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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

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

Chemical Bonds — Ionic

Result from the attraction between ions

with opposite charges

Electrons are gained or lost

Unstable bonds

Example: NaCl

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

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Chemical Bonds — Hydrogen

Weak, numerous bonds; found in:

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.

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

elastic membrane (keeps our membrane moist)

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

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

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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

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

Overall function: main source of energy for living things

Monomer: monosaccharide

Polymer: polysaccharide

Carbohydrates

1 sugar molecule (monomer)

Function: mainly used to form polymers or for cell activities

Most common: glucose C6H12O6

Others:

Fructosefruits

Galactoselactose

RiboseRNA

DeoxyriboseDNA

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Lipids

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

Monomer: fatty acid

Polymer: triacylglycerol

Lipids

Types of lipids:

- Fats - Phospholipids

- Oils - Steroids

- Waxes

Triacylglycerol (formerly triglyceride): the chemical name of fats

and oils; 1 glycerol + 3 fatty acids

Amino Acids and Proteins

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)

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

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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

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

2 types of nucleic acids:

DNA-deoxyribonucleic acid (2 strands)

RNA-ribonucleic acid (1 strand)

Sugars: deoxyribose (DNA) and ribose (RNA)

Prokaryotic Cells

Protists, Fungi, & Animal cells (eukaryotic)

Bacterial cell (prokaryotic)

Comparing & Contrasting the Cell Types

Prokaryotic (Bacteria) Both Eukaryotic (Protist, Fungi, &

Animal)

-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)

- Have genetic material

- Has a plasma/ cell

membrane

- Have organelles

- Have cell walls

-larger cells

- more complex

- have a nucleus and nuclear

envelope that contains the

genetic material (RNA, DNA)

- most organelles have

membranes (mitochondria)

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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 Shapes

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. Spirillum minus

5. Spirochete (corkscrew spiral):

-Ex. Treponema pallidum

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

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

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

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 ONLY; 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 Gram Negative

Cell wall has thick layer of

peptidoglycan & teichoic acid

Cell wall has a thin layer of

peptidoglycan & LPS

Less complex More complex

colors purple colors pink

Gram Positive & Gram Negative

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 first

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 Cell 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: location of

DNA, RNA, & some

protein; some bacteria

have circular DNA called

plasmids

Cytoplasm: site of protein synthesis,

suspends all of the organelles ;

semifluid substance

Ribosomes:

make proteins

Internal Structures

Chromatophores: contain pigments to

capture light; found only in

photosynthetic bacteria or

cyanobacteria

Granules: stores glycogen for energy or

polyphosphate for metabolic processes; no

membrane

Internal Structures

Vesicles: stores substances like

gas or lipid deposits that help

bacterial cells float or store

energy

Vacuoles: small bodies called

granules or vesicles

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

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

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High concentration of sugar molecules Low concentration

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: shrinks

•WHICH CELL LIKES IT BEST: both HATE

it!!!!!!!

Animal cell

Bacterial cell

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Active Transport:

Requires Energy

Active Transport – molecules moving from a LOW to

HIGH concentration & this requires energy

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”

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Types of Active Transport

Exocytosis- the expulsion or release of materials from a cell; exo =

exit