome) that needs the information is outside.



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DNA RNA Protein

Stores genetic material inherited from parents

DNA RNA

Template for DNA replication

Contain genes for specific proteins and serves as template for RNA

Specifically mRNA, carries the genetic information to the protein synthesizing machinery

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1. 2 AIM: How do organisms build/break macromolecules? Chapter 5 – The Structure and Function of...

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