IB BIO Unit 2 - Molecular Biology

includes translation, transcription and DNA replication from unit 7

Dehydration Synthesis

Water molecule H20 is removed and is a product in the reaction

Hydrolysis Reactions

Water molecule H20 is a reactant in the reaction

What are the four most common biological elements

carbon, oxygen, nitrogen and hydrogen!

What are the five trace elements required by living things

iron, sodium, potassium, magnesium and phosphorus

4 macromolecules of life

1.carbohydrates
2. lipids
3. proteins
4. nucleic acids

monomer is the _________ ________

building block

polymer is made up of the _________ units

monomer

2 types of metabolism

catabolism
anabolism

catabolism

* create or require energy
* provide example

the break down of a large molecule into smaller molecules (creating energy)

eg. hydrolysis reaction

anabolism

* energy requirements
* provide example

the reaction of small molecules forming a large molecule (requires energy)

eg. dehydration synthesis

ends in "ase" means

enzyme

ends in "ose" means

sugar

enzyme

type of protein that speeds up chemical reactions by lowering activation energy

activation energy

amount of energy which is needed in order to undergo a specific reaction

carbon advantage

- ability to form large and complect molecules via covalent bonding
- can form 4 bonds
- stable molecule

(Di)polarity in relation to water

H20 has different charges at each "end" because oxygen is more attractive to electrons than hydrogen

intramolecular forces

within molecule
eg. polar-covalent bonding

intermolecular forces

short lived ("ephemeral") attractions
outside molecule
eg. hydrogen bonds

What does the bipolarity of water allow it to do

has the ability to dissolve substances that contain charged particles (IONS) or electronegative atoms (polarity)
- depends on the # of water molecules

organic molecule

contain carbon; and are often found in living things

4 exceptions to organic molecules

- carbides (CaC2)
- Carbonates
- oxides of carbon (CO, CO2)
- cyanides

Aqueous solution

containing H2O
- where most biochemistry occurs!!

body is made up of ____ water

70%

some eg.
- lymph nodes = 94%
- joints = 83%

explain "like dissolves like"

polar, ionic compounds soluble in polar, ionic solutions

non-polar compounds soluble in non-polar solutions

cohesion

when molecule of the same type are attracted together
eg. H-bonds between water molecules
- droplets
- surface tension (some bugs walk on water)
- how able to move as a 'column' in the vascualr tissue of plants

adhesion

2 unlike molecules are attracted together
eg. eg H-bonds
- H2O + cellulose
- in vascular tissues in plants (pull the cohesioning water allong the H-bonds on the sides)

specific heat capacity

amount of heat required to change states

water has a _____ specific heat capacity
...meaning H2O is

HIGH!

excellent temperature moderator

Explain specific heat capacity and hydrogen bonds

h-bonds need to be broken in order for water to change shape
- requires the absorption of energy

this is why sweating = cooling
- when evaporates takes heat absorbed w it

Why are methane and water comparable

similar size + weight
both single covalent molecules

differences between methane and water

water = polar
methane = non-polar

therefore many changes with temp
- lower heat capacity
- less energy taken w evaporation
- range of freezing to evaporation much smaller - sensitive

what is a reducing agent

donates electrons during certain types of reactions

what does "carbs are metabolized through" mean

dehydration/condensation reactions are required to release the energy they hold

what is the monomer unit for a carbohydrate

monosaccharides

what is the monosaccharide ratio

1:2:1 carbon, hydrogen, oxygen

common examples of monosaccharides and their chemistry

triose C3H6O3
pentose C5H10O5
- ribose!
hexose C6H12O6
- glucose + fructose + galactose

Disaccharide

formed from two monosaccharides through dehydration/condensation reactions

Disaccharide examples (hexoses) - glucose + galactose

LACTOSE
both hexoses
through dehydration synthesis, lactose = C12 H22 O11

Disaccharide examples (hexoses) - glucose + glucose

maltose

Disaccharide examples (hexoses) - glucose + fructose

sucrose

Polysaccharides

formed by 2+ disaccharides via glycocidic bonds

what are the four types of polysaccharides

Starch
- amylose
- amylopectin

glycogen

cellulose

explain structure + function of amylose

- 1,4 bonds
- straight line
- easily metabolized through
- the enzymes don't need to adjust , continue to metabolize through in straight line
- short term energy source

explain structure + function of amylopectin

- 1,4 w some 1,6 bonds
- causes branching
- slightly longer sources of energy
- when eaten makes you feel more full (space it takes up compared to amylose)
- enzyme has to slightly adjust around the sugars
- takes longer to catabolize through

explain structure + function of glycogen

- 1,4 w more 1,6 bonds
- causes extreme branching
- longer source of energy
- enzyme has to adjust more frequently to catabolize the polysaccharide
- used by mammals to store glucose in insoluble state in liver + muscles

where is starch used in nature

- plants to store glucose in an insoluble form so as not to disrupt the osmotic balance of the plant

fatty acids are the _____ ______ for lipids

building blocks

structure of a fatty acid

- carboxyl group one end (-COOH)
- methane group other end (-CH3)
- variable length of hydrocarbons in the middle , usually between 11-23 carbons long

types of fatty acids

SATURATED

UNSATURATED
monounsaturated
polyunsaturated
- cis
- trans

LDL

Low density lipoproteins

* carry cholesterol/dietary fats from liver to rest of body BAD
* get caught in arteries = bc less dense, don’t travel compactly

HDL

High density lipoproteins

* carry cholesterol from around body back to liver to be disposed of
GOOD
* compacted, easy travel, don’t clog

Saturated FAs

- saturated because they carry as many hydrogen atoms as possible
- single covalent bonds between Carbons
- straight/LINEAR in structure

Increase LDL levels = decreased HDL therefore Increase cholesterol levels BAD

found in - tend to be solid at room temp
- dairies fats
- animal fats

where are saturated FAs found in

- dairy fats
- animal fats
(not good for cholesterol levels)

Unsaturated

- missing one or more H's
- at least one double bond between C's
- CAN result in a bend

monounsaturated

one double bond between carbons

polyunsaturated

multiple double bonds between carbons

2 polyunsaturated types of fatty acids

Cis
Trans

Cis unsaturated fats

* hydrogens are bonded to carbons on the SAME SIDE of double bond
* results in a bend

Increases HDL levels = decreases LDL levels / cholesterol levels

found in - tend to be liquid at room temp

* veggies oils
* fish
* leafy greens
* nuts

Trans fats

* hydrogens atoms are bonded to carbons on opposite sides of the double bond
* the Hs don't repel so the fatty acid chain is LINEAR
* INDUSTRY MADE through partial hydrogenation

increases LDL levels = decreases HLD therefore increases Cholesterol levels

found in - solid at room temp

* fast foods
* processed foods

Hydrogenation

adding hydrogens (saturating the hydrocarbon chain) or switching the side their on (trans isomer)

3 main types of lipids

1. Triglycerides
2. phospholipids
3. steroids

Triglycerides structure + function

- formed via condensation reactions
3 fatty acids + 1 glycerol
- functions as long term energy source
- fats + oils are triglycerides (largest class of lipid)
- their health benefits depend on the types of fatty acids

phospholipids

2 fatty acids + 1 glycerol + phosphorus group
- found in mostly in membranes
- structural

steroids

- all have similar structure of four fused rings
eg. testosterone, estrogen, CHOLESTEROL, progesterone

what is a gene

one gene is the code for one protein synthesis

what is a polypeptide?

a long chain of amino acids
makes up proteins

what is DNA

a series of genes that code for making different protiens that execute different functions in the cell

how many active genes to humans have

20 000-25 000 active genes

why do different organisms have a different number of active genes

the more adaptable an organism is, the more genes it will have

Genome

the entire set of DNA instructions that are unique to each human therefore we all synthesis different types and amounts of proteins

Proteome

the entire set of proteins expressed by an organism at a certain time

Rubisco

- enzyme that catalyzes first reaction of photosynthesis

insulin

* hormone, made by pancreas, allows sugar to enter cell (reducing blood plasma sugar)
* Globular protein

immunoglobin

\-antibody, recognizes antigens during immune response

* globular protein

Rhodopsin

pigment in retina, useful for low light

haemoglobin

in your red blood cells that carries oxygen to your body's organs and tissues and transports carbon dioxide from your organs and tissues back to your lungs

* globular protein

collagen

structural part of connective tissue

most abundant protein in the body

* fibrous protein

spider silk protein

structural component of webs

what are the 2 classes of protein

fibrous
globular

fibrous protein

- long, narrow strands
- structural role
- repetitive amino acid sequence meaning the same reactions are occurring over and over again = shape is long chain
- less sensitive to changes (temp, ph)
- generally insoluble in water

eg. collagen

"they ARE something"

globular protein

- generally more compact and rounded
- functional role
- irregular amino acid sequence meaning different reactions occurring = shape is globular ball constant bends
- more sensitive to changes (temp, ph)

eg. enzymes, hemoglobin, immunoglobin

"They DO something"

Structure of amino acid (1 peptide)

He - Never - Could - Chant - OH

Dipeptide

2 amino acids bonded together via dehydration synthesis reaction

Formation of Proteins - primary structure

- long chains of amino acids held together by peptide bonds = polypeptide
- the sequence of amino acids is determined by the gene

hoe many R groups are there

20 - one for each amino acid
- what makes them unique

Secondary Structure

interactions between the R groups
- forming H bonds

1. beta plated sheet
2. alpha helix

the sequence of amino acids determines structure

Tertiary structure

covalent, ionic, disulphide bridges, h-bonds between R groups

- twists and form specific shape to the molecule

FIBEROUS stop synthesizing at this point
a.a sequences needs to be correct, structure dictates function

Enzymes

- globular proteins
- biological catalysis (facilitate metabolic reaction)
- lowers activation energy
- can be used many times because it doesn't chemically change in the reaction

substrate

reactant molecule(s) for the reaction

active site

area of enzyme w specific shape due to careful folds of globular protein
where reaction occurs

enzyme substrate complex

describes the interaction of the enzyme and substrate while reaction happens

how to substrates and enzymes bind successfully

successful collision

-both substrates and enzymes(if not immobilized)(slower) move freely

this allows the binding to take place

what are the 2 hypothesis on enzyme/substrate binding

1) Lock and Key - fit perfectly each enzyme only works with ONE substrate

2) induced fit (approved)
- both enzyme and substrate change shape due to the attractive forces between them
- better explanation bc although enzymes are specific to their substrate, some can facilitate more than one type of reaction

Factors that affect enzyme activity

- temp
- ph
- substrate conc.

how does temp affect enzyme activity

- most are most effective at 37C
- increase in rate of speed = stronger attractive forces w enzymes
- increased collision rate
- too much heat = denaturation

how does ph level affect enzyme activity

- most are most effective at neutral (7)
- donates H+ or OH- affecting attractions of R groups = denaturation

how does substrate concentration affect enzyme activity

platos bc too many substrates for enzymes

Denaturation of enzymes and proteins

ENZYMES
- globular therefore tertiary structures involved
- tertiary maintained by bonds - the factors affecting those bonds changes shape
- when active site changes = wont attract substrate = functionless protein

- structure dictates function
- Hbonds, covalent, ionic bonds
- when bonds change via temp or ph the structure changes = function changes

enzymes in industry

food
paper
medicine
textiles
brewing

EXAMPLE =
lactose

what does immobilized enzyme mean explain in terms of LACTOSE INTOLERANCE

alginate beads
- confining the enzyme molecule to a solid support over which a substance is passed and converted into products

LACTOSE INTOLERANCE
- inefficient lactase(enzyme) in body = gas

make lactose free milk
- Lactase is purified from yeast or bacteria
and then bound to an inert substance
(such as alginate beads)

Milk is then repeatedly passed over this
immobilised enzyme, becoming
lactose-free