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General Biology

BI 102, Fall 2014

CRN 22608

Instructor: Bill Thomas (Instructor website under Thomas, William)

Email: [email protected]

Learning Objectives – Week 1 • Properties of life

• The 3 domains of life – Archaea, Bacteria, Eukarya

• Biological Themes – Evolution, Flow of Energy, Cooperation, Structure Determines Function,

Homeostasis

• Scientific process

• Unifying Theories of Biology – Cell Theory, Gene Theory, Theory of Heredity, Theory of Evolution

• Atoms: Structure and properties

• Electron shells and orbitals

• How are ions formed?

• The types of bonds: ionic, covalent, hydrogen bonds (and van der Waals forces)

• Biological importance of the special properties of water

• Become familiar with the terms “hydrophilic” and “hydrophobic” and understand their biological

importance

• Understand the basics of the pH scale

• Logarithmic

• Lower Higher = Acidic Basic

• Learn the four main types of biological macromolecules and their components

• What is a monomer?

• Two reactions: dehydration synthesis and hydrolysis

• Which requires energy input? Which releases energy?

• Understand the basics of protein structure (primary, secondary, etc.)

• See how the structure of a macromolecule determines its function

First-day business • Introductions

• Syllabus

• Read safety instructions in lab packet for Thursday

• McGraw Hill Connect resources

http://connect.mheducation.com/class/w-thomas-bi-102-lbcc-fall-14-1

LearnSmart: Objective: Familiarize yourself with material we will be covering in class

Homework: Weekly Activity

LearnSmart and online homework together make up 10% of your grade—don’t

forget about them!

















Course Objectives

• Hands-on lab experience

DNA extraction, genetics, electrophoresis!

• Gaining a better understanding of biological systems

Cell structure and function

Genetics and heredity

Evolutionary processes

• Understanding the scientific method

Scientific inquiry

• Impact of cell biology on your life

Photo : Frank Wojciechowski

The Domains of Life

• Historically, life was grouped into three kingdoms.

• Modern taxonomy divides life into three domains

textbookofbacteriology.net

The six kingdoms of life

What is Life?

• What qualifies something as “living” versus “non-living?”

• Consider these points complexity

movement

response to stimulation

• A life-defining property must be exclusive to living things

Are these properties

unique to living things?

Properties of Life

• 1. Cellular organization

all living things are comprised of at least one cell

• 2. Metabolism

all living things process energy which is used to power other processes

• 3. Homeostasis

all living things maintain relatively stable internal environments to optimize conditions for metabolism and other processes

Properties of Life

• 4. Growth and reproduction

all organisms have the capacity

for growth and reproduction

• 5. Heredity

all organisms pass genetic

information to future generations

from parents to offspring

Does this possess the

properties of life?

The Organization of Life

• Living things function and interact with

each other on many levels

• The organization of life is a hierarchy of

levels of increasing size

cellular

organismal

populational

Figure 1.4 Levels of organization:

cellular level

Alternative example:

1. Atoms (C, H, N, O, S)

2. Molecule (amino acid)

3. Macromolecule (protein;

e.g., actin)

4. Organelle (Cytoskeleton)

This level of organization is where

we will spend most of our time!


organismal level


populational level

On which of these three levels

(cellular, organism, population)

do you think evolution takes

place?

The Organization of Life

• At higher levels of the living hierarchy, new properties become apparent that were absent at the lower levels

• These emergent properties result from the interaction of diverse but simpler components

• Many higher order processes that are hallmarks of life are emergent properties

metabolism

consciousness

Biological Themes: Evolution

Evolution is genetic change in a

species over time

The mechanism for evolution is

natural selection

The diversity of life is explained by

evolutionary processes

Biological Themes: Flow of Energy

All living things require energy

Energy from the sun flows through the living world

Organisms acquire energy differently

How much energy is available determines how many and what kinds of organisms can live together in an ecosystem

biology.tutorvista.com

Biological Themes: Cooperation

As energy and other resources are

limiting, many organisms have

evolved cooperation as a means of

survival

Symbiosis describes when two

species live in direct contact

Biological Themes: Structure Function

Structure Determines Function

Evolution favors structures that

function in an adaptive manner

Many structures are specialized for a

particular function

tiger.towson.edu

naturedocumentaries.com

Biological Themes: Homeostasis

Homeostasis is a physiological condition of “steady-state”

The internal environment of organisms is relatively stable

Organisms act to control their internal environments so that the complex processes of metabolism function efficiently

Scientific Investigation

Scientists systematically

conduct experiments to

evaluate hypotheses about

observed phenomena

• You’ve probably used the

scientific method without

realizing it!

Copyright © 2011 Pearson Education, Inc.

What’s missing from

this experimental

design?

Fig.1.5 The scientific process

Stages of a Scientific Investigation

The scientific process has six stages

1. Observation

science begins with careful observation of natural phenomena

2. Hypothesis scientists make an educated guess that might be true

often scientists formulate multiple ideas about a phenomenon; these are called alternative hypotheses


3. Predictions

if a hypothesis is correct, then specific

consequences can be expected

4. Testing

scientists conduct experiments to attempt to

verify predictions made by hypotheses

• 5. Controls

experiments usually employ a parallel design • scientists use a control to assess the influence of

potential factors, called variables

• conditions stay the same in the control in comparison to the variable condition

• 6. Conclusion

a hypothesis that has been tested and not rejected is tentatively accepted


The

Experiments

of Francesco

Redi

Copyright © 2011 Pearson Education, Inc.

Scientific Method in Action

Theory and Certainty

• The term “theory” means different things

to different audiences

To scientists

• A theory represents certainty and is a unifying

explanation for a broad range of observations

To the general public

• A theory implies a lack of knowledge or guess

Theory and Certainty

• Scientists’ acceptance of theory is

provisional

the possibility always remains that future

evidence will cause a theory to be revised

• The process of science is not just trial-

and-error but involves judgment and

intuition

Four Theories Unify Biology as a

Science

• 1. The Cell Theory

• 2. The Gene Theory

• 3. The Theory of Heredity

• 4. The Theory of Evolution

The Cell Theory

• All organisms are composed of

at least one cell

• The cell is the most basic unit

of life

• All cells come from pre-

existing cells

The Gene Theory

• Genetic information is encoded in

molecules of deoxyribonucleic acid

(DNA)

• Genes encode specific proteins

• The proteins encoded by an organism’s

genes determine what it will be like in

terms of form and function

The Theory of Heredity

Genes are passed down generations

as discrete units

Mendel’s theory of heredity

gave rise to the field of genetics

Chromosomal theory of

inheritance located Mendelian

genes on chromosomes

The Theory of Evolution

• All living organisms are related to one another in a common tree of descent

The six kingdoms of life are grouped into three domains

• Theory of evolution explains the unity and diversity of life

The Theory of Evolution

• Charles Darwin attributed evolution to natural selection

Organisms best able to respond to

the challenges of living will leave

more offspring, thus their traits

become more common in the

population

• Scientists have been able to identify

changes in individual genes that are

responsible for differences among

individuals

Figure 1.13 The theory of evolution

Figure 2.2 Basic structure of an atom

Atoms - Properties • An atom is characterized by the

number of protons it has or by its overall mass

atomic number

• the number of protons in the nucleus

• Why not the number electrons?

mass number

• the number of protons plus neutrons in the nucleus

• electrons have negligible mass www.chemistry.wustl.edu

Table 2.1

“Organic”

Electrons

• Electrons determine the chemical behavior of atoms

These subatomic components are the parts of the atom that come close

enough to each other in nature to interact

• Electrons are associated with energy

Electrons have energy of position, called potential energy

Electrons occupy energy levels, or electron shells, of an atom, which

are actually complex, three-dimensional volumes of space called

orbitals

• orbitals are where electrons are most likely to be found

Electron Shells & Energy

• As electrons move to a

lower energy level, closer

to the nucleus, energy is

released

• Moving electrons to

energy levels farther out

from the nucleus requires

energy

Figure 2.3 The electrons of

atoms possess potential energy

Electron Shells & Orbitals

• Electron shells have specific numbers of orbitals that may be filled

with electrons

atoms that have incomplete electron orbitals tend to be more reactive

atoms will lose, gain, or share electrons in order to fill completely their

outermost electron shell

these actions are the basis of chemical bonding

Ions

Ions – atoms that have gained or lost one or more electrons

Isotopes

Isotopes – atoms that have the same number of protons but different

numbers of neutrons

most elements in nature exist as mixtures of different isotopes

Isotopes & Radioactivity

• Some isotopes are unstable and break up into particles with lower

atomic numbers

this process is known as radioactive decay

• Radioactive isotopes have multiple uses

dating fossils

medical procedures

Figure 2.7 Using a

tracer to identify cancer

Molecular bonds

A molecule is a group of atoms held together by energy in the form of a chemical bond

• There are 3 principal types of chemical bonds 1. Ionic

2. Covalent

3. Hydrogen

• van der Waals forces are a kind of weak chemical attraction (not a bond) that come into play when atoms are very close to each other

Ionic compounds

• Ionic bonds involve the

attraction of opposite electrical

charges

• Molecules comprised of these

bonds are often most stable as

crystals

Fig. 2.8(a) The formation of

ionic bonds in table salt

Molecules – Covalent bonds

Covalent bonds form between two atoms when they share

electrons

The number of electrons shared varies depending on how many

the atom needs to fill its outermost electron shell

Covalent bonds are stronger than ionic bonds because they are

directional

Single

covalent

bond

Double

covalent

bond

Oxygen gas (O2)

Methane gas (CH4)

C H H

H

H

O O O

–

H H

H

H

–

–

–

– –

– –

–

–

– –

–

–

– –

–

– –

– –

–

O –

–

–

–

C

Polar molecules

• Some atoms may be better at attracting the shared electrons of a covalent bond

This creates tiny partial negative and positive charges within the molecule, now called a polar molecule

Polar covalent bonds form when the shared electrons of a covalent bond spend more time in the vicinity of a particular atom

What is this important polar

molecule?

Hydrogen bonding

Hydrogen bonds are weak electrical attractions between the positive

end of one polar molecule and the negative end of another

each atom with a partial charge acts like a magnet to bond weakly to

another polar atom with an opposite charge

the additive effects of many hydrogen bonding interactions can add

collective strength to the bonds

Example?

Electrons – Big Picture

• Electrons can be “energized”; this energy can be used

by cells to do work

• The number of electrons and the way they are shared by

atoms give molecules biologically important properties:

Charge: the charge on an ion restricts its movement in a cellular

environment, can be used in transport

Polarity: polar molecules interact with ions and other polar

molecules, are repelled by nonpolar molecules

Nonpolarity: nonpolar molecules repel polar and charged

molecules, “hide” from water

Polarity of Water

Water can form hydrogen bonds

Hydrogen bonding confers on water many different special properties

Unique Properties of Water

Why is this

important?

Evaporative

cooling

Hydrophilic vs. Hydrophobic

• High polarity

In solution, water molecules tend to form the maximum number of hydrogen bonds

• hydrophilic molecules are attracted to water and dissolve easily in it

– these molecules are also polar and can form hydrogen bonds

• hydrophobic molecules are repelled by water and do not dissolve

– these molecules are nonpolar and do not form hydrogen bonds

Figure 2.14 How salt dissolves in water

Water Ionizes

• The covalent bond within a water molecule sometimes breaks spontaneously

• This produces a positive hydrogen ion (H+) and a negatively charged hydroxide ion (OH-)

H2O OH- + H+

Water Hydroxide Hydrogen

Figure 2.15 The pH scale

• The amount of ionized

hydrogen from water in a

solution can be measured

as pH

• The pH scale is

logarithmic, which means

that a pH scale difference of

1 unit actually represents a

10-fold change in hydrogen

ion concentration

Acids & Bases

• Pure water has a pH of 7 there are equal amounts of [H+] relative to [OH-]

• Acid – any substance that dissociates in water and increases the [H+] acidic solutions have pH values below 7

• Base – any substance that combines with [H+] when dissolved in water basic solutions have pH values above 7

Biological pH

• The pH in most living cells and their environments is fairly close to 7 proteins involved in metabolism are sensitive to any

pH changes

• Organisms use buffers to minimize pH disturbances

a buffer is a chemical substance that takes up

or releases hydrogen ions

Blood is an example of a biological buffer

Organic Molecules

Carbon is the basis of all organic molecules

Carbon core has attached

groups of atoms called functional groups

• The functional groups confer specific chemical properties on the organic molecules

Macromolecules

Macromolecules are actually assembled from many similar small components, called monomers

the assembled chain of monomers is known as a polymer

• There are four types of macromolecules: 1. Proteins

2. Nucleic acids

3. Carbohydrates

4. Lipids

Fig. 3.3 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

O

N

H

C

H H

C

O P

O

–O

O– O

O C C

N C

N

C H

H

H

H H H H

P

P

P

P

P

P P

P

P

P

P

P

P

P

P

G

C

G

C

T

A

A

A

A

T

T

H H

H H

H

O

H O H H H H H H H H H H

H O C C C C C C C C C C C C

H H H H H H H H H H H

Polymer: Starch

Polymer: Fat molecule

(d) Lipid (b) Nucleic acid

Monomer:

Nucleotide

(a) Protein

Monomer:

Amino acid

Alanine

Ala

Val Ser Val

Ala

Monomer:

Monosaccharide

(c) Carbohydrate

Polymer: Polypeptide

Polymer: DNA strand

Monomer:

Fatty acid

OH

OH OH

HO

CH2OH

OH

NH2

CH2

OH

CH3

Which of these monomers is polar? What does that mean for the

polymer/macromolecule?

Dehydration synthesis

All macromolecules are assembled the same way

A covalent bond is formed between two subunits by

removing a hydroxyl group (OH) from one subunit and a hydrogen (H) from another subunit

Because this amounts to the removal of a molecule of water (H2O), this process is called dehydration synthesis

Figure 3.4(a) Dehydration synthesis

Figure 3.4(b) Hydrolysis

Which process releases energy: dehydration synthesis or hydrolysis?

Proteins

Complex macromolecules that are polymers of many subunits called amino acids

Figure 3.3(a) Polymers are built from monomers: protein

Amino acids

Small molecules with a simple basic structure, a carbon atom to which three groups are added

• an amino group (-NH2)

• a carboxyl group (-COOH)

• a functional group (R)

20 different

R groups

Figure 3.6(b) The formation of a peptide bond

Protein structure

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Tertiary

structure

Secondary

structure

β-pleated sheet

Primary

structure

Amino

acids

α-helix

Quaternary

structure

Protein structure: Primary

Primary structure –

the sequence of amino

acids in the polypeptide

chain

• This determines all

other levels of protein

structure

Figure 3.7 Levels of protein

structure: primary structure

Primary

structure

Amino

acids


Protein structure: Secondary

Secondary structure – the

initial folding of the amino acid

chains

• Occurs because regions of

the polypeptide that are non-

polar are forced together

• The folded structure may

resemble coils, helices, or

sheets


structure: secondary structure

Secondary

structure

β-pleated sheet

α-helix


Protein structure: Tertiary

Tertiary structure – the final 3-D shape of the protein

• The final twists and folds that lead to this shape are the result of polarity differences in regions of the polypeptide


structure: tertiary structure

Tertiary

structure


Protein structure: Quaternary

Quaternary structure

– the spatial

arrangement of

component

polypeptides in

proteins comprised of

more than one

polypeptide chain


structure: quaternary structure

Quaternary

structure


Figure 3.8 Protein denaturation

Heat

pH

Inactive

Figure 3.9 Protein structure

determines function

Nucleic Acids

Nucleic acids are very long polymers that

store information

comprised of monomers called nucleotides

Figure 3.3(b) Polymers are built from monomers: nucleic acid

Figure 3.10

The structure

of a nucleotide

Each nucleotide has 3 parts

1. a five-carbon sugar

2. a phosphate group

3. an organic nitrogen-

containing base

• There are five different types of

nucleotides

• information is encoded in

the nucleic acid by

different sequences of

these nucleotides

Dehydration reaction

DNA & RNA

There are two types of nucleic acids

Deoxyribonucleic acid (DNA)

Ribonucleic acid (RNA)

• RNA is similar to DNA except that

it uses uracil instead of thymine

it is comprised of just one strand

it has a ribose sugar (instead of deoxyribose)

Figure 3.11 How DNA structure

differs from RNA

The Double Helix

The structure of DNA is a

double helix because

there are only two base pairs

possible

• Adenine (A) pairs with

thymine (T)

• Cytosine (C) pairs with

Guanine (G)

the bonds holding together a

base pair are hydrogen

bonds

a sugar-phosphate backbone

comprised of phosphodiester

bonds gives support

Structure of DNA

The hydrogen bonds of the base pairs can be broken

to unzip the DNA so that information can be copied

• each strand of DNA is a mirror image so the DNA contains

two copies of the information

Having two copies means that the information can be

accurately copied and passed to the next generation

Carbohydrates

Carbohydrates are used for energy or as

structural molecules

a carbohydrate is any molecule that contains the

elements C, H, and O in a 1:2:1 ratio

the sizes of carbohydrates varies

• simple carbohydrates – made up of one or two monomers

• complex carbohydrates – long polymers

Figure 3.3(c)

Polymers are built

from monomers:

carbohydrate

Figure 3.14 The structure of glucose

Mono- & Disaccharides

• Simple carbohydrates are

small

monosaccharides consist of

only one monomer subunit

• an example is the sugar

glucose (C6H12O6)

disaccharides consist of two

monosaccharides

• an example is the sugar

sucrose, which is formed by

joining together two

monosaccharides, glucose

and fructose

Polysaccharides

Complex carbohydrates are

long polymer chains

because they contain many

C-H bonds, these

carbohydrates are good for

storing energy

• these bond types are the

ones most often broken by

organisms to obtain energy

the long chains are called

polysaccharides

Carbohydrate storage

• Plants and animals store energy in

polysaccharide chains formed from

glucose

plants form starch

animals form glycogen

• Some polysaccharides serve structural

functions and are resistant to digestion by

enzymes

cellulose is found in the cell walls of

plants

chitin is found in the exoskeletons of

many invertebrates and in the cell walls of

fungi

Lipids

Lipids – fats and other molecules that are not soluble in water

lipids are nonpolar molecules

lipids include fats, phospholipids, and many other molecules

Figure 3.3(d) Polymers are built from monomers: lipid

Fats Used for long-term energy

storage

fats have two subunits

1. fatty acids

2. glycerol

fatty acids are chains of C

and H atoms

Glycerol contains three

carbons and forms the

backbone to which three

fatty acids are attached

Glycerol

Fatty acids How is the energy released?

Figure 3.17 Saturated and

unsaturated fats

What

forces are

at work

here?

Lipid membranes

• Biological membranes use lipids

phospholipids make up the two layers of the membrane

cholesterol (a steroid) is embedded within the membrane

• Lipids also include oils, other steroids, rubber, waxes,

and pigments

Figure 3.16 Lipids

are a key

component of

biological

membranes

What properties of

phospholipids

make them work as

a membrane?

Steroids

Lipids that have rings in their

structure

• Structural components of

membranes (cholesterol)

• Signaling molecules

(testosterone, estrogen)

Testosterone

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