Biological molecules03-30-16

Announcements

• Turn in the student safety form

• On Monday, we saw most of chapter 1

• Today we will mainly see chapter 3, and only some concepts from chapter 2

Review

• What makes something a living thing?• Being made of one or more cells• Responding to stimuli• Being able to reproduce• Being able to grow and develop• Having genetic code that is heritable• Carrying out metabolism/regulation• Maintaining internal balance/homeostasis• Being organized in the cellular and ecosystem level• Adapt in the short term• Evolve in the long term

Continuing review

• Science is done using the scientific method• The Scientific method has six steps

1. Observation

2. Question

3. Hypothesis

4. Prediction

5. Experiment

6. Conclusion

Scientific reasoning: inductive

• Inductive reasoning related observations to arrive at a general conclusion

• This type of reasoning is common in descriptive science• Make observations and record them

• These data can be qualitative or quantitative

• Infer conclusions (inductions) based on evidence

• Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data

Inductive reasoning - examples

• This cat is black. That cat is black. A third cat is black. Therefore all cats are black.

• This marble from the bag is black. That marble from the bag is black. A third marble from the bag is black. Therefore all the marbles in the bag black.

• Most universities and colleges in Utah ban alcohol from campus. That most universities and colleges in the U.S. ban alcohol from campus.

Scientific reasoning: deductive

• Deductive reasoning logical thinking that uses a general principle or law to forecast specific results• Extrapolate and predict the specific results that would

be valid as long as the general principles are valid

Deductive reasoning - examples

• Physics - electric circuits• first premise: The current in an electrical circuit is directly

proportional to the voltage and inversely proportional to the resistance (I=V/R).

• second premise: The resistance in a circuit is doubled.• inference: Therefore, the current is cut in half.

• Chemistry - element classification• first premise: Noble gases are stable.• second premise: Neon is a noble gas.• inference: Therefore, neon is stable.

• Biology – plant classification• first premise: Monocot flower parts are in multiples of three.• second premise: Apple flowers have five petals.• inference: Therefore, apple trees are not monocots.

You do not need to know from chapter 2• The structure of an atom

• Atomic mass and number

• Isotopes

• The periodic table

• Electron Shells and the Bohr Model

• Electron Orbitals

Matter and elements

• Matter is a substance that occupies space and has mass

• Elements are unique forms of matter

• An atom is the smallest unit of matter that retains all of the chemical properties of an element

• Matter is made up of combinations of elements

Matter and elements

• Matter is made up of combinations of elements

• The most abundant element are carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus

• These form the biomolecules: nucleic acids, proteins, carbohydrates, and lipids - fundamental components of living matter

Chemical reactions and molecules

• Elements are most stable when their outermost shell is filled

• But, not all elements have enough electrons to fill their outermost shells

• So, atoms of elements form chemical bonds with other atoms to fill their outer shell

• When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule

Chemical reaction

• When two or more atoms bond together to form molecules

• or

• when bonded atoms are broken apart

• The substances used in the beginning of a chemical reaction are called the reactants

• The substances found at the end of the reaction are known as the products

Bonds

• A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms• Polar covalent bonds form when the electrons are unequally

shared by the atoms• The e are attracted more to one nucleus than the other • A slightly positive (δ+) and a slightly negative (δ–) charge develops

• Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally

Why Is Carbon So Important in Biological Molecules?• Organic refers to molecules containing a carbon

skeleton bonded to hydrogen atoms• All macromolecules are organic molecules

• Inorganic refers to carbon dioxide and all molecules without carbon

• Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen

Hydrocarbon chains

• Hydrocarbon chains are formed by successive bonds between carbon atoms

• May be branched or unbranched

• The overall geometry of the molecule is altered by the different geometries of single, double, and triple covalent bonds

• Linear chains are known as aliphatic hydrocarbons

Hydrocarbon rings

• Aromatic hydrocarbons, consists of closed rings of carbon atoms

Isomers

• Molecules that share the same chemical formula but have a different structure of their atoms and/or chemical bonds are known as isomers

• Structural isomers differ in the placement of their covalent bonds

Isomers

• Geometric isomers have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. • Butene (C4H8) has two methyl groups (CH3) that can be

on either side of the double covalent bond central to the molecule

• When the carbons are bound on the same side of the double bond, this is the cis configuration

• When they are on opposite sides of the double bond, this is the trans configuration

Enantiomers

• Share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms

• They are mirror images of each other

• In nature, only L-forms of AA are seen

• Some bacterial forms of AA are D-form

Why Is Carbon So Important in Biological Molecules? • The unique bonding properties of carbon are key to

the complexity of organic molecules

• It can bond covalently with up to 4 different atoms

C

hydrogen

carbon

nitrogen

oxygen

C C C

N

O O

N N

Why Is Carbon So Important in Biological Molecules?

• The unique bonding properties of carbon are key to the complexity of organic molecules• Functional groups: groups of atoms that occur

within molecules and confer specific chemical properties to those molecules• Classified as hydrophobic or hydrophilic depending on their

charge or polarity characteristics

Table 3-1

How Are Organic Molecules Synthesized?• Small organic molecules (called monomers) are

joined to form longer molecules (called polymers)

• Biomolecules are joined or broken through dehydration synthesis or hydrolysis

How Are Organic Molecules Synthesized?• Biological polymers are formed by removing water

dehydrationsynthesis

How Are Organic Molecules Synthesized?• Biological polymers are split apart by adding water

hydrolysis

How Are Organic Molecules Synthesized?• Biological polymers are formed by removing water

and split apart by adding water

• All biological molecules fall into one of four categories• Carbohydrates

• Lipids

• Proteins

• Nucleotides/nucleic acids

What Are Carbohydrates?

• Carbohydrate molecules are composed of C, H, and O in the ratio of 1:2:1• Can be represented by the stoichiometric formula

(CH2O)n

• If a carbohydrate consists of just one sugar molecule, it is a monosaccharide

• Two linked monosaccharides form a disaccharide

• A polymer of many monosaccharides is a polysaccharide

What Are Carbohydrates?

• Carbohydrates are important energy sources for most organisms

• Carbohydrates provide energy to the body, particularly through glucose

• Glucose is a component of starch and an ingredient in many staple foods

• Most small carbohydrates are water-soluble due to the polar OH functional group

What Are Carbohydrates?

• Simple carbohydrates = sugars• Monosaccharides

• In categories based on number of carbons

• Number of carbons determines beginning of category name

• Most sugar names end in “-ose”

Ex: glucose

Main source of cellular fuelhexose6

7 heptoseEx: sedoheptulose

Intermediate in lipid A biosynthesis

4 tetrose

Ex: D-erythrulose

Used in some self-tanners

Reacts with aa in skin and turns brown

5 pentoseEx: ribose

Building block for RNA

Number of carbon atoms Monosaccharide Category Biologically Relevant

3 trioseEx: glyceraldehyde

Important in cellular respiration

What Are Carbohydrates?

• There are several monosaccharides with slightly different structures• The basic monosaccharide structure is a

backbone of 3–7 carbon atoms

• Glucose (C6H12O6) is the most common monosaccharide in living organisms• It’s a hexose

Figure 3-5 Depictions of glucose structure

Chemical formula

Ring, ball and stick

Linear, ball and stick

Ring, simplified

123456

1

23

4

5

6

1

23

4

5

6

What Are Carbohydrates?

•Additional hexose sugars are • Fructose (“fruit sugar” found in fruits, corn

syrup, and honey)

• Galactose (“milk sugar” found in lactose)

• Ribose and deoxyribose (found in RNA and DNA, respectively)

Figure 3-6 Some six-carbon monosaccharides

fructose galactose

1

2

34

5

6

1

23

4

5

6

Figure 3-7 Some five-carbon monosaccharides

ribose deoxyribose

Note “missing”oxygen atom

1

23

4

5

1

23

4

5

Hexose sugars

• Dozens of hexose sugars exist

• All have the same chemical formula

• Differ in the arrangement of atoms• Therefore also shape, enzymes, absorbability

• Termed structural isomers

What Are Carbohydrates?

• Disaccharides consist of two monosaccharides linked by dehydration synthesis • The fate of monosaccharides inside a cell can be

• Some are broken down to free their chemical energy

• Some are linked together by dehydration synthesis

What Are Carbohydrates?

• Disaccharides consist of two monosaccharides linked by dehydration synthesis• Disaccharides are two-part sugars

• More efficient way to store energy

• Commonly encountered in our diets

• Require enzymatic digestion to be absorbed

Figure 3-8 Synthesis of a disaccharide

glucose

dehydrationsynthesis

sucrosefructose

Lactose galactose and glucose 1-4 glycosidic

Maltose glucose and glucose 1-4 glycosidic

Disaccharide Monosaccharide Units Type of Bond

Sucrose glucose and fructose 1-2 glycosidic

What Are Carbohydrates?

• Polysaccharides are chains of monosaccharides• Storage polysaccharides include

• Starch

• Glycogen

• Both starch and glycogen are polymers of glucose molecules

Figure 3-9 Starch structure and function

starch grains

Potato cells

A starch molecule Detail of a starch molecule

What Are Carbohydrates?

• Polysaccharides are chains of monosaccharides• Many organisms use polysaccharides as a structural

material

• Cellulose (a polymer of glucose) is one of the most important structural polysaccharides

Figure 3-10 Cellulose structure and function

Cellulose is a majorcomponent of wood

Detail of a cellulose molecule

A plant cell witha cell wall

A close-up ofcellulose fibersin a cellwall Hydrogen bonds

cross-linkingcellulose molecules

Alternating bondconfiguration differsfrom starch

bundle ofcellulosemolecules

cellulose fiber

What Are Carbohydrates?

• Polysaccharides are chains of monosaccharides• Chitin (a polymer of modified glucose units) is found in

• The outer coverings of insects, crabs, and spiders

• The cell walls of many fungi

What Are Lipids?

• Lipids are a diverse group of molecules that contain regions composed almost entirely of hydrogen and carbon• All lipids contain large chains of nonpolar hydrocarbons

• Most lipids are therefore hydrophobic and water insoluble

What Are Lipids?

• Lipids are diverse in structure and serve a variety of functions• They are used for energy storage

• They form waterproof coverings on plant and animal bodies

• They serve as the primary component of cellular membranes

• Still others are hormones

What Are Lipids?

• Lipids are classified into four major groups• Oils, fats, and waxes

• Phospholipids

• Steroids containing rings of carbon, hydrogen, and oxygen

What Are Lipids?

• Oils, fats, and waxes are lipids containing only carbon, hydrogen, and oxygen• Oils, fats, and waxes are made of one or more fatty acid

subunits

• Waxes are made up of long fatty acid chains esterified to long-chain alcohols

What Are Lipids?

• Oils, fats, and waxes are lipids containing only carbon, hydrogen, and oxygen • Fats and oils

• Are used primarily as energy-storage molecules, containing twice as many calories per gram as carbohydrates and proteins

• Are formed by dehydration synthesis

• Three fatty acids glycerol triglyceride

• Glycerol is an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups.

Forming a fatty acid

• Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached

• The number of carbons in the fatty acid may range from 4 to 36 (12–18 carbons usually)

• In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through an oxygen atom

• Ester bond is when you bond an alcohol with another organic molecule

Figure 3-12 Synthesis of a triglyceride

triglyceride

fatty acids glycerol

Figure 3-13a Fat

Fat

What Are Lipids?

• Fats that are solid at room temperature are saturated (the carbon chain has as many hydrogen atoms as possible, and mostly or all C–C bonds); for example, beef fat

• Saturated or unsaturated with hydrogens

• Carbon needs 4 bonds to be stable

• Has 3 options to get them

C C C

Carbon Saturation

Figure 3-14a A fat

A fat

What Are Lipids?

• Fats that are liquid at room temperature are unsaturated• The more saturated fatty acids an oil has, the higher its

melting point• For example, palm oil, which has mostly saturated fatty acids, is

semi-solid at room temperature

What Are Lipids?

• Unsaturated trans fats have been linked to heart disease

What Are Lipids?

• Oils, fats, and waxes are lipids containing only carbon, hydrogen, and oxygen • Waxes are highly saturated and solid at room

temperature

• Waxes form waterproof coatings such as on• Leaves and stems in plants

• Fur in mammals

• Insect exoskeletons

• Waxes are also used to build honeycomb structures

Figure 3-13b Wax

Wax

What Are Lipids?

• Phospholipids have water-soluble “heads” and water-insoluble “tails”• These form plasma membranes around all cells

• Phospholipids consist of two fatty acids glycerol a short polar functional group

• They have hydrophobic and hydrophilic portions

fatty acid tails

phosphategroup

variablefunctional

group

glycerolbackbone

polar head(hydrophilic) (hydrophobic)

What Are Lipids?

• Steroids contain four fused carbon rings• Steroids are composed of four carbon rings fused

together with various functional groups protruding from them

Figure 3-16 Steroids

Estrogen

Testosterone Cholesterol

What Are Proteins?

• Proteins are molecules composed of chains of amino acids

• Proteins have a variety of functions

• Enzymes are proteins that promote specific chemical reactions

• Structural proteins (e.g., elastin) provide support

Table 3-3

Figure 3-17 Structural proteins

SilkHorn Hair

What Are Proteins?

• Proteins are molecules composed of chains of amino acids

• Proteins have a variety of functions

• Enzymes are proteins that promote specific chemical reactions

• Structural proteins (e.g., elastin) provide support

SilkHorn Hair

What Are Proteins?

• Proteins are molecules composed of chains of amino acids • Proteins are polymers of amino acids joined by peptide

bonds

• All amino acids have a similar structure

hydrogen

aminogroup

variablegroup (R)

carboxylicacid group

Figure 3-19 Amino acid diversity

glutamic acid (glu) aspartic acid (asp)

phenylalanine (phe) leucine (leu)

Hydrophilic functional groups

cysteine (cys)

Hydrophobic functional groups Sulfur-containing functional group

What Are Proteins?

• Amino acids are joined by dehydration synthesis

amino acid

aminogroup

amino acid peptide water

aminogroup

peptidebond

carboxylicacid group

dehydrationsynthesis

What Are Proteins?

• A protein can have as many as four levels of structure• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

Figure 3-21 The four levels of protein structure

hydrogenbond

Tertiary structure:Folding of the helix resultsfrom hydrogen bonds with surrounding water moleculesand disulfide bridges betweencysteine amino acids

Quaternary structure:Individual polypeptides arelinked to one another byhydrogen bonds or disulfidebridges

Secondary structure:Usually maintained byhydrogen bonds, whichshape this helix

Primary structure:The sequence of aminoacids linked by peptidebonds

heme group

helix

pro

lys

val

ala

lys

his

lys

val

gly

lys

leu

Figure 3-22 The pleated sheet and the structure of silk protein

hydrogenbond

Pleated sheet Structure of silk

stack of pleated sheets disorderedsegment

strandof silk

What Are Proteins?

• Precise positioning of amino acid R groups leads to bonds that determine secondary and tertiary structure

• Disruption of secondary and tertiary bonds leads to denatured proteins and loss of function

What Are Nucleotides and Nucleic Acids?• Nucleotides are the monomers of nucleic acid

chains • Deoxyribose nucleotides

• Ribose nucleotides

What Are Nucleotides and Nucleic Acids?• All nucleotides are made of three parts

• Phosphate group

• Five-carbon sugar

• Nitrogen-containing base

What Are Nucleotides and Nucleic Acids?• DNA and RNA, the molecules of heredity, are

nucleic acids• Nucleic acids are polymers formed by monomers strung

together in long chains by dehydration synthesis

What Are Nucleotides and Nucleic Acids?• DNA and RNA, the molecules of heredity, are

nucleic acids • There are two types of polymers of nucleic acids

• DNA (deoxyribonucleic acid)

• RNA (ribonucleic acid)

Figure 3-25 Deoxyribonucleic acid

hydrogenbond

Lab 1

Reminders:

• Pre-lab 1 due now

• Lab write-up due Monday

• Quiz 1 is next Wednesday

Learning Goals

• From lab book• Understand the distinction between prokaryotic and

eukaryotic cells

• Understand how structure relates to function in cells

• Understand how diffusion and osmosis relate to the way cells function

• My interpretation• Predict which direction water will move relative to cells

• Explain how diffusion and osmosis are important for cells

• Gain some hands on experience in viewing cells

• Interpret scientific data and reach conclusions from that data

Parts of the lab

• Part 1: cell models• Skip this part – we will cover parts of the cell next week• Use the pictures to help identify possible cell parts in

part 3 of the lab

• Part 2: osmosis• 2a dialysis: set this up first• 2b plasmolysis: to be done with plant cells

• Part 3: putting cells in perspective (observing cells)• 3a prokaryotic cells (bacteria)• 3b eukaryotic cells (plants, your own cheek cells,

paramecium)

Osmosis and Cells

• Osmosis is the diffusion of water across selectively permeable membranes• Water diffuses from a region of high water

concentration to one of low water concentration across a membrane

• Dissolved substances (solutes) reduce the concentration of free water molecules (solvent)

Water moves in or out of cells depending on the relative tonicity of the solution

• Isotonic solutions have equal concentrations of water (solvent) and equal concentrations of dissolved substances (solutes)• No net movement of water across the membrane

• A hypertonic solution is one with a greater solute concentration • Water moves across a membrane toward the

hypertonic solution

• A hypotonic solution has a lower solute concentration• Water moves across a membrane away from the

hypotonic solution

Osmosis and cells

hypertonicisotonic hypotonic

10% salt90% water

10% salt90% water

10% salt90% water

10% salt90% water

0% salt100% water

30% salt60% water

Osmosis and red blood cells

Fig. 5-9