Biochemistry

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 molecular building blocks )- Occurs by dehydration synthesis the removal of a H+ ion and OH- ion, forming a chemical bond between

monomers.

I. Organic POLYMERSI. Organic POLYMERSA. CarbohydratesA. Carbohydrates

B. Lipids B. Lipids

C. ProteinsC. Proteins

D. Nucleic acids D. Nucleic acids

(DNA and RNA)(DNA and RNA)

A. Carbohydrates (C,H,O)A. 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. Polysaccharides … examples3. Polysaccharides … examples-- many sugar units chemically bonded together many sugar units chemically bonded together

1. 1. starchstarch ( (synthesized in plants: bread, potatoessynthesized in plants: bread, potatoes) ) - for energy- for energy

2.2. glycogen glycogen ( ( synthesized in animals: in animal musclessynthesized in animals: in animal muscles) ) – – for structure & energyfor structure & energy

3. 3. cellulose cellulose - plant wall structure- plant wall structure

4. 4. chitinchitin – component of exoskeletons …structure – component of exoskeletons …structure

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

glucoseglucoseglucoseglucose

cellulosecellulose

A. Carbs provide quick energy

(remember: 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

CARBS: FunctionsCARBS: 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 (C,H,O)B. Lipids (C,H,O)

Lipid … a Lipid … a triglyceride triglyceride - 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

=

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

• FATS

1.1. Saturated fatsSaturated fats … no double bonds in fatty acid … no double bonds in fatty acid chain (bad)chain (bad)

2.2.Unsaturated fatsUnsaturated fats… double bonds in fatty acid … double bonds in fatty acid chain(good)chain(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

FunctionsFunctions 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) Amino Acids – the monomer “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

PROTEINs: FUNCTIONS

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

b. Transport b. Transport hemoglobinhemoglobin: : bonds with 0 bonds with 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 AntibodiesAntibodies to fight foreign to fight foreign “invaders” to living tissues “invaders” to living tissues

C. C. ProteinsProteins The synthesis (making) of a proteinThe synthesis (making) of a protein

- goes through 3 foldings- goes through 3 foldings

aa.. Primary (1°) structurePrimary (1°) structure

b.b. Secondary (2°) structureSecondary (2°) structure

c.c. Tertiary (3°) structureTertiary (3°) structure

d.d. Quaternary (4°) structureQuaternary (4°) structure

Primary Form (1°)• Amino acids bond together in long, linear chains by in long, linear chains by

dehydration synthesis dehydration synthesis reactions. reactions.

• Process called Process called protein synthesisprotein synthesis– Process starts at Process starts at nucleus nucleus & finishes at & finishes at ribosomesribosomes

aa1 aa2 aa3 aa4 aa5 aa6

Peptide Bonds – specific name for chemical bonds between amino acids

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°)

• secondary protein forms may now bendbend and fold: fold: attaching to themselves and/or others, forms a attaching to themselves and/or others, forms a Tertiary Form Tertiary Form – ““Side chain” bonding Side chain” bonding (disulfide bonds) (disulfide bonds)

• This makesThis makes them more compactthem more compact..

WHY is this of benefit to a cell? WHY is this of benefit to a cell?

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

Alpha HelixAlpha Helix

Beta Pleated SheetBeta Pleated Sheet

Quaternary Form (4°)Quaternary Form (4°)• 2 or more tertiary units may then join together

= A globular PROTEIN molecule!

could be a digestive enzymes, enzymes, steroids, hemoglobin, hair, nails, steroids, hemoglobin, hair, nails,

3° subunits3° subunits

Subunits

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. Nucleic acids … Functions

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 – structure2. A Nucleotide – structure

- a - a phosphate group +phosphate group +

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

- one of the nitrogenous bases … - one of the nitrogenous bases …

Purines: Purines: (double rings) (double rings)

adenine (A) guanine (G)adenine (A) guanine (G)

Pyrimidines: Pyrimidines: (single rings)(single rings)

thymine (T) cytosine (C) thymine (T) cytosine (C) andand

(uracil (U) replaces thymine (T) in RNA) (uracil (U) replaces thymine (T) in RNA)

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