Organic Molecules for Physiology

Organic Molecules for Physiology

The main groups of organic molecules we will be covering include the:

1 Carbohydrates

2 Lipids

3 Proteins and

4 Nucleic Acids

This is only a small portion of all organic molecules.

Organic Molecules

Contain carbon and hydrogen

Some Organic Groups We Will Use

-CH3 methyl group

-COH aldehyde group

-COOH carboxyl group or organic acid

H O H

H-C-C-C-H ketone

H H

H

-C-H

H

H

-C=O

O

-C-O-H

Inorganic Molecules

All the molecules that are not organic

Inorganic Groups We Will Use

-OH alcohol

-PO4= phosphate

-NH2 amino or amine

H+ proton or hydrogen ionOH- hydroxyl ion

Organic molecules in physiology

• Name elements ratios

• Carbohydrates C,H,O H:O is 2:1

• Lipids C,H,O H:O is many:1

• Proteins C,H,O,N

• Nucleic Acids C,H,O,N,P

Metabolismall the reactions in the body

• Reactions that build up• Anabolism• examples include• glycogenesis - combining

glucose units to make glycogen

• building fats• protein synthesis• DNA replication

• Reactions that tear down• Catabolism• examples include• glycogenolysis - splitting

glucose molecules off of a glycogen molecule

• glycolysis - spitting a glucose into two molecules

• burning fats

Vocabulary builder genesis - creation of lysis - splitting of

Metabolism

• Anabolism• uses dehydration synthesis

to join molecules• remove a H from one

molecule and an OH from another

• form water, H2O

• the other molecules join where the water left to form one molecule

• Catabolism • uses hydrolysis to separate

molecules

• separate a water, H2O into H and OH

• add the H to an oxygen in one molecule

• add the OH to a carbon in the molecule, separating the molecule into two molecules

Hydro - water

lysis - splitting

Dehydration - remove water

synthesis - put together

Carbohydrates • Sugars and starches

• basic building block is the

• monosaccharide - one sugar - C6H12O6

– glucose, galactose, fructose

• isomers - same molecular formula, different structural formulas

H

H-C-OH

H C OHO OH C C H H C C HO H HO H

H

H-C-OH

H C OH OH C C HO H C C HO H HO H

H H

H C OH O H C OH

H C C OH

H C C H

HO OH

Carbohydrates

• Disaccharide - two sugars• formed by dehydration synthesis• glucose + fructose sucrose + water

table sugar

• glucose +galactose lactose + water milk sugar

• glucose + glucose maltose + water malt sugar

Carbohydrates• Polysaccharide - glycogen

• many glucose units in a branching pattern

• liver and skeletal muscle are good sources

• hormone insulin stimulates glycogen production (glycogenesis)

• hormone glucagon stimulates glycogen breakdown (glycogenolysis)

• glycogen is found in animal cells as an inclusion

Carbohydrates

• Starches are complex carbohydrates, often two polysaccharide chains

• plants make starches, including the indigestible cellulose

• examples - wheat, rice, corn, potato, cassava, rye, barley

Lipidsnot water soluble, oxygen poor molecules

• Waxes • Fats• Steroids• Phospholipids• Glycolipids• Lipoproteins • Eicosanoids

• Candles, honeycomb• butter, lard• cholesterol,sex hormones, Vit D• cell membranes • cell membranes • HDLs and LDLs, lipid transport• prostaglandins, leukotrienes

Lipids - fats

• Neutral Fats• triglyceride• glycer - 3 carbons• glycerol - 3 carbon alcohol• tri - three fatty acids• fatty - chain of carbons and

hydrogens• acid - organic acid, the

carboxyl group

• In combined form, not acidic• usual form of neutral fat• H H H

H - C - C - C - H . OH OH OH

• H H H H H H H H - C - C - C - C - C - C - C - . H H H H H H H

• O C - OH

Lipids - fats• One glycerol

• dehydration synthesis with one fatty acid forms a

• monoglyceride

• dehydration synthesis with a second fatty acid

• diglyceride

• dehydration synthesis with a third fatty acid

• triglyceride

• three water molecules are produced

Lipids - fats• Saturated fats• produced by animals and

some tropical plants• contains no carbon-

carbon double bonds• carbon bonds are

saturated with hydrogens

• Unsaturated fats• produced by animals and

plants• contains carbon-carbon

double bonds• carbon bonds are not

saturated with hydrogens

• polyunsaturated

O H H H H H H H H H H H H H O H H H H H H H H H H H H H H HO-C-C-C-C-C-C-C-C-C-C-C-C-C-C-H HO-C-C-C-C-C-C-C=C-C-C-C-C=C-C-C-H H H H H H H H H H H H H H H H H H H H H H H H

Lipids - steroids

• Basic building block - cholesterol

• examples are:

• vitamin D

• sex hormones - testosterone, estrogen, progesterone

• glucocorticoids - hydroxycortisone

• mineralocorticoids - aldosterone

Outline of a steroid molecule

Lipids - phospholipids

• One glycerol

• two fatty acids• one phospho group - phosphate, may have amino groups

• fatty acids are hydrophobic - water fearing

• phospho end is hydrophilic - water loving

Lipids - phospholipids• Cells are wet inside and outside

• phospho end will face the water

• lipid ends will face each other

• phospholipid bilayer is formed

• water water

• outside cell inside cell• phospho fatty acids

• hydrophilic hydrophobic

Lipids - glycolipids

• Like phospholipids with a carbohydrate in place of the phospho group

• carbohydrate end of the glycolipids are usually found on the outer surface of a cell membrane

carbohydrate glycerol two fatty acids

• outside of cell inside of cell

Lipids - lipoproteins

• HDL high density lipoproteins

• LDL low density lipoproteins

• mobilizes fats

• deposits fats

Proteins - C, H, O, N

• The basic building block of a protein is the amino acid.

• Many amino acid molecules link together to form a polypetide.

• A very large polypeptide is a protein.

• The structure may be relatively simple for a small polypeptide, but quite complex for a large protein.

Amino Acids

The basic building block of a protein is the amino acid

There are four main parts in an amino acid

1 a central carbon atom

2 the amine or amino group -NH2

3 the carboxyl or organic acid group -COOH

4 an R group that is different for each of the . . twenty amino acids

Amino Acids

• All amino acids follow this basic plan

• The R groups can be polar or nonpolar, charged, or neutral. One amino acid, cystine, contains sulfur and can form a bond, the disulfide bridge.

H H O

N - C - C-O-H

H H-C-H

H

Central carbon

Carboxyl group

R group

Radical or “rest of the molecule”

Amino group

Proteins

Two amino acids can form a peptide bond by dehydration synthesis.

H H O H H O H H O H O

N-C-C-O-H +N-C-C-O-H N-C-C-O-N-C-C-O-H

H H H H H H H H

H-O

+ H

amino acid + amino acid dipeptide + water

Peptide Bond

Proteins

• Many amino acids joined in a chain will form a polypeptide.

• The sequence of the 20 amino acids in the polypeptide chain is called the primary structure of a protein.

• This sequence or primary structure will determine the shape and characteristics of the final protein.

Proteins The primary structure will determine the twists

(ex. alpha helix) and folds (ex. pleated sheets) that are the secondary structure

of a protein.

Proteins• The polypeptide, unless it is very small, will

also fold and twist the secondary structure for another level of complexity. You might imagine a toy slinky being the secondary structure of a protein, and the slinky being tied in a knot as the tertiary structure of that protein.

Proteins• The tertiary structure of a protein gives it a unique

shape and function.

• Some proteins are even more complex, and are made of two polypeptides that are twisted and folded together.

• This is the quaternary structure of a protein.

• Hemoglobin is a good example of this kind of protein with an alpha polypeptide and a beta polypeptide folded together

Proteins

• Proteins are produced by structures called ribosomes in our cells by a process called protein synthesis.

• If you change the shape of a protein, you usually change its’ function.

• These proteins may be structural proteins, enzymes or hormones to name a few of their uses.

Nucleic Acids• Deoxyribonucleic Acid• Ribonucleic Acid• Adenosine Triphosphate• Adenosine Diphosphate• Cyclic Adenosine

Monophosphate• Nicotinomide Adenine

Dinucleotide• Flavoprotein version of NAD

• DNA• RNA• ATP• ADP• C-AMP

• NAD

• FAD

Nucleic Acids C, H, O, N, P

• Nucleotide

• one phosphate group• one sugar • one nitrogen base

• Basic building block of the nucleic acid

• 5 C or pentose sugar

Nucleic Acids

phosphate group connects the sugar molecules in the “backbone” of the molecule

Deoxyribose or Ribose sugar (5 C pentose)

nitrogen baseDNA 4 types

RNA 4 types

makes DNA or RNA

DNA - adenine, thymine, cytosine, guanine

RNA - adenine, uracil, cytosine, guanine

. Three hydrogen bonds .

Nucleotides - bases

. Two hydrogen bonds .

• Purines - larger• adenine • guanine

• Pyrimidines - smaller• thymine - uracil• cytosine

A

G

T

C

U

Deoxyribonucleic Aciddouble helix

Sugar phosphate backbone

Two stranded or double helix

Nitrogen bases

DNA RNA

• Double strand• helix• thymine• much larger than RNA• in nucleus and

mitochondria• genetic material of the

cell

• Single strand• various shapes• uracil• smaller than DNA• made in nucleus (nucleolus)

functions in cytoplasm• used in protein synthesis

– r-RNA (ribosomal)

– t-RNA (transfer)

– m-RNA (messenger)

High energy phosphate bonds

• ATP - triphosphate• ADP - diphosphate

• High energy molecule• lower energy molecule

adenine

Ribose sugar

P P

Phosphate groups

High energy phosphate bonds

P P energy released from

. phosphate bond and . . used in reactions like . . protein synthesis

Left arrow once to repeat energy release

c-AMP

• AMP - monophosphate • Second messenger in cell membranes

• changes shape in response to an enzyme adenine

Ribose sugar

P