The Chemistry of Life- Organic Molecules

Polymer

Chains of similar units (monomer or building blocks)

Dehydration synthesis

A hydrogen atom is removed from one monomer and a hydroxyl is removed from the other = a water molecule removed from every bond formed

Hydrolysis

a water molecule id added to each bond to be broken

How are polymers formed and broken

Formed through dehydration synthesis

Broken through hydrolysis

Organic molecules what

Contain carbon

Electroneutral

Never lose or gain electrons (always shares electrons)

What carbon compounds are inorganic

CO₂ and CO

Why are carbon compounds unique to living systems

They have

Carbohydrates, Lipids, Proteins, Nucleic Acids ( DNA, RNA, Adenosine Triphosphate)

Carbohydrates

Are the sugars and starches of the body

Contain C, H, and O 1:2:1 ration

Three types monosaccharides, disaccharides, polysaccharides

Functions

Major source of cellular fuel

Structural molecules

Ex. Ribose sugar in RNA

Monosaccharides

Simple Sugars containing 3 to 7 C atoms

Cross over cell membranes

One Sugar

The only carbs our body can digest

Disaccharides

Two sugars

Too large to pass through cell membranes

How we ingest carbs

Polysaccharides

Many Sugars

Ingest and Store

Examples of Monosaccharides

Glucose

Fructose

Galactose

Pentose

Five Carbon

Hexose

Six Carbon

Important Disaccharides

Sucrose (Table Sugar)

• Glucose + Fructose

Lactose (Milk sugar)

• Glucose + Galactose

Maltose

• Glucose + Glucose

Oligosaccharides

Short Chains of three or more monosaccharides (At least 10)

Polysaccharides

Long chains of monosaccharides (At least 50)

What are three important polysaccharides

Glycogen, Starch, Cellulose

Glycogen

Energy storage in cells of the liver, muscle, brain, uterus, vagina,

Starch

Energy Storage in plants that is digestible by humans

Cellulose

Structural Molecule in plants that is important for human dietary fiber ( humans cannot digest)

Conjugated Carbohydrates

Lipid and protein molecules at the external surface of the cell membrane often have chains of sugars attached to them

Glycolipids

Sugar attached to fat

Glycoproteins

Sugar attached to protein

Major component of mucus

Proteoglycans

Gels that hold cells and tissues together; fill umbilical cord and eye

Join lubrifaction; responsible for the rubbery texture of cartilage

More carbohydrates than protein

Lipids

Contains C,H,O and sometimes P (Less O than in a carbohydrate

Insoluble in water

• Keep the water in our bodies

What are the main types of lipids

Neutral fats or triglycerides

Phospholipids

Steroids

Eicosanoids

Triglycerides

Neutral Fats

• Solids are fats and liquids are oils

Composed of three fatty acids bonded to a glycerol molecule

Fatty acid

linear chain of carbon and hydrogen chain with a -COOH group

Glycerol

Modified simple sugar

Main functions of a triglycerides

Energy storage (most efficient and compact)

Insulation (found mainly beneath the skin Ex. Subcutaneous fat)

• Maintain body temp

Protection (from mechanical trauma

• Fat around kidneys

Saturated

Solid at room temperature

Have a single carbon bond

All bonds have a hydrogen attached

Unsaturated

Liquid at room temperature

Has at least one double carbon bonds

Not all bonds have a hydrogen

Trans-fatty acids

Two covalent single C-C bonds angle in opposites on each side of the C = C double bond

[blank] = across from each other

Resists enzymatic breakdown in the human body, remain in circulation, longer, deposits in the arteries; thus, raises the risk of heart disease

Cis-fatty acids

Two covalent C-C bonds angle in the same direction adjacent to the C=C double bond

Phospholipids

Modified triglycerides

• Glycerol+ two fatty acids and a phosphorus (P) containing group

“Head” and “tail” regions have different properties

Important in the cell membrane structure

Eicosanoids

20 Carbon compounds derived from arachidonic acid

Hormone-like chemical signals between cells

• Local chemical messengers

Includes prostaglandins

What do prostaglandins do

They play an important roles in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter

Steroid

Lipid with 17 carbon atoms in 4 rings

Cholesterol

The “parent” steroid from which other steroids are synthesized

Important for nervous system function and structural integrity of all cell membranes

Where does cholesterol come from

15% of [blank] comes from diet

85% is internally synthesized (mostly in the liver)

What are some examples of steroids

Cortisol (stress hormone), progesterone, estrogens, testosterone, and bile acids

Proteins

Polymers of amino acids

Contains C,H,O,N and sometimes S and P

Basic structural material of the body

How are amino acids bound

They are joined by peptide binds

Amino Acid

Central carbon with three attachments

[blank] group (-NH₂)

Carboxyl Group (-COOH)

Radical Group (R group)

What determines the properties of amino acids

The R group

What is identical about proteins and what makes them different

All proteins are made up of the same 20 different amino acids. What is different is the Radical group

How much cell mass is protein

10-30%

Peptide Bond formation

Dehydration synthesis creases a [blank] bond that joins the amino acid of one group to the carboxyl group of the next

• Unique name for a covalent bond between amino acids

What are the four structural levels of proteins

Primary, Secondary, Tertiary, Quaternary

Primary Structure

Sequence of amino acids within protein molecule

Primary structure is encoded by genes

Secondary Structure

Coiled or folded shape held together by hydrogen bonds

• Hydrogen bonds between slightly negative C=O and slightly positive N-H groups

Types of Secondary Structures

Alpha helix- Spiral coil

• Elasticity to fibrous proteins (Ex. Skin and hair)

Beta Sheet- Planar pleat arrangement

• Flexibility to globular proteins (Ex. Enzymes)

Tertiary Structure

3rd protein structure level. Comprised of Globular and Fibrous proteins.

Globular proteins

Compact tertiary structure for proteins within cell membrane and proteins that move freely in body fluids.

Specific functional regions (active sites)

• Ex. Antibodies, hormones, molecular chaperones, and enzymes.

Play a crucial role in virtually all biological processes

Unstable.

Functional protiens

Fibrous Proteins

Slender filaments suited for roles in muscle contraction and strengthening skin and hair

• Ex. Keratin, Elastin, Collagen, and certain contractile fibers

Chief building material of the body

Stable

Structural proteins

Quaternary Structure

Associations of two or more polypeptide chains due to ionic bonds and hydrophobic-hydrophilic interactions

Occurs only in some proteins

• Ex. Hemoglobin has four peptide subunits

Comprised of 2 or more separate proteins (all twisted together)

Protein Function: Structure

Keratin: Tough structural protein of hair, nails, skin surface

Collagen (Most abundant in body): Contained in deeper layers of skin, bones, cartilage, and teeth.

Protein Function: Communication

Neurotransmitters, some hormones, and other signaling molecules are proteins

The receptors to which the signaling molecules bind are also proteinsPr

Ligands

Signaling molecules that exert their effects by reversibly binding to a receptor molecule

Protein Function: Membrane Transport

Channel proteins allow hydrophilic substances to diffuse across cell membranes

Carrier proteins help solutes cross cell membranes via active or passive transport

Allows cells to take in what they need

Protein Function: Catalysis

The enzymes that catalyze physiological reactions are usually globular proteins

Protein Function: Recognition and protection

Glycoproteins are important for immune recognition

Protein Function: Movement

Motor proteins are molecules with the ability to change shape repeatedly

Protein Function: Cell Adhesion

Proteins bind cells together

CAMs= cell to cell

ECM=attachment to the cytoskeleton and extracellular matrix

Enzymes

Globular proteins

Biological catalyst

• Lower the activation energy, increase the speed of reaction (millions of reactions per minute)

What are the three steps of an enzyme reaction

1) Substrate approaches the active site

2)The substrate binds, and forms an enzyme substrate complex

3) The reaction occurs, the products are created

Are enzymes reusable

Yes enzymes are not consumed by the reactions. However if denatured they can no longer be used

What is the enzyme speed

One enzyme molecule can catalyze millions of reactions per minute

What factors can affect an enzyme

Temperature, pH and other factors can change enzyme shape and function

• Alter the ability of enzyme to bind to substrate

• Each enzyme has an optimum pH (Ex. Salivary works best at pH 7 while pepsin in the stomach works best at pH 2)

• Temperature optimum for human enzymes is usually near body temperature

Denaturation

Conformational change in protein

Disturbs protein activity

Usually irreversible

May occur due to increased temperatures

[blank] can also be caused pH changes

• Interfere with electrostatic interactions and other intramolecular bonds

• Changes in blood pH can be lethal

Nucleic Acids

DNA and RNA

• Largest molecules in the body

Contains C,H,O,N,P

Nucleotide

Building block of DNA or RNA

Composed of N-containing base, a pentose sugar, and a phosphate group

Ex. ATP, cAMP (Cyclic adenosine monophosphate)

What are polymers of nucleotides

Nucleic acids

DNA

Deoxyribonucleic acid

• Contains millions of nucleotides

• Constitutes genes

  • Instructions for synthesizing proteins

Double stranded helical molecule in the cell nucleus

Typically found in the nucleus

What are the four bases of DNA

Adenine, Guanine, Cytosine, and Thymine

A=T C=G

What are the major functions of DNA

Provides instructions for protein synthesis

Replicates before cell division, ensuring genetic continuity

RNA

Ribonucleic acid

70 to 10,000 nucleotides long

Carries out genetic instructions for synthesizing proteins

Assembles amino acids in the right order to produce proteins

Single stranded molecule mostly active outside of the nucleus

What are the three types of RNA

Messenger RNA (mRNA), Ribosomal RNA (rRNA), and Transfer RNA (tRNA)

These three varieties of RNA carry out the DNA orders for protein synthesis

What are the four bases for RNA

Adenine, Guanine, Cytosine, and Uracil

A=U C=G

Adenosine Triphosphate

[Blank] is the body’s most important energy-transfer molecule

Stores energy gained from exergonic reactions

Releases it within seconds for physiological work

Holds energy in covalent binds

• Second and third phosphate groups have high energy bonds

• Most energy transfers to and from [blank] involve adding or removing the third phosphate group

Hydrolysis of ATP is catalyzed by what

ATPases

• Breaks the third high energy phosphate bond

• Separates ATP into ADP+ P_i + Energy

Phosphorylation

Addition of free phosphate group to a molecule

Carried out by enzymes called kinases