Biochemistry SOL BIO 3 b,c. Organic Compounds 1.Molecules 1.Molecules containing the atom carbon ( C...

BiochemistryBiochemistry

SOL BIO 3 b,c

Organic CompoundsOrganic Compounds

1.1. MoleculesMolecules containing the atom carbon ( C )

Ex: C6H12O6 glucose

2. Most are macromolecules called polymers

3. Polymerization the process of organic polymers being built with

monomers ( single molecule building blocks )

I. Organic POLYMERSI. Organic POLYMERS

A. CarbohydratesA. Carbohydrates

B. Lipids (B. Lipids (fats)fats)

C. ProteinsC. Proteins

D. Nucleic acids D. Nucleic acids

(DNA and RNA)(DNA and RNA)

A. Carbohydrates C,H,OA. Carbohydrates C,H,O

Built with monomers like:

1.1. monosaccharides (1 sugar)monosaccharides (1 sugar)

- glucose- glucose ( (simple sugar)

- - galactosegalactose (milk sugar) (milk sugar)

- - fructosefructose (honey) (honey)

2.2. disaccharides (disaccharides (2 sugars bonded together2 sugars bonded together))

- - sucrosesucrose = glucose + fructose = glucose + fructose

(table sugar)(table sugar)

3. Polysaccharides3. Polysaccharides- - many sugar units bonded togethermany sugar units bonded together

1. 1. starchstarch (bread, potatoes) - for energy (bread, potatoes) - for energy 2.2. glycogenglycogen (beef muscle) – (beef muscle) – for structure & for structure &

energyenergy

3. 3. cellulosecellulose (lettuce, corn) – for structure(lettuce, corn) – for structure 4. 4. chitinchitin (exoskeletons) – for structure (exoskeletons) – for structure

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

cellulosecellulose

A. Carbs provide quick energy

(breaking chemical bonds release energy)

Ex: starch

B. Carbs make up cell structures

Ex: Plant cell walls are cellulose = “fiber”

Ex: External skeletons are chitin

C. Carbs can store energy for cells to use later

Ex: glycogen

CARB Examples & FunctionsCARB Examples & Functions – – why do living cells need them?why do living cells need them?

GO Pack!

- Built with the monomers . . . - Built with the monomers . . .

oneone glycerol glycerol molecule molecule

bonded to bonded to

threethree fatty acid fatty acid moleculesmolecules

B. Lipids ( “fats” ) C,H,OB. Lipids ( “fats” ) C,H,O

• One “triglyceride” One “triglyceride” II

– the smallest lipid molecule the smallest lipid molecule

– 1 glycerol1 glycerol & 3 fatty acids3 fatty acids molecules bonded together

H

H-C----O

H-C----O

H-C----O

H

1 glycerol

O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=

3 fatty acids

O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=

O

C-CH2-CH2-CH2-CH=CH-CH2 -CH

2 -CH2 -CH

2 -CH3

=

• Two types of fatty acidsfatty acids may be bonded to the glycerol molecule:

1.1. Saturated fatty acids:Saturated fatty acids: no double bonds no double bonds (bad)(bad)

2.2. Unsaturated fatty acids:Unsaturated fatty acids: double bonds double bonds (good)(good)

- liquid at room temperature- liquid at room temperature

O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=saturatedsaturated

O

C-CH2-CH2-CH2-CH=CH-CH2-CH

2-CH2-CH

2-CH3

=

unsaturated

Examples of lipid molecules Examples of lipid molecules

1. Fats - 1. Fats - in foods, both saturated and unsaturatedin foods, both saturated and unsaturated

2. Phospholipids – 2. Phospholipids – cell membrane structurecell membrane structure

3. Oils – 3. Oils – lubricants, cooking, fuellubricants, cooking, fuel

4. Waxes – 4. Waxes – protective coatingsprotective coatings

5. Steroids / hormones – 5. Steroids / hormones – regulate cell activitiesregulate cell activities

6. Polyglycerides –6. Polyglycerides – in make-up, body lotions in make-up, body lotions

Examples & FunctionsExamples & Functions of Lipids of Lipids

a. Long term energy storagea. Long term energy storage

(fats)(fats)

b. Protection against heat lossb. Protection against heat loss (lipid storage in specialized (lipid storage in specialized

cells)cells)

c. Protection against water loss & germsc. Protection against water loss & germs (skin oils)(skin oils)

d. Chemical messengersd. Chemical messengers

(hormones & steroids)(hormones & steroids)

e. Major structural component of cell e. Major structural component of cell membranesmembranes

(phospholipids)(phospholipids)

C. Proteins C H O N S C. Proteins C H O N S 1. Monomer building blocks

a. amino acids – the “building blocks”

20 total

1) 9 essential amino acids

- Essential amino acids need to be obtained through our diet

2) 11 non-essential amino acids

- amino acids that can be

synthesized by our body

C. C. ProteinsProteins

2. 2. 4 protein forms4 protein forms::

aa.. Primary (1°)Primary (1°)

b.b. Secondary (2°)Secondary (2°)

c.c. Tertiary (3°)Tertiary (3°)

d.d. Quaternary (4°)Quaternary (4°)

Primary Form (1°)• Amino acids bond together with peptide bonds peptide bonds in a in a

long, single chain by a process called long, single chain by a process called

protein synthesisprotein synthesis

aa1 aa2 aa3 aa4 aa5 aa6

Peptide Bonds

Amino Acids (aa)

Secondary Form (2°)Secondary Form (2°)• The first 3-dimensional folding of a

primary structureprimary structure into

»coils (alpha helix)coils (alpha helix) and

»pleats (beta pleats)pleats (beta pleats)

hydrogen bonds hold the secondary form together so they don’t uncoil

Secondary Form (2°)Secondary Form (2°)

The 2 typesThe 2 types

Alpha HelixAlpha Helix

Beta Pleated SheetBeta Pleated Sheet

Hydrogen BondsHydrogen Bonds

Alpha Helix

Beta Pleated Sheets

Tertiary Form (3°) Tertiary Form (3°)

• Now cells bendbend and foldfold the coiled or pleated proteins into a 3-D package 3-D package

called a “subunit”“subunit”

• This makesThis makes them them more compactmore compact

WHY? so more proteins can float around WHY? so more proteins can float around inside a small cell. inside a small cell.

C.C. Tertiary Form (3°)Tertiary Form (3°)

Alpha HelixAlpha Helix

Beta Pleated SheetBeta Pleated Sheet

Quaternary Form (4°)Quaternary Form (4°)• Finally, 2 or more subunits fold and join

together.

= A PROTEIN molecule!

digestive enzymes, steroids, enzymes, steroids, hemoglobin, hair, nails, hemoglobin, hair, nails,

3° 3° subunitssubunits

Subunits

PROTEIN FUNCTIONS

a. Energy a. Energy albumin (egg white), meatalbumin (egg white), meat

b. Transport b. Transport hemoglobinhemoglobin = transports 0= transports 022

c. Regulatoryc. Regulatory hormones, steroids hormones, steroids

d. Movementd. Movement major component of muscle cellsmajor component of muscle cells

e. Structurale. Structural cell membranes, hair, nailscell membranes, hair, nails

f. Controlf. Control EnzymesEnzymes turn on and turn off turn on and turn off all all cellular biochemical reactionscellular biochemical reactions

g. Defenseg. Defense antibodies to fight foreign antibodies to fight foreign “invaders” to living tissues “invaders” to living tissues

Enzymes: Special ProteinsEnzymes: Special Proteins

D. Nucleic Acids C, H, O, N, PD. Nucleic Acids C, H, O, N, P

A. Two types:A. Two types:

1. DNA deoxyribonucleic acid 1. DNA deoxyribonucleic acid

(double helix)(double helix)

2. RNA ribonucleic acid 2. RNA ribonucleic acid

(single strand)(single strand)

B. STRUCTUREB. STRUCTURE – – the monomers arethe monomers are

nucleotides nucleotides

1. FunctionsNucleic acids …

a. Control our hereditary messages

b. Control the overall function of a cell

c. Control the making of all cell proteins

d. Control cell reproduction

e. Control the metabolic rate of a cell

2. A Nucleotide – the monomers of 2. A Nucleotide – the monomers of nucleic acids nucleic acids

- a - a phosphate group +phosphate group +

- a - a sugar molecule (5-carbon ring) +sugar molecule (5-carbon ring) +

- a - a nitrogenous base … eithernitrogenous base … either

adenine (A)adenine (A)

thymine (T) - uracil (U) in RNAthymine (T) - uracil (U) in RNA

cytosine (C)cytosine (C)

guanine (G)guanine (G)

a single nucleotidea single nucleotide

OO=P-O O

PhosphatePhosphate GroupGroup

NNitrogenous baseNitrogenous base (A, G, C, or T)(A, G, C, or T)

CH2

O

C1C4

C3 C2

5

SugarSugar(deoxyribose)(deoxyribose)

DNA – the double helix formDNA – the double helix form

P

P

P

O

O

O

1

23

4

5

5

3

3

5

P

P

PO

O

O

1

2 3

4

5

5

3

5

3

G C

T A

Q: What keeps us alive?

A: the sum total of biochemical reactions in every cell termed …

A: Metabolism

“We’re just one big ‘ole

chemical factory on

legs!”

II. Cell Metabolism the sum total of all the chemical reactions

in a cellular organism

1. Anabolic reactions building UP (requires energy) Ex: many sugar molecules a carbohydrate

2. Catabolic reactions breaking DOWN (energy released)

Ex: a carbohydrate molecule ????

Metabolism:Metabolism: influencing factors influencing factors

1. TEMPERATURE1. TEMPERATURE

- low temperatures,- low temperatures,• reaction rates decreasereaction rates decrease

- high temperatures,- high temperatures,• speed up reactionsspeed up reactions

andand

• can alter protein structurescan alter protein structures

2.2. The pH of an cell’s environmentThe pH of an cell’s environment

- - extremes of pH can irreversibly extremes of pH can irreversibly change the functioning of enzymes change the functioning of enzymes

… stop ‘em cold … stop ‘em cold

- most cells function best within a - most cells function best within a narrow range of temperature and pH.narrow range of temperature and pH.

III. Review Basic Cell Biochemistry A. The atoms

that make up the molecules in a cell

1. carbon C2. hydrogen H3. nitrogen N4. oxygen O

AND some phosphorus P and sulfur S

• Inside every cell is a concentrated mixture of thousands of different macromolecules forming a variety of specialized structures that carry out cell functions

III. Basic Cell Biochemistry Facts

B. The mix of molecules

III. Basic Cell LifeC. Necessary metabolic functions

1. Energy production2. Transportation of molecules

- within the cell- in and out of the cell

3. Waste disposal4. Protein Synthesis 5. Safe storage of genetic material6. Reproduction7. Defensive protection