IB HL BIO YR 1 UNIT THREE

carbon compounds

building blocks of life

four covalent bonds

can form chains and rings

variety: length, arrangement (linear, branching patterns, rings), number and locations of double and triple bonds

macromolecules

large molecules made up of monomers

crucial role in structure/function of living organisms

formed by condensation reaction

broken down into monomers through hydrolysis

carbohydrates, lipids, proteins, nucleic acids

monomers

individual subunits that can be linked together to form polymers

condensation reaction

polymerisation reaction in which two molecules join together

one loses hydroxyl group (-OH)

one loses hydrogen atom (-H)

forms water molecule

polysaccharide

more than two glucose molecules join together

long chains of monosaccharides connected with glycosidic linkages

energy storage (starch & glycogen)

structural material (cellulose & chitin)

complex carbohydrates

hydrolysis

reverse reaction for condensation

water molecules used to break covalent bonds between monomers

carbohydrates

macromolecules essential to life

organic molecules with carbons, hydrogens, & oxygens

C×n H×2n O×n

monosaccharide

fundamental biological molecules

serve as a source of energy for cells

involved in various cellular processes

single sugar unit that can't be broken down by hydrolysis

classified by number of carbon atoms and locations of the carbonyl group

triose (3 carbons), pentose (5 carbons), hexose (6 carbons)

can be linear or ring structure

glucose

hexose, C6 H12 O6

most common monosaccharide found in nature

two isomers which vary in the orientation of the hydroxyl group on the first carbon atom (alpha-glucose and beta-glucose)

soluble molecule because of polarity (like dissolves like, polar dissolves polar), makes it easily transported in blood plasma

can be oxidized to create ATP energy for cell during cellular respiration

stable, great material to build polysaccharides (starch, glycogen, cellulose)

alpha glucose

hydroxyl group on the first carbon atom oriented downwards

beta glucose

hydroxyl group on the first carbon atom oriented upwards

starch

serves as primary storage of glucose/energy in plants

two types (amylose and amylopectin)

compact structure allows for efficient storage

relatively insoluble

polymer of alpha-glucose

amylose

linear polysaccharide

made of alpha-glucose monomers

coiled structure

amylopectin

highly branched polysaccharide

alpha-glucose

complex 3d structure allows for more efficient glucose storage

major component of starch

glycogen

serves as primary glucose/energy storage in animals

branched polymer of alpha-glucose molecules

stored mainly in liver and muscle cells

mostly insoluble

cellulose

complex polysaccharide

polymer of beta-glucose, glycosidic linkages are different (humans are unable to break them down)

structural polysaccharide found in plant cell wall

straight long unbranched chains

glycoproteins

proteins that have one or more carbohydrates attached to them

sugar-protein molecule

cell signaling and communication (cell-cell recognition, receptors, logands, structural support)

receptors for chemical signals/chemical signals for other cells

provide structural support

lipids

class of macromolecule that are united because of their hydrophobic properties

non-polar

not polymers, not made of monomers

low solubility in water (hydrophobic, can’t form hydrogen bonds with water)

dissolve in non-polar solvents

very low proportion of oxygen to carbon

triglycerides

type of lipid

consumed in food (butter, lard, ghee)

synthesized by liver

formed by condensation of one glycerol molecule and three fatty acid molecules (ester bond)

effective thermal insulators in many organisms (help regulate body temperature)

wax

class of diverse lipids

generally long hydrocarbon chains

completely water insoluble

low melting point

solid at room temperature

ex: bee honeycombs, plants/animals use waxes to waterproof

steriods

type of lipid

four carbon rings fused together (three hexose rings and one pentose ring)

naturally occurring hormone

regulate physiological functions

non-polar

can pass through cell membrane

functional groups added to framework to give different properties

phospholipids

type of lipid

forms by condensation

one glycerol molecule modified with a phosphate group and two fatty acids (ester bond, formed during condensation reactions)

negatively charged phosphate interacting with water molecules

head = hydrophilic, tail = hydrophobic, amphipathic

major component of cell membranes in the form of a phospholipid bilayer

saturated fatty acids

straight linear shape

all single bonds

packed tightly together

solid at room temperature

typically from mammals

high melting point

aka “fats”

unsaturated fatty acids

single and double bonds

bends and kinks in chain which prevent packing closely together

liquid at room temperature

less viscous

lower melting points (more double bonds = lower melting point)

can be monounsaturated or polyunsaturated

monounsaturated fats

unsaturated fatty acid with one double bond

polyunsaturated fats

unsaturated fatty acid with more than one double bonds

endotherms

organisms that regulate body temperature

rely on metabolic reactions to generate heat and maintain constant internal temperature

require constant supply of energy (food)

phospholipid bilayer

major structural component of cell membrane

made of double layer of phospholipids

hydrophilic heads on either side of membrane

hydrophobic tails in the middle

covalent bond

electron pairs are shared between 2 atoms

hydrogen bond

interaction between slightly positing hydrogen and slightly negative other atom

ionic bond

electrons are completely transferred from one atom to another

organic chemistry

study of compounds that contain carbon

carbon

forms covalent bonds

has tetravalence

tetravalence

ability to form total of 4 covalent bonds

valence electrons

electrons in outermost shell

valence

number of covalent bonds an atom can form

carbon skeleton

provides framework for other atoms/functional groups to attach to

hydrocarbons

molecules that only contain carbon and hydrogen

functional groups

add different chemical properties to the molecule

metabolism

all chemical reactions in a cell

anabolic/catabolic pathways

anabolic pathways

synthesize (build up) large molecules from smaller ones

many monomers → polymer (forms bonds between monomers)

condensation reactions (dehydration synthesis)

endergonic (stores/requires energy)

catabolic pathways

break down complex molecules into simpler ones

polymer → many monomers (breaks bonds between monomers)

hydrolysis reactions

exergonic (releases energy)

monomers

small building block molecules

make up polymers

nucleic acid → nucleotide

carbohydrate → monosaccharide

protein → amino acid

polymers

large molecules consisting of the same/similar building blocks (monomers)

nucleic acid → polynucleotide

carbohydrate → polysaccharide

protein → polypeptide

simple sugars

monosaccharides and disaccharides

polusaccharides

energy storage

structural building material

electronegativity

“c

non-polar covalent bond

almost same electronegativity

electrons are evenly shared

C-H bond

polar covalent bond

different electronegativity

electrons shared unequally

higher electronegativity side is slightly negative

lower electronegativity side is slightly positive

basis of ability to form hydrogen bonds, O-H & N-H

hexose

6 carbons in ring

glucose, galactose (dairy), fructose (fruit)

pentose

5 carbons in ring

ribose

deoxyribose

disaccharide

2 monosaccharides (can be same or different) join during condensation reaction

connected by glycosidic linkages

simple sugar

sucrose

disaccharide

table sugar

glucose + fructose

lactose

disaccharide

sugar in milk

glucose + galactose

maltose

disaccharide

sugar in malt

glucose + glucose

chitin

structural polysaccharide

found in cell walls of fungi & exoskeletons of arthropods

polymer of modified glucose

ABO blood typing

determined by specific glycoproteins on surface

hydrophobic

does not interact with water

cant form hydrogen bonds with water

hydrophillic

interacts with water

can form hydrogen bonds with water

amphipathic

having both hydrophilic and hydrophobic parts

proteins

complex macromolecules

composed of 1+ chains of amino acids

made of carbon, hydrogen, oxygen, nitrogen (CHON)

do just about everything in terms of function

amino acids

monomers that are used to make proteins

20 unique ones

central carbon (alpha carbon) is covalently bonded to carboxyl group (-COOH) amino group (-NH2) hydrogen atom (-H) and a side chain (-R)

join together through a condensation reaction (when two join, one water molecule is released)

essential amino acids

amino acids that your body can't produce and you must obtain from food

necessary for proper growth, maintenance, and repair

animal proteins are best source, most easily absorbed

non-essential amino acids

can be produced by body from other amino acids or by breaking down proteins

have important functions

codons

groups of three nucleotides that specify the type of amino acid/stop signal required

makes up genetic code

64 different total codons, only 20 amino acids, causes silent mutations

silent mutations

a change in the DNA sequence that does not result in a change in the amino acid sequence

polypeptide

chain of 3+ amino acids

linked together by peptide bonds

makes up proteins

amino end = N-terminus

carboxyl end = C-terminus

ex: lysozyme, glucagon, myoglobin, alpha-neurotoxins

lysozyme

enzyme

129 amino acids

present in tears and saliva

antimicrobial

alpha-neurotoxins

group of polypeptides

60-75 amino acids

snake venom

target-disrupt nervous system

glucagon

hormone

29 amino acid residues

regulates blood sugar levels

myoglobin

type of protein

153 amino acid residues

oxygen-binding

stores/releases oxygen to muscle fibers

denaturation

process in which structure of a protein is altered, causing it to lose function

caused by change in pH or temperature

if temperature gets too high or pH gets too low (acidic) or too high (basic), the structure will unravel and change, which changes function

primary structure of proteins

specific sequence of amino acids joined together to form polypeptide chain

position of each amino acid determines 3D structure

secondary structure of proteins

refers to local folding patterns within polypeptide chain

alpha helices and beta-pleated sheets

hydrogen bonding between backbone (not side chains) causes coils and pleats

alpha helix

secondary structure of proteins

forms coils

hydrogen bond forms between amine hydrogen of one amino acid and carboxyl oxygen of another amino acid that is four residues away

beta-pleated sheets

secondary structure of proteins

pleated sheet-like structure

sections of polypeptide chain are parallel

hydrogen bonds form between adjacent strands

tertiary structure of proteins

further folding of the polypeptide

dependent on interaction between R-groups

includes hydrogen, ionic, and disulfide covalent bonds and hydrophobic interactions

stabilize structure

hydrogen bonds (tertiary structure of proteins)

holds distant regions of polypeptide chain together

stabilizes

ionic bonds (tertiary structure of proteins)

forms between oppositely charged ions

can undergo binding (positive charge) or dissociation (negative charge) of hydrogen ions

stabilize overall protein

disulfide covalent bonds (tertiary structure of proteins)

forms between pairs of cysteine amino acid residues

forms covalent bonds that maintain overall 3D shape

hydrophobic interactions (tertiary structure of proteins)

occur between non-polar amino acids

stabilize tertiary/quaternary structures

quaternary structure

arrangement and interaction of 2+ polypeptide chains

forms functional protein

non-covalent bonds and interactions

ex: hemoglobin and rubisco

hemoglobin

conjugated protein

transports oxygen and binds oxygen to lungs

has a quaternary structure (two alpha chains and two beta chains)

non-conjugated proteins

consist of only polypeptide subunits

conjugated proteins

have non-protein components (metal ions or carbs) in addition to polypeptide subunits

globular proteins

complex prooteins

usually spherical in shape with irregular folds

held together by hydrogen bonds, hydrophobic interactions and disulfide bonds

soluble in water

insulin

hormone

regulates amount of glucose in blood

produced by pancreas

hydrophilic exterior and hydrophobic interior

globular shape

fibrous proteins

simpler than globular proteins

long narrow shape

repeating structures designed for strength/stability

insoluble in water

collagen

main component of connective tissue in animals (skin, cartilage, bones)

3 polypeptide chains

triple helix structure

contain proline/hydroxyproline residues

strong and flexible

cis-unsaturated fatty acids

type of fatty acid

hydrogens attached to double-bonded carbon are on the same side

created bend

harder to pack

liquid at room temperature

typically from fish and plants

low melting point

aka “oils”

trans-unsaturated fatty acids

type of fatty acid

hydrogens attached to double-bonded carbon are on opposite sides

no bend

easier to pack

solid at room temp

produced during industrial process (hydrogenation)

functions of fats/oils

long term energy storage, energy released slowly

insulation, reduce heat loss

protection/cushioning/support of internal organs

adipose tissue

fat storage in mammals

can be broken down to provide cell with ATP energy

fats/oils in plants

used for long term energy storage

high levels in seeds to provide seeding with energy until photosynthesis

cholesterol

steroid

found in animal cell membranes

reduces permeability of cell membrane by reducing fluidity at high temps

increases permeability of cell membrane by increasing fluidity at lower temps

modified into other steriods

steroid hormones

class of hydrophobic hormone molecules that control wide range of physiological functions

hydrophobic so can easily pass through cell membrane to give instructions

ex: estrogen and testosterone

catalyst

substance that increases rate of (speeds up) chemical reactions

is not changed or used up in the reaction

enzymes

biological catalysts

speed up metabolic reactions in all living organisms

different enzymes required by different organisms

complex globular proteins

catalyze metabolic reactions by binding to a substrate(s)

lower activation energy, allows reaction to happen faster

most reactions in living organisms would not occur without enzymes

active site

where catabolic reactions occur

where the substrate minds

order of amino acids in polypeptide chain determines 3D structure

protein folding ensures overall 3D structure is correct

side chain

aka r-group

20 different side chains

gives amino acid properties

hydrophobic