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Unit 2 From the Atom to the Cell

Organisms + Chemistry

• Organic chemistry: the study of carbon-containing compounds (help make up our bodies)

• Biochemistry: the study of chemical reactions that occur in living systems

Periodic Table Review

• Elements are substances that cannot be broken down or converted into another substance...gold, carbon, oxygen, silver, etc.

• They are composed of atoms which are the smallest units of matter

Atoms & Subatomic Particles

• An atom is composed of a nucleus, an electron cloud, and 3 subatomic particles:

– Protons (p+)

– Neutrons (n0)

– Electrons (e-)

• Protons and neutrons are

located in the nucleus of an

atom and electrons in the

electron cloud

p+

n0

e-

Nucleus

Electron

cloud

What are Ions?

• Ions are charged atoms that are made when an atom gains or loses one or more electrons

– Loss of electrons = cation

– Gain of electrons = anion

• Anion: negatively charged ion

• Cation: positively charged ion

Chemical Bonds — Ionic

• Result from the attraction between ions with opposite charges

• Electrons are gained or lost

• Unstable bonds

• Example: NaCl

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Chemical Bonds — Covalent

• Result from ions sharing electrons

– Equal sharing = nonpolar compounds

• Strong bonds; stable molecule

• Common in organic molecules

– Hydrogen, oxygen, carbon, & nitrogen commonly do this

Chemical Bonds — Hydrogen

• A weak attraction between a partially positively charged H atoms and electronegative O or N atoms

• Weak, numerous bonds

– DNA

– Protein folding

– Enzyme/substrate binding

– Makes H20 a polar compound

Cellular Chemical Reactions

• Catabolic (Decomposition)

– Bonds are broken

– Energy is released

– Ex. Breaking down food for energy

• Anabolic (Synthesis)

– Bonds are created

– Energy is required

– Ex. Making proteins

The Importance of Water

• Water is a polar compound which means it can dissolve a lot of ionic compounds.

– It has both positive and negative regions that can work with both positively charged and negatively charged ions

Properties of Water

• Surface tension: how the surface of water acts as a thin, invisible, elastic membrane

– keeps our membrane moist

Properties of Water

• High specific heat: can absorb or release large amounts of heat energy with little temp change

– Helps stabilize the temp of living organisms

• Acts as a medium for most chemical reactions

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Water & Mixtures

• Solutions:

– Composed of a solvent (liquid that dissolves) and a solute (particle being dissolved)

– Water is a universal solvent

– Glucose, CO2, O2, & small proteins are common solutes

• Colloids:

– when large particles aren’t readily dissolved

– Ex. cytoplasm

Acids & Bases

• Every liquid you see will probably have either acidic or basic traits.

• Acid: a hydrogen ion (H+) donor

– In organisms, HCL

• Base: a H+ acceptor or hydroxyl ion (OH-) donor

– In organisms, amino groups in proteins

pH Scale

• pH scale: measures how acidic or basic (alkaline) something is

• pH 1-6: acidic; 7: neutral; 8-14:basic

Synthesizing Complex Organic

Molecules

Carbon & Organic Molecules

• Molecules are particles composed of atoms (from elements) held together by chemical bonds

– Classified as organic (contains carbon) and inorganic (doesn’t contain carbon)

• Organic molecules are important because they are general types of molecules that all living organisms synthesize and use; they are essential for life

Carbon & Biomolecules

• Although they have a common structure and function, the tremendous variety of organic molecules contributes to the diversity of structures within an individual organism and even individual cells

• The reason for this?

– Carbon’s structure is very versatile when it comes to forming bonds with other atoms

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Modular Approach

• The modular approach involves building organic molecules piece by piece (like a train with individual cars):

– Monomer: individual subunits (car)

– Polymer: long chains of monomers (train)

• Mono- means “one”

• Poly- means “many”

• Organic molecules: carbohydrates, lipids, proteins, & nucleic acids

Complex Organic Molecules

Molecule Monomer Polymer

Carbohydrate Monosaccharide Polysaccharide

Lipid Fatty acid Triacylglycerol

Protein Amino Acid Proteins

Nucleic Acid Nucleotide Nucleic Acid

Carbohydrates-Sugars

• Composed of carbon, hydrogen, and oxygen

• Overall function: main source of energy for living things

• Monomer: monosaccharide

• Polymer: polysaccharide

Carbohydrates-Monosaccharides

• 1 sugar molecule (monomer)

• Function: mainly used to form polymers or for cell activities

• Most common: glucose C6H12O6

• Others:

– Fructosefruits

– Galactoselactose

– RiboseRNA

– DeoxyriboseDNA

Carbohydrates-Disaccharides

• 2 sugar molecules linked together

• Function: mainly used for short-term energy

• Examples:

– Sucroseglucose + fructose

– Lactoseglucose + galactose

– Maltoseglucose + glucose

Carbohydrates-Polysaccharides

• Many sugar molecules linked together (polymer)

• Function: used for long-term energy storage

• Examples:

– Starch: found in plant seeds & roots (FYI: 1000 to ½ million glucose)

– Glycogen: found in animal muscles & liver (much smaller than starch)

– Cellulose: found in plant cell walls • Animals can’t digest it, has to be broken down by microbes so its

usually just roughage/fiber for us

– Chitin: found in exoskeletons and fungi cell walls

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Cellulose Structure & Location

Chitin Structure & Location

Lipids

• Composed of mainly carbon and hydrogen

• Overall function: help make up a cell & can be used for energy

• Monomer: fatty acid

• Polymer: triacylglycerol

Oils, Fats, and Waxes

Types of lipids: - Fats - Phospholipids

- Oils - Steroids

- Waxes

Triacylglycerol (formerly triglyceride): the chemical name of fats and oils; 1 glycerol + 3 fatty acids

Saturated Fats

• Saturated fats are solid and are made of mainly hydrogen so the FA chains are “saturated” in hydrogen

• Where we get them from: butter, bacon fat, steak; tends to come from animals

Unsaturated Fats

• Unsaturated fats are liquids and have a smaller amount of hydrogen in their FA chains

• Where we get them from: the seeds of plants (they’re stored for the embryo) such as corn oil, peanut oil, etc.

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FYI: Saturated & Unsaturated Fats

Saturated

Unsaturated

Waxes

• Function: used as a waterproof covering for:

– plant leaves and stems

– mammalian fur

– insect exoskeletons

– to construct beehives

Fats & Waxes Phospholipids

• Make up the plasma (cell) membrane

– Head is hydrophilic or “water loving”

– Tail is hydrophobic or “water fearing”

Steroids

• Structurally different from all other lipids because it is a ring while the others were chains

• Common steroid: cholesterol

– Component of animal cell membranes

Amino Acids and Proteins

• Composed of: amino group & carboxyl group

• Overall function: structural functions for cells, cell parts, and membranes or making enzymes

• Monomer: amino acids (AAs); there are 20 different AAs in all

• Polymer: protein (chains of AAs)

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Amino Acids and Proteins

• Bond between the AAs when they are making polymers is known as a peptide bond

• Peptide: short chains of AAs (2-49 AAs)

• Polypeptide: long chains, aka a protein (50 or more AAs)

Protein Structure

• Primary structure (1o)-the chain of AAs that make up the protein

• Secondary structure (2o)- when the protein takes on a coiled or pleated shape

Primary Secondary

Protein Structure

• Tertiary structure (3o)-the 3-D shape a polypeptide becomes (like balling up a piece of paper)

• Quaternary structure (4o)-when polypeptide chains link together

Tertiary/Quaternary Levels

Tertiary

Quaternary

Protein Disruption

• Denaturation: disruption of the 2o, 3o, or 4o structures caused by extreme heat or chemicals.

• This is why cultures are autoclaved before disposal.

• Main reason why chemicals used as antimicrobial agents work

Types of Proteins

1.Structural

2. Enzymes: proteins that speed up almost all chemical reactions that occur inside the cell

3. Hormones

4. Antibodies

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Types of Proteins

• FYI: Structural--

– Elastin: gives skin its elasticity

– Keratin: main protein found in hair, nails, horns, scales, and feathers

– Gossamer: the silk protein in spiders and silk moth cocoons

Nucleic Acids

• Overall function: stores the genetic material of an organism which contains the directions for protein synthesis

• Monomers: nucleotides

• Polymers: nucleic acids (NAs)

• Adenosine triphosphate (ATP): main energy storing molecule in organisms

Types of Nucleic Acids

• Nucleotides are made of 3 parts: a nitrogenous base, a sugar, and one or more phosphate groups

• Nitrogenous bases: adenine, thymine (in DNA only), cytosine, guanine, and uracil (in RNA only)

• 2 types of nucleic acids:

– DNA-deoxyribonucleic acid (2 strands)

– RNA-ribonucleic acid (1 strand)

• Sugars: deoxyribose (DNA) and ribose (RNA)

Comparing DNA and RNA

DNA RNA

Strands 2-double helix 1

Sugar Deoxyribose Ribose

Types of

Bases/Base

Pairs

A-T

C-G

DNA – RNA

A-U

C-G

So why is RNA important? Because DNA is too big to leave

the nucleus and it uses RNA to take its message out into the

cytoplasm so that proteins can be made.

CHARACTERISTICS OF

PROKARYOTIC &

EUKARYOTIC CELLS

CH. 4

Protists, Fungi, & Animal cells

(eukaryotic)

Bacterial cell (prokaryotic)

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Prokaroyte Both Eukaryote

-Have genetic material

-Has a plasma/ cell

membrane

-Have organelles

-Have cell walls

Two Cell Types

-Ex. bacteria

-ALWAYS unicellular

- smaller cells

- less complex (simple)

- Do not have a nucleus

- Genetic material (RNA, DNA)

is found free within the

cytoplasm

- Organelles do not have

membranes (ribosomes,

vacuoles)

Prokaryotes

Eukaryotes

Two Cell Types

-Ex. plants, animals, protists,

fungi

- larger cells

- more complex

- have a nucleus and nuclear

envelope that contains the

genetic material (RNA, DNA)

- most organelles have

membranes (mitochondria)

Eukaryotes Prokaryotes

Prokaryotic Cells

Prokaryotic Size, Shape, & Arrangement

Size

Prokaryotic cells are among the smallest

organisms

Ex. Most range from 0.5-2.0 mm

Human RBCs are 7.5 mm

Prokaryotic Size, Shape, & Arrangement

Shape

1. Coccus/cocci (spherical):

- Ex. Streptococcus & Staphylococcus

2. Bacillus/bacilli (rod):

- Ex. E.coli

3. Vibrio (comma shaped spiral)

- Ex. Vibrio cholerae

4. Spirillum/spiralla (rigid, wavy spiral):

- Ex. syphilis

5. Spirochete (corkscrew spiral):

- Ex. Syphilis

**Pleomorphism: how the same bacteria can vary in shape within a single culture

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Prokaryotic Shapes Prokaryotic Size, Shape, & Arrangement

Arrangements (usually only cocci & bacilli)

Diplo- Pairs

Strepto- Chains

Staphylo- Clusters

Tetrads 4 cells in a cube

Sarcinae 8 cells in a cube

Without Using Your Notes…

Draw the following:

1. Staphylococcus

2. Streptobacillus

3. Diplococcus

4. Streptococcus

5. Spirochete

6. Vibrio

Typical Prokaryotic Cell

Bacterial cells have the following:

1. A cell membrane

2. Internal cytoplasm with ribosomes, a nuclear region,

and sometimes vesicles

3. A variety of external structures such as capsules, pili,

and flagella

Typical Prokaryotic Cell Cell Wall

Outside the cell membrane in nearly all

bacteria; semi-rigid and porous (things can

enter it)

Function:

1. maintain cell shape

2. prevent the cell from bursting if it takes in too

much water via osmosis

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Cell Wall Components

Peptidoglycan (also called murein): a structural

polymer that forms a supporting net; most

important component; in Gram positive cells, it is

accompanied by teichoic acid

Outer Membrane: selectively permeable; has

receptors and binding sites for certain molecules;

found mainly in Gram-negative cells

Cell Wall Components

Lipolysaccharide A (LPS) (also called endotoxin):

part of the cell wall in Gram-negative cells; Lipid

A/endotoxin is released when cells are dying so it

can make infections worst if treated late; helps

identify different Gram-negative bacteria

Periplasmic space: active site of cell metabolism; gap

between the cell wall and membrane; contains

peptidoglycan, digestive enzymes, & transport

proteins

Distinguishing Bacteria by Cell Walls

Gram staining:

Gram positive:

Cell wall has thick layer of peptidoglycan

Lack an outer membrane & periplasmic space

colors purple (retains crystal violet)

Distinguishing Bacteria by Cell Walls

Gram staining:

Gram negative:

Cell wall has a thin layer of peptidoglycan; more complex

Has an outer membrane & large periplasmic space

colors pink (doesn’t retain crystal violet)

Distinguishing Bacteria by Cell Walls

Acid-Fast Bacteria:

Mycobacteria:

Cell wall is thick, but mostly lipid based and only a small

percentage of peptidoglycan

Use carbolfuschin as a dye for a red staining

Will stain as Gram-positive

Brain Check…

1. What is peptidoglycan? Where is it found?

2. What takes place in the periplasmic space? Which

organisms have such a space?

3. Compare the cell walls of Gram-positive, Gram-

neagtive, and acid-fast bacteria.

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Cell Membrane aka Plasma Membrane

The Plasma Membrane-- also called a Phospholipid Bilayer: a

flexible boundary between the cell and its environment; it’s

selectively permeable b/c it only allows certain things in or out

Cell Membrane aka Plasma Membrane

Fluid-mosaic model: Fluid: means that the membrane is flexible

Mosaic: means that proteins are embedded in the membrane and form a pattern

Polar Head-water loving or hydrophilic

Non polar tail- made of fat so it’s water fearing or hydrophobic

Internal Structures of the Cell

Organelles: internal structures within cells that

have specific functions to help maintain the cell

(“little organs”)

Internal cytoplasm with ribosomes, a nuclear

region, and sometimes vesicles

Nuclear region or

Nucleoid: DNA,

RNA, & some

protein; sometimes

bacteria have

circular DNA called

plasmids

Cytoplasm: site of protein

synthesis, suspends all of the

organelles ; semifluid

substance

Ribosomes:

make proteins; made of RNA

and protein

Internal Structures

Inclusions: small

bodies called granules

or vesicles

Chromatophores: contain

pigments to capture light;

found only in photosynthetic

bacteria or cyanobacteria

Granules: contain glycogen for

energy or polyphosphate for

metabolic processes; no membrane

Internal Structures

Vesicles/Vacuoles:

contain substances like

gas or lipid deposits

that help bacterial cells

float or store energy

Internal Structures

Endospores (Bacillus or Clostridium):

Found in stasis (resting state) versus vegetative state

(metabolizing nutrients)

Medically significant genera: tough to kill

Resistances: to heat, drying, pH, certain disinfectants, &

radiation

Contain dipicolinic acid: helps with heat resistance

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External Structures Flagella: aid in locomotion;

long, whip-like

Cilia: aid in locomotion;

short, hair-like

Why Move?

• Chemotaxis: movement from or

to substances in the environment

• Positive: to the substance

• Negative: away from the

substance

• Phototaxis: movement from or to

light in the environment

• Positive: to the light

• Negative: away from the

light

External Structures

Pili (pilus): not used for

movement; tiny, hollow projections

Conjugative pili: allow the

transfer of DNA between

bacteria, in the process

of bacterial conjugation.

Attachment pili: attach bacteria

to surfaces; also called fimbriae;

contribute to pathogenicity

External Structures

Glycocalyx: coating that covers the outside of many prokaryotic cells

Capsule: protective structure outside the cell wall; prevents host cell defense mechanisms from destroying it (phagocytosis); not every bacteria secretes it; unique to the strain making it

Slime layer: protects the cell against drying, helps trap nutrients, sometimes binds cells together, helps bacteria attach to surfaces as a biofilm; less tightly bound to the cell wall

Eukaryotic Cells

Golgi Apparatus: Modifies, sorts, &

packs proteins into vesicles; Vesicles:

transport things around the cells

Centrioles: have

a role in cell

division

Nucleus: control

center of the cell

because it directs all

cellular activities;

Nucleolus: makes

ribosomes

Mitochondria: makes

energy so it’s known as the

“powerhouse”

ER: site of

chemical

reactions, helps

transport

proteins

Ribosomes:

make proteins

Fig. 4.18 p.96

Internal Structures

Cytoskeleton: forms the

framework of the cell;

made of microfilaments

and microtubules

Lysosome: contains digestive

enzymes to get rid of cell wastes

Plasma

Membrane:

maintains cell

balance

Cytoplasm: site

of protein

synthesis,

suspends all of

the organelles

Vacuole: temporary storage

site for food, water, or wastes

(not found in a lot of animal

cells) Peroxisome: contains enzymes to

breakdown amino acids; convert

hydrogen peroxide to water

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Cilia & flagella: aid in

locomotion External Structures

Pseudopodia: “false feet;” cytoplasmic

extensions that organisms like amoebas use

to move

Cell wall: provides extra

support and protection for

certain protists, fungi, and

plants

Movement Across the Membranes

Passive Transport

Passive Transport –molecules moving from a high to low concentration & this DOES NOT REQUIRE ENERGY

Passive Transport: Diffusion and Osmosis

1) Diffusion: molecules moving from a high to low concentration

2) Facilitated diffusion: molecules move from high to low concentrations, but need transport proteins in the cell membrane to help them

3) Osmosis: the diffusion of water across a selectively permeable membrane

Types of Transport Proteins

Act as gatekeepers of the cell because they are within

the cell membrane and help molecules enter or exit

the cell.

Channel Proteins- form channels that allow specific

molecules to flow through.

Carrier Proteins - change shape to allow a substance to pass

through the plasma membrane.

High concentration of sugar molecules Low concentration

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Osmosis

Why do we need to regulate osmosis?

To maintain homeostasis because the plasma membrane is NATURALLY permeable to water

How long does water diffuse in a solution?

- Until it is evenly distribution, or causes solutes to reach

equilibrium

Osmosis in Microbes

Bacterial cells have cell walls that prevent them

from bursting or shrinking in different watery

environments.

Protists have contractile vacuoles that will expel the

water.

Isotonic Solution ISO means EQUAL

•SOLUTE: equal inside & outside

the cell

•WATER: moves equally in both

directions

•ANIMAL CELLS: stays the same

•BACTERIAL CELLS: slightly firm

•WHICH CELL LIKES IT BEST:

Animal

Animal

cell

Bacterial

cell

Hypotonic

Solutions HYPO means LESS

•SOLUTE: more inside the cell

•WATER: enters the cell

•ANIMAL CELLS: swells

•BACTERIAL CELLS: very firm

•WHICH CELL LIKES IT BEST:

BACTERIAL

Animal

cell

Bacterial

cell

Hypertonic

Solution HYPER means MORE

•SOLUTE: more outside the cell

•WATER: leaves the cell

•ANIMAL CELLS: shrinks

•BACTERIAL CELLS: wilts

•WHICH CELL LIKES IT BEST:

they both HATE it!!!!!!!

Animal

cell

Bacterial

cell

Active Transport:

Requires Energy

Active Transport – molecules through a

membrane from LOW to HIGH & this

requires energy

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Active Transport & Energy

2 reasons we need active

transport:

1. To move large molecules

2. When a high concentration

of molecules are needed and

there are already enough

there

Active Transport & Energy

The mitochondria is the organelle that makes the

energy for active transport; in bacterial cells, there

are high energy molecules that provide energy

Types of Active Transport

Endocytosis- cell membranes making vesicles to

absorb molecules; endo = enter

Types of Active Transport

Phagocytosis- the engulfing and ingesting of

solid molecules- “cell eating”

Very important in microbiology

Types of Active Transport

Pinocytosis- the ingestion of fluid into a cell- “cell

drinking”

Types of Active Transport

Receptor mediated- molecules are taken in at

receptor sites specific to the molecule

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Types of Active Transport

Exocytosis- the expulsion or release of materials

from a cell; exo = exit

Active Transport & Transport Proteins

Active transport also uses transport proteins to move

molecules across the membrane.