Slide 1 / 140 Slide 2 / 140 Biology Large Biological Molecules 2015-08-28 www.njctl.org Slide 3 / 140 amino acid carbohydrate amphiphilic cellulose denaturation disaccharide DNA fatty acid fructose glucose glycogen hydrocarbon lipid monosaccharide nucleic acid nucleotide peptide bond phosphodiester bond polysaccharide primary structure protein purine pyrimidine quaternary structure RNA saturated secondary structure starch steroid sucrose tertiary structure trans fat triglyceride unsaturated waxes Vocabulary Slide 4 / 140 Large Biological Molecules Unit Topics · Organic Chemistry, Hydrocarbons · Amino Acids, Proteins · Nucleic Acids Click on the topic to go to that section · Lipids · Carbohydrates, Polysaccharides · Review Slide 5 / 140 Organic Chemistry, Hydrocarbons Return to Table of Contents Slide 6 / 140 Carbon is the backbone of biological molecules. Organic chemistry is the chemistry of carbon compounds. Carbon has the ability to form long chains, enabling the creation of large molecules: proteins, lipids, carbohydrates, and nucleic acids. Carbon
Organic compounds range from simple molecules to colossal ones.
H
C
Organic compounds contain:
Always Often Occasionally
N
O
S
P
Si
Halogens
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Organic Chemistry
Carbon atoms can form diverse molecules by bonding to four other atoms which are in different directions.
This allows the molecule to take on a 3D configuration. It is this 3D structure that defines the molecule's function.
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Electron Configuration
You should remember from chemistry, electron configuration is the key to an atom’s characteristics.
Electron configuration determines the kinds and number of bonds an atom will form with other atoms.
Carbon has four valence electrons to make covalent bonds.
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1 Organic chemistry is a science based on the study of _____. A functional groups.
B carbon compounds.
C water and its interaction with other kinds of molecules.
D inorganic compounds.
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2 Which property of the carbon atom gives it compatibility with a greater number of different elements than any other type of atom?
A Carbon has 6 to 8 neutrons.B Carbon has a valence of 4.C Carbon forms ionic bonds.D A and C only.E A, B, and C.
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3 What type(s) of bond(s) does carbon form?
A ionicB hydrogenC covalentD A and B onlyE A, B and C
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4 How many electron pairs does carbon share to complete its valence shell?
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5 Which of the following is an organic compound?
A H2OB NaClC C6H12O6
D O2
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Hydrocarbons
These molecules consist of only carbon and hydrogen atoms.
Each carbon atom makes 4 bonds. Each hydrogen atom makes 1 bond. Carbon-hydrogen bonds are non-polar, so those bonds are hydrophobic.
Fossil fuels are examples of hydrocarbons that are formed from decaying organic matter.
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Saturated Hydrocarbons
In saturated hydrocarbons:
· every carbon atom is bonded to four different atoms· no new atoms can be added along the chain
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Unsaturated Hydrocarbons
double bond
In unsaturated hydrocarbons:
· some of the carbon-carbon bonds are double or triple bonds
· those can be broken and replaced with a single bond
· at that point, additional atom(s) can be added
H C C CC
H
H
H
H
H
H
H
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6 Hydrocarbons _____.
A are polarB are held together by ionic bondsC contain nitrogenD contain only hydrogen and carbon atoms
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7 What is the reason why hydrocarbons are not soluble in water?
A The majority of their bonds are polar covalent carbon to hydrogen linkages
B The majority of their bonds are nonpolar covalent carbon to hydrogen linkages
C They are hydrophilicD They are lighter than water
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8 Hydrocarbons containing only single bonds between the carbon atoms are called __________.
A saturated
B polar
C non-polar
D unsaturated
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9 Hydrocarbons containing double or triple bonds between some of the carbon atoms are called __________.
A saturated
B polar
C non-polar
D unsaturated
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10 Gasoline and water do not mix because gasoline is __________.
A less dense than waterB non-polar and water is polar
C volatile and water is not
D polar and water is non-polar
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Hydrocarbons form the framework from which the 4 different classes of macromolecules (large molecules) have been derived. We have mentioned these 4 types of molecules before . List them below.
Biological Macromolecules
· _____________
· _____________
· _____________
· _____________
(See the first slide in this chapter for a hint)
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Three of the classes of life’s organic molecules are polymers: carbohydrates, nucleic acids, and proteins. Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of how their monomers are used to make polymers.
An immense variety of polymers can be built from a small set of monomers.
Polymers
Polymer : Monomer they're made from:
Proteins Amino acids
Carbohydrates Simple sugars (monosaccharides)
Nucleic acids Nucleotides
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Review: Dehydration Synthesis
longer polymer
monomershort polymer
OH
OHH
H
water
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11 ____________ are to carbohydrates as ___________ are to proteins.
A nucleic acids; amino acids
B monosaccharides; amino acids
C amino acids; nucleic acids
D monosaccharides; nucleic acids
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12 Dehydration synthesis reactions join monomers to form polymers. Which of the following illustrates a dehydration synthesis reaction?
A C6H12O6 + C6H12O6 --> C12H22O11 + H2O
B C3H6O3 + C3H6O3 --> C6H12O6
C C6H12O6 + H2O --> C3H6O3 + C3H6O3
D C3H6O3 + H2O --> C3H6O4
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Carbohydrates,Polysaccharides
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Slide 29 / 140
Carbohydrates are compounds consisting of carbon, hydrogen and oxygen.
Simple carbohydrates also called
sugars also called
saccharides.
Carbohydrates
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The general formula for a carbohydrate is
C x H 2x O x
So some possible formulas for carbohydrates are:
C6H12O6 C 8H16O8 C9H18O9
Formula for Carbohydrates
Carbohydrates have equal amounts of carbon and oxygen atoms, but twice as many hydrogen atoms.
Monosaccharides are the simplest carbohydrates. They are the monomers that are used to build more complex carbohydrates. The most common of these are glucose and fructose.
Disaccharides are formed by combining two monosaccharides. Table sugar, (sucrose) is made up of glucose and fructose.
Polysaccharides are formed by combining chains of many monosaccharides.
Carbohydrates
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Monosaccharides are the simplest sugars. Examples include glucose and fructose
In solution, they form ring-shaped molecules.
The basic roles of simple sugars are as:· fuel to do work, · the raw materials for carbon backbones· the monomers from which larger
carbohydrates are synthesized.
Monosaccharides
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Sugars all have several hydroxyl (OH-) groups in their structure that makes them soluble in water.
C
Glucose Fructose
(monosaccharides)
Carbohydrate Solubility
Note: the names of sugars typically end in "ose"
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In solution, sugars form cyclic structures.
These can form chains of sugars.
Carbohydrate Structures
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Cells link 2 simple sugars together to form disaccharides
Disaccharide formation is another example of a dehydration synthesis reaction.
Disaccharides
The most common disaccharide is sucrose (glucose + fructose)
What other molecule is produced when sucrose is formed?
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16 Which of the following is an example of a monosaccharide?
A sucroseB glucoseC fructoseD B & C
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17 Disaccharides are formed by combining how many monosaccharides?
A 2B 3C 4D 5
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18 What is another name for a simple carbohydrates?
A sugars
B saccharides
C monosaccharides
D all of the above
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Polysaccharides are polymers of glucose.
Different organisms link monosaccharides together, using dehydration reactions, to form several different polysaccharides.
The most important 3 are starch, glycogen, and cellulose.
Polysaccharides
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Polysaccharides: Starch
Starch is used for long term energy storage in plants.
A starch can be branched or unbranched.
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Polysaccharides: GlycogenGlycogen has the same kind of bond between monomers as starch but it is always highly branched.
It is used for long term energy storage in animals. It's used in muscles to provide a local supply of energy when needed.
Glycogen is broken down to obtain glucose.
What kind of reaction is used?
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Polysaccharides: Cellulose
Cellulose has a different kind of bond between monomers, forming chains that are cross-linked by hydrogen bonds.
Cellulose is a carbohydrate used to make cell walls in plants.
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Breakdown of Cellulose
Because cellulose is the principle structural molecule in cell walls of plants, it needs to be strong.
Animals cannot break down cellulose without the help of intestinal bacteria. It is commonly referred to as fiber.
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In order for cells to obtain energy from polysaccharides, they must be first broken down into monosaccharides.
____________ occurs, breaking the polysaccharide into glucose molecules.
Getting Energy
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19 The fundamental unit of a polysaccharide is
A fructoseB glucoseC sucroseD A and B
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20 Simple sugars do not include
A monosaccharidesB disaccharidesC polysaccharidesD glucose
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21 Starch and glycogen are similar molecules because
A they are both disaccharides
B they are both structural molecules
C they are both used to storage energy
D they are both highly branched
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22 A necropsy (an autopsy on an animal) is performed by a veterinarian. The stomach contents contain large amounts of cellulose. We can conclude that this animal is a/an ________________.
A carnivore
B herbivore
C omnivore
D decomposer
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23 In plants ____________ is used to for energy storage and ______________ is found in cell walls.
A glucose; starch
B starch; glycogen
C starch; cellulose
D cellulose; starch
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Nucleic Acids
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Nucleic acids are compounds consisting of carbon, hydrogen, oxygen, nitrogen, and phosphorus.
Nucleic Acids
The two main types of nucleic acids are DNA and RNA
The bonds between nucleotides are called phosphodiester bonds.
Like bonds between saccharides, they are formed by dehydration synthesis.
Phosphodiester bond
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Nucleotides have three parts:
a sugara base (a nitrogen compound)
a phosphate
Parts of a Nucleotide
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Sugars
Ribonucleic Acid (RNA) uses the sugar ribose, while Deoxyribonucleic Acid (DNA) uses the sugar deoxyribose.
Here's the difference.
Ribose Deoxyribose
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Slide 61 / 140 Slide 62 / 140
Each strand is unique due to its sequence of bases. In this way, genetic information is stored in the sequence of nucleotides.
Since the bases are not part of the sugar or the bond, the base sequence is independent of them. Any base sequence is possible.
Nucleotides
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25 The creation of a phosphodiester bond involves the removal of ____ from the nucleotides:
A phosphates
B glucose
C water
D nucleic acids
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26 Which of the following is not a component of a nucleotide?
A phosphate groupB nitrogenous baseC 5-carbon sugarD glucose
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27 Which base is found in RNA but not DNA?
A CytosineB UracilC GuanineD Adenine
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28 The only structural difference between RNA and DNA is in their nitrogenous bases.
TrueFalse
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29 Adenine would be characterized as a purine.
True
False
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30 Uracil is a purine.
True
False
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31 Pyrimidines are bases with single carbon rings.
True
False
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RNA
RNA is a single strand of nucleotides.
This strand folds in on itself, hydrogen bonds forming between the bases, and between bases and surrounding water. These bonds cause RNA to form different shapes.
Different sequence of bases = different shapes
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RNA base pair bonding
Bonds form between bases in a predictable pattern.
A nucleotide with an adenine base (A) will hydrogen bond with a nucleotide with a uracil (U) base. A nucleotide with a guanine (G) base bonds with a nucleotide with a cytosine (C) base.
A UC G
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RNAIn early life, RNA played many roles that have now been taken over by more specific molecules. RNA's role is still essential, but more limited than it once was. Think back to last chapter and fill in the molecules which control these functions now.
Function Then Now
catalyze reactions RNA
store energy RNA
store genetic information RNA
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DNA is double-stranded.
It only forms one shape: the double-helix.
Pair bonding between nucleotides still occurs, but in DNA it is between guanine (G) and cytosine (C) and between adenine (A) and thymine (T)
DNA
Adenine
Thymine
Cytosine
GuanineA TC G
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Instead of nucleotides being attracted to other bases in the same strand, to create shapes, they bond to matching nucleotides in a second strand, to create the double stranded helix.
Double Helix
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But it also means that DNA can't directly work in the cell. It is a library of information, but the only way that information can be used is via RNA.
RNA is chemically active in the cell, DNA is not.
DNA v. RNAThis makes DNA a better archive for genetic information since the bases are on the inside of the helix, protected. Thymine is also more stable than uracil.
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Storage and Implementation of the Genetic Code
So DNA is more useful and stable as an archive, while RNA is more useful working in the cells.
RNA carries genetic information from DNA to where it can be used.DNA is maintained in a safe environment to maintain the integrity of the genetic code.
RNA is used throughout the cell to implement the genetic code that's stored within DNA.
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DNA and RNA
RNA strands are shorter and less durable than DNA strands, but they are critical to communicate the instructions of the DNA code to the cell where they can be executed.
Without RNA, the information stored in DNA could not be used. And without DNA, the information would not be as stable.
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33 DNA is more stable than RNA because _____.
A it can form a double helixB it contains the base uracilC it can form a double helix and contains the
base uracilD it can form a double helix and contains the base
thymine
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34 DNA _______________. RNA _____________
A is a polymer of nucleic acid; is a polymer of glucose
B is always a double helix; forms many shapes
C has hydrogen bonds between its bases; bases do not form bonds
D acts as an enzyme; stores genetic code
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DNA RNA
DNARNA
and
double-stranded
double helix
ribose sugar
single stranded
phosphate groupfound inside and
outside the nucleus
guanine base
multiple shapes
uracil base
thymine base
remains in nucleus cytosine
basedeoxyribose sugar
adenine base
made up of nucleotides
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Proteins
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Slide 83 / 140
Proteins are compounds consisting of carbon, hydrogen and oxygen, nitrogen, and sometimes sulfur.
Proteins also called
peptides also called
polypeptides.
Proteins
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Proteins are chains of amino acids. There are 20 amino acids used to construct the vast majority of proteins.
While there are a few others that are sometimes used, these 20 are the "standard" amino acids.
All life on Earth uses virtually the same set of amino acids to construct its proteins.
Amino Acids always include an amine group (NH3), a carboxyl group (COOH) and a side chain that is unique to each amino acid.
Components of Amino Acids
The side chain (sometimes called the R-group) determines the unique properties of each amino acid. Here it is symbolized by the letter "R".
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The chemical bond that is formed between amino acids is called a peptide bond.
Hydroxyl group H atom Water
Peptide Bonds
Like bonds between saccharides and nucleotides, they are formed by dehydration synthesis.
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Peptide chain with 50 or more amino acids can form an individual protein.
Peptide bonds
1
1
2
2
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The 3 in the light blue box are basic ("amine" group in the side chain).
The 2 in the magenta box are acidic ("carboxyl" group in the side chain).
The 8 amino acids in orange are nonpolar and hydrophobic.The others are polar and hydrophilic.
The unique side chains are shown in blue.
The common "amine" group (NH3) and "carboxyl" group (COOH) are shown in black.
Amino Acids
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35 Glucose molecules are to starch as ___________ are to proteins.
A oils
B fatty acids
C amino acids
D nucleic acids
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36 Which of the following is not a component of amino acids?A R-group
B Amine Group
C Hydroxyl Group
D Carboxyl Group
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37 Which component of amino acids varies between the 20 different kinds?
A Amine group
B Carboxyl group
C Hydroxyl group
D R-group
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Protein Shape and Structure
Shape is critical to the function of a protein. A protein's shape depends on four levels of structure:
· Primary · Secondary · Tertiary · Quaternary
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The primary structure of a protein is the sequence of amino acids that comprise it.
Each protein consists of a unique sequence.
Proteins: Primary Structure
Alanine Lysine
Valine
Leucine Serine
Leucine Leucine Alanine
Lysine Alanine Serine Lysine
or
or
or...
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Changes in Primary Structure
Changes in the primary structure of a protein are changes in its amino acid sequence. Changing an amino acid in a protein changes its primary structure, and can affect its overall structure and ability to function.
Sickle Cell disease is an example of a single amino acid defect
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Sickle Cell Disease
Sickle Cell Disease is a blood disorder specifically involving hemoglobin, which carries oxygen in the blood.
A single glutamate amino acid is replaced in the primary sequence by a valine.The result changes the overall shape of the hemoglobin molecule and does not allow it to properly carry oxygen.
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Secondary Structure
Secondary Structure is a result of hydrogen bond formation between amine and carboxyl groups of amino acids in each polypeptide chain.
Depending on where the groups are relative to one another, the secondary structure takes the shape of an alpha helix or a pleated sheet.
Note: R-groups do not play a role in secondary structure.
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alpha helix
pleatedsheets
Secondary Structure
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Tertiary Structure
Tertiary Structure is the overall 3-D shape of the polypeptide.
It results from the clustering of hydrophobic and hydrophilic R-groups and bonds between them along the helices and pleats.
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Structure Determines Function
The function of proteins is determined by their shape: it's tertiary structure. It's shape is driven by chemistry, but it is the shape, not the chemistry, that dictates function.
Each sequence of amino acids folds in a different way as each amino acid in the chain interacts with water and the other amino acids in the protein uniquely.
For instance, upon contacting water, a protein can fold into grooves that function as binding sites for other molecules.
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Denaturation
Changes in heat, pH, and salinity can cause proteins to unfold and lose their functionality, known as denaturation.
This egg's protein has undergone denaturation and loss of solubility, caused by the high rise in the temperature of the egg during the cooking process.
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38 The tertiary structure of a protein refers to:
A its size
B the presence of pleated sheets
C its over all 3D structure
D the number of R-groups it contains
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39 The __________ structure of a protein consists of a chain of amino acids assembled in a specific order.
A primary
B secondary
C tertiary
D quaternary
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40 Hydrophobic interactions have occurred between R groups of adjacent amino acids in a protein. This is the ___________ structural level and forms a/an _____________.
A secondary; alpha helix
B secondary; pleated sheet
C tertiary; 3D shape
D primary; alpha helix
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Quaternary Structure
Some proteins have a Quaternary Structure.
Quaternary structure consists of more than one polypeptide chain interacting with each other through hydrogen bonds and hydrophobic/hydrophilic interactions.
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Level Structure Notes
Primary bonds between amino acids
single chain of amino acids
Secondaryhydrogen bonds between amine and carboxyl groups
alpha helix, pleated sheet
Tertiaryclustering of hydrophobic or hydrophilic R groups
disulfide bonds
Quaternaryattractions between multiple peptide chains
not present in all proteins
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41 Denaturation causes a protein to
A lose its shape
B lose its function
C both A and B
D none of the above
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42 At which structural level does a protein get its function?
A Primary
B Secondary
C Tertiary
D Quaternary
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Types of Proteins
Structural hair, cell cytoskeleton
Contractile as part of muscle and other motile cells
Storage sources of amino acids
Defense antibodies, membrane
Transport hemoglobin, membrane
Signaling hormones, membrane
Enzymatic/ regulate speeds of chemical reactions
Type Function
Proteins have 7 different roles in an organism.
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43 Hormones are an example of what class of protein?
A structural
B defense
C transport
D signaling
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44 Hemoglobin is an example of what class of proteins?
A Transport
B Signaling
C Enzymatic
D Structural
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Lipids
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Lipids are the one class of large biological molecules that do not consist of polymers.
Lipids
Main functions of lipids include
· energy storage· the major component of cell membrane· involved with metabolic activities
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Recall the definitions of hydrophobic and hydrophilic.
Review: molecules and water
water
Hydrophilicmolecules
water
Hydrophobic molecules
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Lipids are either hydrophobic or amphiphilic.
Amphiphilic
hydrophobic
hydrophilic
Amphiphilic molecules have a hydrophobic "tail" and a hydrophilic "head". So one of its ends is attracted to water, while the other end is repelled.
What molecule did we already learn about that was amphiphilic?
Triglicerides are hydrophobic. They are constructed from two types of smaller molecules: a single glycerol and three fatty acids
Fatty acids are carboxylic acids with a very long chain of carbon atoms. They vary in the length and the number and locations of double bonds they contain.
Triglicerides: Hydrophobic Lipids
a fatty acid
CH2OH
CH2OH
CH2OH
glycerol
C C C CC
H H H H
HH
H
HHH
C C C COOHC
H H H
H H H
H
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3 fatty acids added to glycerol produce a trigliceride.
Triglicerides
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Phospholipids have 2 fatty acids and 1 phosphate group.
The phosphate end is polar and hydrogen bonds with water. The fatty acids are made of long chains of carbon and hydrogen, making them non-polar.
As a result, the phosphate end is hydrophilic and the fatty-acid end is hydrophobic. Overall, phospholipids are amphiphilic.
Phospholipids: Amphiphilic Lipids
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45 How are lipids different from other large biological molecules?
A they do not contain carbon
B they contain oxygen
C they are hydrophillic
D they are not polymers
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46 Lipids can be _____.
A hydrophobicB hydrophilicC amphiphilicD hydrophobic and amphiphilicE hydrophilic and amphiphilic
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47 A phospholipid is an example of a/an _____.
A hydrophobic moleculeB hydrophilic moleculeC amphiphilic moleculeD hydrophobic and amphiphilic
molecule
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Have the maximum number of hydrogen atoms possible
Have no double bonds in their carbon chain
They are solid at room temperature
Saturated Lipids
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Have one or more double bonds.
Oils are liquids at room temperature.
When hydrogenated (by adding more hydrogen) they become solid and saturated.
Unsaturated Lipids
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Saturated fatty acids
Fatty Acid Bonding Structure
Unsaturated fatty acids
double bond
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Trans Fats
Trans unsaturated fatty acids(transfats)
The chemical process that's used to saturate unsaturated fatty acids can lead to transfats.
These have a double bond that is rotated, resulting in a linear chain. These do not function well in biological systems and are a health hazard.
twisted double bondclick here to see a
video on lipids
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Trans Fat: Margarine
Margarine is a trans fat which which developed during World War II
Due to a milk and butter shortage, scientists took corn oil and hydrogenated it. The double bonds became single bonds and a solid was formed
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Health Hazards of Trans Fats
Trans fats tend to stay in the bloodstream much longer than saturated or unsaturated fats. Trans fats are much more prone to arterial deposition and plaque formation.
Trans fats are thought to play a role in the following diseases and disorders: cancer, alzheimers disease, diabetes, obesity, liver dysfunction, and infertity.
The hydrophobic end of a soap or detergent is repelled by water, but attracted to other non-polar molecules, like grease and oil.
The hydrophilic end of the soap or detergent hydrogen bonds with water.
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Soaps and Detergents
So the soap or detergent bonds with many stains (oil, grease, etc.) and pulls them from the surface being cleaned and into the surrounding water.
The water then goes down the drain, along with the oil or grease, leaving the surface clean.
fabricbeing washed
DIRT
DIRT REMOVED
detergent
hydrophobic end
hydrophilic end
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Waxes are effective hydrophobic coatings formed by many organisms (insects, plants, humans) to ward off water. They consist of 1 long fatty acid attached to an alcohol.
Waxes
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Steroids are lipids with backbones which form rings. Cholesterol is an important steroid as are the male and female sex hormones, testosterone and estrogen.
Steroids
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48 Fatty acids with double bonds between some of their carbons are said to be:
A saturated
B unsaturated
C triglycerides
D monoglycerides
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49 Which of the following is not a lipid?
A wax
B cellulose
C cholesterol
D triglyceride
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50 Cellulose is a lipid found in cell membranes.
True
False
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51 Which of the following is not one of the four major groups of molecules found in living organisms?
A glucoseB carbohydratesC lipidsD proteinsE nucleic acids
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Review
Return toTable ofContents
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carbon-hydrogen-oxygen1:2:1
plants (autotrophs)
primary source of energy
monosaccharides
monosaccharidespolysaccharides
simple sugar
long chains of monosaccharides
GlucoseFructose ring shaped
table sugarStarchCelluloseGlycogen
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types foun
d in
carbon, hydrogen,nitrogen, oxygen, phophorus
sugar
phosphate
Nitrogenous base
DNA
make proteins
nucleotides
RNA
store geneticinformation
uracildeoxyribose
ribose
thymine
guanine
adenine
cytosine
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have
and sometimes
amino acids
body to functionproperly
enzymes
control the rate of chemical reactions
carbon, hydrogen,oxygen, nitrogen, sulfur
muscle, haircartilage, nails,meat we eatamine group
