3- chemistry of life ii

The Chemistry of Life II

Chapter 2

Outline for Today

I. Carbon and Organic MoleculesB. Classes of Biomolecules

3. Lipids

4. Proteins

5. Nucleotides and Nucleic Acids

Lipids

Lipids - Basics• Contains C, H, O, and

sometimes P– High ratio of H to O– e.g. tristearin C57H110O6

• Mostly or completely insoluble in water– Hydrophobic

• Used for fuels, structure, insulation and as hormones

• More variable structure than carbs

• More calories than carbs

Fig. 2.19

Organic Compounds : Lipids

TriglyceridesDehydration

Synthesis

If all carbons have full complement of H atoms, fat is saturated

If some carbons do not have full complement of H atoms, fat is

unsaturated

C = C

Most fatty acids have 16 – 18 carbons

Fatty acids can have between 14 – 22 carbons

Fatty Acids: What’s the big deal?

http://www.tennoji-h.oku.ed.jp/tennoji/oka/2004/04ko3-05.htm

http://www.sonic.net/~mueller4/mike/

saturated

unsaturated

Lipids - Triglycerides

• In general – fats are solid at room temp. and oils are liquid

• Primary function is fuel (energy) but can provide thermal insulation as well as cushioning

http://www.drhooman.com/walrus/walrus.jpg

Organic Compounds : LipidsPhospholipids

Fig. 2.20

Glycerol: just like in triglycerides

Fatty Acids: Notice the number

Phosphate group: Charged

Nitrogen group: charged

Charged and uncharged regions


Hydrophilic head region

Hydrophobic tail region

Fig. 2.20


Hydrophilic head region

Hydrophobic tail region

Fig. 2.20

Organic Compounds : LipidsSteroids

Steroid HormonesSex hormones (estrogen, progesterone, testosterone)

CortisolVitamin D

Fig. 2.22

Cholesterol

Polypeptides/Proteins

http://www.medical-definitions.net/hemoglobin.htm

http://www.nofadz.com/nofadz_history_x/177.html

Polypeptides - Basics

• Contains carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur

• Basic unit is the amino acid

http://www.agron.iastate.edu/courses/Agron317/AA_inhibitors.htm

(Radical group)

Fig. 2.23a

Amino group

AcidGroup

R group

Amino acids and peptide bonds

20 common amino acids


N terminus

C terminus

Fig. 2.23b


N terminusC terminus

Fig. 2.23b

What type of reaction is this?

Dehydration Synthesis/

Condensation Reaction

Since the C-N bond is a peptide bond, you will commonly hear of polypeptides


Fig. 2.23b

Conformation and denaturation

1 2 3 4

Levels of structural complexity

Fig. 2.24

Levels of Protein Structural Complexity

Held together by

Hydrogen bonds!!

Held together by

Hydrogen bonds!!

Fe

Saladin, 3rd. Ed.

• 3-D structure is extremely important– If the conformation of the

protein changes the function can be altered

• Denaturation is a drastic change in 3-D structure– Change in pH,

temperature, or addition of chemicals

http://www.cookacetic.de/secret_ingredients.htm

http://www.harcourtschool.com/glossary/science/define/gr2/irrev2e.html

Protein Structure - Denaturation

3-D structure is changed due to heat

Receptor on membrane

Ligand

• Why are high fevers so dangerous?

• Denature proteins in the body!

Protein Structure - Denaturation

• Structure– Collagen (bones, skin)

and keratin (skin)

• Movement– Actin and myosin

Functional Types

• Transport– Of ions via channels or

carriers

• Communication– hormones

Fig. 2.25

Functional Types

Fig. 3.8

• Recognition/ Protection– Receptors– Immune system

• Catalysis/Enzyme

Fig. 2.27

Functional Types

• Fibrous– Structure and contraction– e.g. Collagen

• Globular– Amorphous– Varied 3-D structure– e.g. pepsin

Shape/Conformation

http://dwb.unl.edu/Teacher/NSF/C10/C10Links/main.chem.ohiou.edu/~wathen/chem302/protein.html

• Biological catalysts that speed up existing chemical reactions– Don’t run “new reactions’

• Vital for life– Reactions won’t occur fast

enough or under conditions compatible with life without them

• Reusable– Not used up in the reaction

• Very specific– One enzyme for each

reaction

Enzymes

Fig. 2.27

• Active site – Area of enzyme where

substrate binds

• Enzyme substrate complex

• When the ES complex forms there is strain on the bonds or they are brought in to a new proximity– Gives proper orientation

Enzymes – how they work

Fig. 2.27

• Activation Energy– Energy needed to get

a reaction started

• Enzymes lower the activation energy of the reaction.

Enzymes – how they work

Fig. 2.26

• Usually end in the suffix “ase”

• Typically named according to– Type of reaction they catalyze (hydrolase)– Substrate in the reaction (DNase, lactase, protease,

ATPase)

• Can be synthesized in a precursor form– Ending is “ogen”

• Pepsinogen is the precursor to pepsin• True for other things besides enzymes

Enzymes – Nomenclature

Nucleotides and Nucleic Acids

http://ianandmanda.typepad.com/blog/2004/08/a_park_fit_for_.html

DNA Tower, Perth, Australia

• Contain the elements C, H, O, N and P

• Building block is nucleotide

• Examples of important nucleic acids are DNA and RNA

• Examples of important nucleotides are ATP, cAMP, NADH

http://sbchem.sunysb.edu/msl/DNA.html

Nucleic Acid composition

http://sbchem.sunysb.edu/msl/dna.gif

• Sugar– Pentose sugar

• Ribose or deoxyribose

• Nitrogen base– Purines (2 rings)

• Adenine• Guanine

– Pyrimidines (1 ring)• Cytosine• Thymine• Uracil

• Phosphate group

http://courses.agri.huji.ac.il/71065/1/pages/c-03-nucleotides.htm

Nucleotide composition

Sugar-phosphate “backbone”

Double stranded helix

interaction between bases holds

strands together

More specifically hydrogen bonds

Single stranded

Nucleic Acid composition – DNA and RNA

nucleotide

Nucleic Acid Structure : DNA

Denaturation occurs at100 C

Denaturation is the basis for PCR

Nucleic Acid composition – DNA and RNA

Forms/Types: B form helix twists to right

Ribosomal RNA (rRNA)

Messenger RNA (mRNA)

Transfer RNA (tRNA)

Modified Nucleotides – adenosine triphosphate (ATP)

Fig. 2.29a

High Energy bonds!!!

Main form of energy used in the cell

Source and Uses of ATP

Modified Nucleotides

Cellular respiration

ATP

• Entire amount in body would support life for under a minute

• Even if you never got out of bed you’d need 45 kg (99 lb) of ATP just to stay alive for a day

• Effects of cyanide

Fig. 2.29a


ATP cycle

ATP

ADP

Pi

EnergyPi

Energy


cAMP

• Cyclic AMP or cyclic adenosine monophosphate

• It is a second messenger in some hormone pathways

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/Hormones.html


Fig. 2.29b

NADH

• Serves as a hydrogen/electron carrier during cellular metabolism

• Important in cellular respiration

http://www.pdrhealth.com/drug_info/nmdrugprofiles/nutsupdrugs/nad_0179.shtml


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