intro to biochem

8/13/2019 intro to Biochem

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Biochemistry

- study of the structure, organizations,

chemical compositions, functions and

processes in a living organisms.- Chemistry of life

Suggested Reading: Pace, N. R. 2000. The universal nature of biochemistry.

Proc. Natl. Acad. Sci. USA98:805-808.


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What makes a living thing 'alive'?

exhibit high degree of complexity &organization

ability to extract, transform & utilize energy

capacity to precisely self-replicate and/or

self-assemble

all three attributes are ultimately due to

biomolecular st ructure and funct ion,

which is the essence of Biochemistry


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A brief overview of

organic chemical principles

You should already be familiar with the

following concepts from organic chemistry:

- functional groups (names & how to draw)- electronegativity & partial charges

- chirality (assigning R vs S stereochemistry),

enantiomers & diastereomers

- acids & bases (pH values); protonation & pKa values


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The types of reactions most frequently

encountered in living systems are:

1. Oxidation-reduction reactions involving carbon-oxygen, carbon-carbon, or carbon-nitrogen bonds.

2. Intramolecular or intermolecular functional group-transfer reactions.

3. hydrolysis of esters, ethers, and amides.

4. Elimination or addition reactions.

5. Isomerization reactions.

6. Formation of ester, thiol ester, and amide

linkages.


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Biochemical reactions utilize a limited number of

elements, most prominently carbon, hydrogen,

oxygen, nitrogen, sulfur, and phosphorus. Many

biochemical reactions are simple organicreactions.

Biochemical reactions of different types are

localized to different parts in the cell.

Biochemical reactions are carried out under very

mild conditions in aqueous solvent.

An Overview of Biochemical Structures and

Reactions that Occur in Living Organisms


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Biochemical reactions are frequentlyorganized into multistep pathways.

Biochemical reactions are regulatedaccording to need by controlling theamount and activity of enzymes in thesystem.

Most organisms depend on otherorganisms for their survival.

An Overview of Biochemical Structures and

Reactions that Occur in Living Organisms


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H, O, C and N make up 99+% of atom s in th e human bod y

Essential Elements in Living Systems


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Biochemist ryfocuses

on these levels in the

hierarchy of biological

structure

Structural Heirarchy of Living Systems


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THE CELL

- structural andfunctional unit of

living organisms

smallest organisms (unicellular)

larger organisms (multicellular)

human contains ~1014cells


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Types of Cell

1) Prokaryotic cell

- small, simple in structure, lacks some organelles

and contains only one single chromosome

ex. Bacteria and blue-green algae

Eubacteria=commonly encountered

in soil,water and living in or on larger

organisms

Archaebacteria= grows in unusualenvironment like salt brines, hot acid

springs and ocean depths


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Parts of the Cell

Parts Functions

membranes -bound the cell and made up of lipids andproteins

- regulates the transport of molecules in and out

of the cell

nucleus- site for the manufacture of nucleic acids

nucleolus - within the nucleus

- center for RNA and proteins biosynthesis

ribosomes - tiny particles in the cell

- site for manufacture of proteinslysosomes - storage of catalytic proteins

endoplasmic

reticulum

- central part for the biosynthesis of

macromolecules


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Parts of the Cell

Parts FunctionsGolgi apparatus - storage house of the cell

- involved in packaging, transport and synthesis

of carbohydrates

mitochondria - Powerhouse of the cell- its inner membrane is the site for oxidativephosphorylation and electron transport


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All cellular life has the following

characteristics in common: All cells have a CELL MEMBRANEthat

separates the CHAOSoutside a cell from thehigh degree of organization within the cell.A cellwithout a cell membrane is NOT A CELL.

All cellular life CONTAINS DNAas its geneticmaterial. All cells contain several varieties ofRNAmolecules and PROTEINS, most of the

latter are enzymes.

All cells are composed of the same BASICCHEMICALS: carbohydrates, proteins, nucleicacids, lipids
http://www.slic2.wsu.edu:82/hurlbert/micro101/pages/101_prologue.htmlhttp://www.slic2.wsu.edu:82/hurlbert/micro101/pages/101_prologue.html


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All cells REGULATEthe flow of nutrients

and wastes that enter and leave the cell.

All cells REPRODUCEand are the resultof reproduction.

All cells require a SUPPLY OF ENERGY.

The most commonsource of chemical

energy used.

All cellular life has the following

characteristics in common:


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ORGANELLESPLASMA MEMBRANE

(CELL MEMBRANE)

-Separates cell from itsenvironment

-Provides mechanical

strength and shape to the

cell

-Vital function: transport

-Plays a role in

communication between

cells, responsiveness to

extracellular signals,

muscle contraction and

nerve impulse conduction


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ORGANELLES NUCLEUS

-Contains the cellsblueprint: the cells

hereditary info

-Exerts a profound

influence over allcellular metabolic

activities

-Contains the nucleolus

which plays a major

role in the synthesis of

ribosomal RNA


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ORGANELLES Endoplasmic reticulum

ROUGH ER

-Primarily involved in

the synthesis of

membrane proteins &

protein for export fromthe cell

-Rough because of the

ribosomes

SMOOTH ER

- Involved in lipid

synthesis


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ORGANELLESRibosomes

-20 nm in diameter

-Biosynthesis of

proteins

-Composed of proteinsand ribosomal RNA

-Composed of 2

irregularly-shaped sub

units


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ORGANELLESGOLGI COMPLEX

-Involved in thepackaging & distribution

of cell products to

internal and external

compartments-In plants, its functions

include transport of

substances into the cell

wall and expansion ofplasma membrane

during cell growth


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ORGANELLESLYSOSOMES

-Functions in intracellularand extracellular digestion

-Suicide bag of the cell

-Contains digestive

enzymes

-Capable of degrading

most biomolecule

- Typically spherical with adiameter of 500 nm


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ORGANELLESPEROXISOMES

-Small spherical membranousorganelles that contain

oxidative enzymes

-Involved in the generation &

breakdown of toxic moleculessuch as peroxides

-In plants, it is found in leaves

that is responsible for an

oxygen-consuming process inwhich CO2is produced


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ORGANELLES

MITOCHONDRIA

-Powerhouse of the cell

-Aerobic respiration takes

place here

-Usually sausage-shaped

-Has an inner membrane

which is the site for oxidative

phosphorylation & electron

transport chain


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ORGANELLESCHLOROPLASTS

-Found only in plants, algae

and some protists

-Type of chromoplasts that arespecialized for the conversion

of light energy into chemical

energy

THYLAKOID MEMBRANE

- Chlorophyll are bound to

thylakoid membrane proteins


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ORGANELLES VACUOLE

-tend to be very large and are

extremely important inproviding structural support,

as well as serving functions

such as storage, waste

disposal, protection, and

growth.

-Many plant cells have a

large, single central vacuole

that- Smaller in animal cells and

are more commonly used to

temporarily store materials or

to transport substances.


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ORGANELLES VACUOLE

-provides the cell with

structural support,

protection, and acts as a

filtering mechanism

-prevents over-expansion

when water enters the cell

- are found in plants,

bacteria, archaea, fungi,and algae.
http://en.wikipedia.org/wiki/Planthttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Fungushttp://en.wikipedia.org/wiki/Algahttp://en.wikipedia.org/wiki/Algahttp://en.wikipedia.org/wiki/Fungushttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Plant


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ORGANELLES

MITOCHONDRIA

-Powerhouse of the cell

-Aerobic respiration takes

place here

-Usually sausage-shaped

-Has an inner membrane

which is the site for oxidative

phosphorylation & electron

transport chain


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ORGANELLESCHLOROPLASTS

-Found only in plants, algae

and some protists

-Type of chromoplasts that arespecialized for the conversion

of light energy into chemical

energy

THYLAKOID MEMBRANE

- Chlorophyll are bound to

thylakoid membrane proteins


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ORGANELLES VACUOLE

-tend to be very large and are

extremely important inproviding structural support,

as well as serving functions

such as storage, waste

disposal, protection, and

growth.

-Many plant cells have a

large, single central vacuole

that

- Smaller in animal cells and

are more commonly used to

temporarily store materials or

to transport substances.


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ORGANELLES VACUOLE

-provides the cell with

structural support,

protection, and acts as a

filtering mechanism

-prevents over-expansion

when water enters the cell

- are found in plants,

bacteria, archaea, fungi,and algae.
http://en.wikipedia.org/wiki/Planthttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Fungushttp://en.wikipedia.org/wiki/Algahttp://en.wikipedia.org/wiki/Algahttp://en.wikipedia.org/wiki/Fungushttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Plant


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A Comparison of Prokaryotes and Eukaryotes

Organelle Prokaryotes Eukaryotes

Nucleus No definite nucleus; DNA present but not

separate from rest of cell

Present

Cell membrane

(plasma membrane)

Present Present

Mitochondria None; enzymes for oxidation reactions

located on plasma membrane

Present

Endoplasmic

reticulum

None Present

Ribosomes Present Present

Chloroplasts None; photosynthesis localized in

chromatophores

Present in green plants


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(Principles of Biochemistry,Zubay,1995)

Summary of Organelles and Their Function

Organelle Function

Nucleus Location of main genome; site of most DNA and RNA

synthesis

Mitochondrion Site of energy-yielding oxidation reactions; has its own

DNA

Chloroplast Site of photosynthesis in green plants and algae; has its own

DNA

Endoplasmic Reticulum Continuous membrane throughout the cell; rough part

studded with ribosomes (the site of protein synthesis)

Golgi apparatus Series of flattened membranes; involved in secretion of

proteins from cells and in reactions that link sugars to other

cellular components

Lysosomes Membrane-bounded sacs containing hydrolytic enzymes

Peroxisomes Sacs that contain enzymes involved in the metabolism of

hydrogen peroxide

Cell Membrane Separates the cell contents from the outside world; contents

include organelles (held in place by the cytoskeleton) and the

cytosol

Cell Wall Rigid exterior layer of plant cells

Central Vacuole Membrane-bounded sac (plant cells)


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Carbohydrates/Sugars

-energy source

-important components of

genetic materials-synthesized by

photosynthesis in plants

-a gram of digestedcarbohydrate gives about

4 kcal of energy


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Are biological catalysts

(enzymes)

Are antibodies that fightantigens (bacteria and

viruses)

Transport molecules and

ions

Regulate cell function

Provide structural support

and mechanical strength


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- structural components of

biological membranes

- provide energy

reserves,predominantly in the

form of triacylglycerols

- vitamins and hormones


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NUCLEIC ACIDSRNA (ribonucleic acid)DNA (deoxyribonucleic acid)

- information molecules

- into their primary structure is encoded

a set of directions that ultimately governs

intro to biochem

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