AP Biology Unit 1 - Chemistry of Life

What is a covalent bond?

The bond type in which atoms share electrons (eg. water)

How is water polar?

The covalent bond between hydrogen in oxygen results in an unequal sharing of electrons between the two molecules. This is because oxygen is more electronegative.

What type of bonding can result in polarity?

covalent bonding

What does it mean to be polar? (What is polarity?)

There is a difference in the electronegativity of the atoms that are bonded

Hydrogen Bond

• weak

• between the negative and positive regions of two separate molecules

• only occurs between polar molecules

Cohesion

two of the same molecules form a hydrogen bond (eg. two water molecules)

Adhesion

two different molecules forming a hydrogen bond

What can hydrogen bonds result in?

surface tension

Surface tension (Why is it important?)

• increased hydrogen bonds between water molecules

• ONLY at the surface

• eg. water droplet on a penny

• plants need to float on leaves

Water Solvency (Why is it important?)

• water has very high solvency as liquid

• it allows living things to absorb nutrients through water

Ice Floating (Why is it important?)

• water is less dense as a solid than as a liquid

• this is not normal

• fish can survive in frozen over lakes

Water’s Heat Capacity (Why is it important?)

• can absorb a lot of thermal energy before becoming steam

• aquatic animals require this to maintain body temperature

Capillary Actions (Why is it important?)

• adhesive and cohesive properties allow water to climb upwards by attaching to itself

• plants take water from the ground through its roots

Law of Conservation of Energy

• energy can only be transformed

Where is the energy mainly used by living systems stored?

chemical bonds

What are atoms and molecules from the environment necessary for in living systems?

• exchange of matter

• building new molecules

• (eg. carbs, proteins, lipids, nucleic acids)

Which element is used to make all macromolecules?

carbon

What is carbon’s unique bonding ability? What does it help do?

• It can bond to other carbon to create “carbon skeletons”

• Very large and complex molecules

• Used to store energy

• Form basic cell strucutes

Monomers

• chemical sub-unit for polymers

• makes up macro-molecules 

Polymer

macromolecule of monomers

What type of bond connects monomers to each other?

covalent bond

Carbohydrate Monomer

• Monosaccharide

• Carbohydrates are the POLYMER

Protein Monomer

• amino acid

• proteins are the POLYMER

Nucleic Acid Monomer

• nucleotide

• nucleic acids are the POLYMER

Lipid Monomer

• fatty acids (kind of)

• no true monomer

• 1 glycerol + 3 fatty acid chains

Dehydration Synthesis Reaction (What bond is formed? Byproduct?)

• a water molecule is removed from the atoms to combine them

• H from one and OH from the other

• covalent bond is formed

• a water molecule is the byproduct

Hydrolysis Reaction (Opposite of Dehydration Synthesis)

• breaks down polymers 

• covalent bonds are broken

• a water molecule is added back into the monomers

• H is added to one original monomer and OH is added to the other

• eg. digestion

What are dehydration synthesis and hydrolysis used to form/transform?

macromolecules

What factor determines the structure and function of carbohydrates?

• directionality of sub-components 

• eg. (OH on the bottom and H on the top vs. the other way) 

• the type of monomer

What are the different shapes that carbs can be?

• branched and linear 

What is the structure and function of starch and glycogen?

• branched

• energy storage

• (starch can sometimes be linear)

What is the structure and function of cellulose?

• linear

• plant cell wall structure

Monosaccharides

• Glucose

• Frucstose

• Galactose

Disaccharides

• Sucrose

• Lactose

• Maltose

Polysaccharides

• Starch (Amlopectic and Amylose)

• Glycogen

• Cellulose

• Chitin

What are carbohydrates comprised of?

linear chains of sugar molecules connected by covalent bonds

What types of bonds link carbohydrates?

covalent bonds

What are the characteristics of a lipid?

• nonpolar

• hydrophobic

Which lipids contain fatty acids?

triglycerides and phospholipids

What are the two types of fatty acids? What defines them?

• saturated - only single bonds between their carbon acids

• unsaturated - at least one double bond between their carbon atoms

How do double bonds affect a lipids structure an function?

• unsaturated

• kink in the carbon chain

• more kinks = more unsaturated 

• more liquid at room temperature

What are the types of lipids?

• Phospholipids

• Steroids

• Triglycerides (Fats)

What are the uses of fats?

• provide energy storage

• support cell function (heat insulation)

Steroids

• hormones that support physiological functions 

• eg. growth, development, metabolism, homeostasis 

Cholesterol

• common steroid found in cell membranes 

• animal cell membranes 

• maintains structural stability (maintain fluidity) 

Phospholipids

• form cell and plasma membranes

• Hydrophilic head (outside of membrane)

• Hydrophobic tail (inside of membrane)

Similarities between DNA and RNA

• 5-carbon sugar

• phosphate group

• nitrogenous base

• sugar-phosphate backbone

• Connect on the 5 prime end and 3 prime end

DNA (Deoxyribonucleic Acid)

• Deoxyribose (sugar without oxygen)

• Cytosine, Guanine, Adenine, Thymine

• Double-stranded (strands are anti-parallel)

RNA (Ribonucleic Acid)

• Ribose (sugar)

• Cytosine, Guanine, Adenine, Uracil

• Single-stranded

What does it mean that DNA strands are anti-parallel?

• one strand has 5 prime at top and 3 prime on bottom

• the second strand has 3 prime on top and 5 prime on bottom

How is the linear sequence of all nucleic acids characterized?

• 3’ hydroxyl 

• 5’ phosphate

of the sugar in the nucleotide

What type of bonds hold together the nitrogen base pairs?

hydrogen bonds

How many hydrogen bonds are in the A - T pair? the G - C pair?

• A - T has two bonds

• G - C has three bonds (stronger and better for stable structure) 

Which is the only “prime” end that nucleotides can be added to each other on?

3’ end (covalent bond)

What is the are two terminus (ends) of an amino acid?

• amino terminus (NH₂) on left

• carboxyl terminus (COOH) on right

Which terminus are new amino acids added to to form a peptide bond?

• carboxyl group

• amino group of new amino acid attaches to carboxyl group

Peptide Bonds

• covalent bond

• between carboxyl and amino group in amino acids

Primary Protein Structure

• determined by sequence of amino acids

• peptide bonds (covalent bonds)

• not yet functional

Secondary Protein Structure

• folding of the amino acid chain in primary structure

• alpha-helix

• beta-sheets

• not yet functional

Tertiary Protein Structure

• 3D shape of protein 

• one chain wrapped around to make a 3D shape

• many are functional at this level

Quaternary Protein Structure

• many tertiary chains wrapped together to make 3D shape

• needed for some proteins

• eg. hemoglobin in red blood cells 

Receptor Protein

• receives chemical signals

• signal molecule must have a similar structure 

How does change in an amino subunit (such as change in polarity) affect the structure and function of a protein?

• change at the primary level

• changes structure and function of protein

What are amino acids composed of?

• central carbon with hydrogen attached

• amino group

• carboxyl group

• varying R group (hydrophobic/non-polar, ions, disulfide bridges, polar/hydrophillic)

Through what method are peptide bonds formed?

• dehydration synthesis (covalent bond)

What type of bonds are in secondary protein structure?

• hydrogen bonds (oxygen and hydrogen)

• twisting around backbone = alpha helix

• folding back and forth = beta sheet

What type of bonds are in tertiary and quaternary protein structure?

• interactions between the different R-groups

• hydrogen bonds

• hydrophobic interactions

• ionic interactions

• disulfide bridges

What levels of a protein structure determine the function?

all of them!

Chemical Makeup of Carbohydrates

• carbon

• hydrogen 

• oxygen

• 1:2:1 CHO ratio 

Chemical Makeup of Lipids

always

• carbon

• hydrogen

• oxygen

sometimes

• phosphorous (phospholipids) 

• nitrogen

• sulfur

(CHOP “ns”)

Chemical Makeup of Proteins

• carbon

• hydrogen

• oxygen

• nitrogen

sometimes

• sulfur

• phosphorous (less common) 

(CHON “ps”)

Chemical Makeup of Nucleic Acids

• carbon

• hydrogen

• oxygen

• nitrogen

• phosphorous

(CHONP) 

What are purines?

• adenine 

• guanine

• double-ring structure

What are pyrimidines?

• cytosine

• thymine

• uracil

• singe-ring structure

What is the function of carbohydrates?

• main fuel source for cells and organisms

• quick energy (glucose)

• energy storage (starch and glycogen)

• structural support (cellulose and chitin)

What are the functions of lipids?

• energy storage (triglycerides)

• cell membrane structure (phospholipids)

• hormones and signaling (steroids) 

What are the functions of nucleic acids?

• storing genetic material

• building protein

What are the different types of RNA and what are their functions?

• mRNA - carry genetic info from nucleus → ribosomes

• rRNA - in ribosomes

• tRNA - brings amino acids to ribosome for protein construction

What are the functions of protein?

• catalysis

• structure

• transport

• signalling

• defense

• movement