Chem 45 Biochemistry: Stoker chapter 18 Introduction – Cell Structure

Chapter 1

Introduction – Cell

Structure

Biochemistry – An Overview

Section 18.1

The Study of Living Things

• Biochemistry is the systematic

study of the chemical substances

found in living organisms, their

organization & chemical

interactions with each other, and

the principles of their participation

in the processes of life.

• Its importance is due to the

increasing recognition that

underlying each and every

biological function is a chemical

reaction.

• Hundreds/thousands of chemical

reactions are taking place in our

cells every minute of our lives.

• Biochemical investigations have

been directed towards the study of

the chemical composition of cells

and the chemical processes in

which they participate.

• A biochemical substance is a

chemical substance found within a

living organism.

• Two types of biochemical

substances:

– Bioinorganic substances :

water and inorganic salts.

– Bioorganic substances :

carbohydrates, lipids,

proteins, and nucleic acids

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Section 18.1

Biochemical substances • As isolated compounds,

bioinorganic and bioorganic

substances have no life in

and of themselves.

• Yet when these substances

are gathered together in a

cell, their chemical

interactions are able to

sustain life.

• A cell in particular, and a

whole organism in general,

has three basic needs:

materials, information, and

energy.

• Without the daily satisfaction

of these, human life would

be severely constrained.



Section 18.1

Main classes of foodstuffs - Materials

• The bioorganic materials of life

will be considered, starting with

the three main classes of

foodstuffs – carbohydrates,

lipids, and proteins.

• Humans use these molecules to

build and run their bodies and to

try to stay in some state of repair.

• Plants rely heavily on

carbohydrate for cell walls, and

animals obtain considerable

energy from carbohydrates made

by plants.

• Lipids serve many purposes.

They are used, both by plants and

animals, as materials to make cell

membranes and as sources of

chemical energy.

• Proteins are particularly important

in both the structures and

functions of cells.

• Because of the catalytic role of

proteins in regulating chemical

events in cells, the study of

proteins will be immediately

followed with an examination of

enzymes, which make up a

particular family of proteins.



Section 18.1

Information system

• Every cell has an information

system – enzymes, hormones,

and neurotransmitters are

components of the intricate

information system in the body.

• Without information, the materials

and energy delivered to the body

could produce only rubbish.

• Although enzymes are major

players in the cells’ information

system, they do not originate the

cellular script.

• They only help to carry out

directions that are encoded in the

molecular structures of the

nucleic acids, which are

compounds that are able to direct

the synthesis of enzymes.

• Thus the study of the enzyme

makers, the nucleic acids, is

included in any study of the

molecular basis of life.

• Hormones & neurotransmitters,

two other components of cellular

information, depend on the

presence of right enzymes not

only for their existence but for their

functions.



Section 18.1

Biochemical substances

• To supply materials for

any use – parts,

information, or energy –

each organism has basic

nutritional needs.

• These include not just

bioorganic materials,

including vitamins, but

also bioinorganic

materials including

minerals, water, and

oxygen.

• Thus, together with

learning about the

bioorganic materials of

life and how they are

processed and used, the

need for vitamins,

minerals, water, and

oxygen will also be

considered.



Section 18.1

Metabolism

• All life processes consist of chemical

reactions catalyzed by enzymes.

• The reactions of a living cell, which

are known collectively as

metabolism, result in highly

coordinated and purposeful activity.

• Among the most frequent reactions

encountered in biochemical

processes are:

– nucleophilic substitution

– elimination

– addition

– isomerization

– hydrolysis

– oxidation – reduction

• The redox chemistry of

carbohydrates is fundamental

to life.

• Glucose is the most important

carbohydrate in biochemistry.

Almost all cells derive energy

from the oxidation of glucose

through glycolysis, citric acid

cycle, and oxidative

phosphorylation

• The energy yield from the

oxidation of glucose is shown

below.



Section 18.1

The Study of Living Things – The CELL STRUCTURE

• Based on their cell structures,

organisms are divided into two

main groups:

• Prokaryote: Greek - meaning

“before the nucleus”; single-

celled organisms

• Eukaryote: Greek - meaning

“true nucleus”

– contain a well-defined nucleus

surrounded by a nuclear

membrane

– can be single celled, such as

yeasts and Paramecium, or

multicellular, such as animals

and plants

• Five kingdoms:

• Monera - prokaryotic organisms;

includes bacteria and

cyanobacteria

• Protista - unicellular eukaryotes:

yeast, Euglena, Volvox, Amoeba,

and Paramecium

• Fungi - molds and mushrooms

• Plantae

• Animalia

• Fungi, plants, and animals are

multicellular eukaryotes

(with few unicellular eukaryotes)



Section 18.1

The Study of Living Things – The CELL STRUCTURE

• The main difference between prokaryotic and eukaryotic cells is the

existence of organelles, especially the nucleus, in eukaryotes.

• An organelle is a part of the cell that has a distinct function; it is

surrounded by its own membrane within the cell.


Organelle Prokaryotes Eukaryotes

Nucleus

Cell membrane

Mitochondria

Endoplasmic reticulum

Ribosomes

Chloroplasts

No definite nucleus; DNApresent but not separate from the rest of the cell

Present

Present Present

None; enzymes for oxidationare on plasma membrane

None

Present

None; photosynthesislocalized in chromatophores

Present

Present

Present

Present in green plants


Section 18.1



Section 18.1


The CELL STRUCTURE – Functions of the organelles


Section 18.1

The cell membrane

• a semi-permeable membrane

surrounding the cell separating its

internal environment from the

external environment;

• permits and/or enhances the

absorption of essential nutrients

into the cell while preventing the

diffusion of needed metabolites

• a lipid bilayer that mechanically

holds cell together

• component biomolecules:

– Lipids: phospholipids,

cholesterol

– Proteins

– Carbohydrates

• Lipids provide the basic structure

of biological membranes

• Proteins are embedded in the

membranes and provide

channels/carriers for the transport

of ions and nutrients



Section 18.1

The cytoplasm

• structureless and highly

viscous

• the aqueous phase of the

cell in which many

particulate constituents

like mitochondria,

ribosomes, etc. are

suspended

• contains a wide variety of

solutes including proteins,

enzymes, nucleic acids

(RNA), a number of

electrolytes, metabolites

for cellular utilization

(e.g., glucose), and waste

products of cellular

activity (e.g., urea,

creatinine, uric acid, etc.)



Section 18.1

The nucleus

• the “information center” of the cell;

enclosed by a nuclear membrane

and contains the cell’s genetic

information and the machinery for

converting that information into

protein molecules

• site of DNA and RNA synthesis

• contains a comparatively large

amount of nucleoprotein (50%

DNA and 50% proteins, histones

and prolamines located in the

chromosomes, and a small

amount of RNA; >95% of nucleic

acids of the cell is in the nucleus

• nucleolus, - small, round dense

body present within the nucleus;

not surrounded by a membrane;

essentially a cluster of looped

chromosomal segments; contains

10-20% of the total RNA of the

cell, chiefly mRNA

• serve as a storehouse for mRNA

prior to its movement into the

cytoplasm by way of the nuclear

pores



Section 18.1

The mitochondria

• the second largest organelle

• the powerhouse of the cell

where carbohydrates, lipids,

and amino acids are oxidized

to CO2 and H2O by molecular

O2 and the energy set free is

converted into the energy of

ATP

• has a double-membrane

structure, an outer membrane

and an inner membrane

• site for cellular respiration

• The inner membrane, in which

the enzymes of electron

transport and energy

conversion are located, is

convoluted to form shelves

termed cristae.



Section 18.1

The endoplasmic reticulum

• appears to be a system of

interconnected tubules or

canaliculi extending throughout

the cell cytoplasm and is

continuous with the outer nuclear

membrane

• two types: rough and smooth er

• rough er is lined with a number

of small, spheric, electron-dense

particles called ribosomes

– primarily involved in synthesis

of membrane proteins and

proteins for export from the

cell

• smooth er lacks ribosomes

– appears to be involved in

the biosynthesis of

steroids, phospholipids,

and complex

polysaccharides

– functions also include

biotransformation, a

process in which water-

soluble organic molecules

are prepared for excretion



Section 18.1

The ribosomes

• consist of ~50% RNA

(rRNA) and 50% protein

• involved in protein

synthesis in the cell and

are sometimes referred to

as the “workbench” for

protein synthesis

• complex structures

containing two irregularly

shaped subunits of

unequal size

• they come together to

form whole ribosomes

when protein synthesis is

initiated

• when not in use, the

ribosomal subunits

separate



Section 18.1

The golgi apparatus / golgi complex

• structures composed of

flattened sacs with vesicles,

located near the nucleus,

probably continuous with er

• the organelles to which

synthesized proteins are

transported and temporarily

stored before release from the

cell

• the “packaging stations” of the

cell

• the primary site for packaging

and distribution of cell products

to internal and external

compartments

• there is a continuous flow of

substances through the Golgi

apparatus

• responsible for sorting and

packaging several types of

proteins, small molecules, and

new membrane components



Section 18.1

The lysosomes

• membrane-bound organelles

containing a variety of

hydrolytic and degradative

enzymes and having an

optimum pH of 5.0

• has regulatory and defense

function

• function in the digestion of

materials brought into the cell

by phagocytosis and

pinocytosis

• also serve to digest cell

components after cell death

• the “suicide bags” of the cell

• upon death of the cell or its

exposure to environmental

conditions, the lysosomal

membrane disintegrates,

releasing its contents, which

cause the self-digestion or

autolysis of the cell

constituents



Section 18.1

The peroxisomes

• contains oxidative

enzymes that oxidize

amino acids, uric acid,

and various 2-

hydroxyamino acids using

O2 with the formation of

H2O2

• H2O2 is then converted to

H2O and O2 by the

enzyme catalase also

present in the

peroxisomes

• thus the cell protects itself

from the toxicity of H2O2



Section 18.1

Water in the cell

• the solvent

– the agency that enables

water-soluble, water-miscible,

or emulsifiable substances to

be transferred in the body not

only in the blood but also

intercellularly and

intracellularly

• in biochemical reactions

– ionization is a prerequisite to

many biochemical reactions

and ionization takes place in

water



Section 18.1

Water in the cell

• in physiologic regulation of body

temperature

– high specific heat (amount of

heat required to raise the

temperature of 1g of H2O 1oC)

enables the body to store heat

effectively without greatly raising

its temperature

– high heat conductivity permits

heat to be transferred readily

from the interior of the body to

the surface

– high latent heat of evaporation

causes a great deal of heat to be

used in its evaporation and thus

cools the surface of the body



Section 18.1

Characteristics of biochemical reactions

• Chemical reactions occurring

in vivo have the following

properties:

• Speed

– glucose, for instance, is

oxidized in the body with

surprising speed, while in

vitro, the same reaction is

quite a long and tedious

process.

– this is due to the presence of

enzymes, without which life

as we know it would not be

possible

• Mildness

– energy is taken up and

released in a gentle way, not

violently as those occurring in

vitro (because of high specific

heat of water which makes up

a large proportion of the

protoplasm)

• Orderliness

– a high degree of orderliness is

due to the existence of cell

specialization within the

different organs of the body


Education

Chem 45 Biochemistry: Stoker chapter 18 Introduction – Cell Structure