2.2-Biological Molecules (copy)

what groups can biological molecules be placed in?

• carbohydrates
• protein
• lipids
• nucleic acids
• (water)

what are carbohydrates used for?

• slow releasing energy
• structure (plants)

what are proteins used for?

• growth and repair
• enzymes
• hormones
• structure
• antibodies

what are lipids used for?

• insulation
• energy
• hormones
• protection
• nerve cells

what are nucleic acids used for?

• genetic information

  \

what is water used for?

• support
• solvent
• transport

how many covalent bonds does carbon form?

4

how many covalent bonds does nitrogen form

3

how many covalent bonds does oxygen form

2

how many covalent bonds does hydrogen form

1

hydroxyl group

-OH

carboxyl group

-COOH

amine group

-NH₂

variable group

-R

Types of bond formed between biological molecules

• Covalent bonds- electrons shared

• Ionic bonds- electrons transferred

• Hydrogen bonds- unequal sharing of electrons= molecules are polar, bonds are weak but provide strength together

what is a monomer

a single molecule

what is a polymer

lots of monomers joined together

condensation reactions vs hydrolysis

• Hydrolysis

  • H₂O used

  • covalent bonds broken down

  • molecules get smaller

• Condensation reaction

  • H₂O molecules released

  • new covalent bond formed

  • makes bigger molecules

Hydrogen bonding in water

• 1 oxygen atom is covalently bonded to 2 hydrogen atoms

• sharing of electrons between hydrogen and oxygen is uneven as oxygen has more protons

  • oxygen- weak negatively charged region

  • hydrogen- weak positively charged region

• polarity causes hydrogen bonds to form between positive and negative regions of adjacent water molecules

properties of water

• liquid

• density

• solvent

• cohesion and surface tension

• high specific heat capacity

• high latent heat of vaporisation

• (reactant)

why is water a liquid

• hydrogen bonds= difficult for water molecules to escape and turn into a gas

• very polar, so liquid

• low viscosity despite hydrogen bonds

how is waters liquidity useful in biology

• provides a habitat e.g. rivers, lakes

• form major components of tissues in organisms

• reaction medium for chemical reactions

• effective transport medium e.g. blood

density in water

• normally density increases as liquid cools

• water’s density increases until 4°C

• between 4°C and freezing point, the molecules align themselves in a structure less dense than liquid water due to water’s polarity

how is water’s density useful

• provides a stable environment for aquatic organisms to live through winter

• ponds and other bodies of water insulated against extreme cold

  • layer of ice reduce rate of heat loss from rest of pond.

water as a solvent

• polarity of water means that oppositely charged ions are attracted

• water molecules gather around charged areas and separate them

  • particles dissolve and form a solution

• molecules and ions can move around and react

how are water’s solvent properties useful

• allows chemical reactions to take place in cells- dissolved solutes are more chemically reactive when they are free to move around

• metabolites can be transported efficiently

cohesion and surface tension in water

• cohesion →hydrogen bonds between water molecules pull them together → doesn’t spread out

• water molecules on the surface are hydrogen bonded to the ones below them

  • more attracted to water molecules than air above them→ molecules pulled inwards so more resistance on surface=surface tension

uses of water’s cohesion and surface tension

• columns of water in plant vascular tissue are pulled up the xylem tissue together from roots

• insects e.g. pond skaters can walk on water

water’s high specific heat capacity

• hydrogen bonds= lots of heat energy required to increase E_k and temp of water → high shc

• doesn’t heat up/cool down quickly

uses of water’s high shc

• living things require stable temperatures for enzyme controlled reactions to happen properly

• aquatic life needs stable environment in which to live

high latent heat of vapourisation

• molecules break away from each other to become a gas when water evaporates

• large amount of energy needed for water molecules to evaporate

uses of water’s high latent heat of vapourisation

helps cool things down and keep temp stable

uses of carbohydrates

• energy store

• provide energy

• structural units

• form larger molecules

general formula for carbohydrates

C_n(H₂O)_n

simple carbohydrate (subsections and examples)

• sugars-small, sweet tasting, soluble

1. Monosaccharides→ glucose, fructose, galactose

2. Disaccharides→ sucrose, maltose, lactose

polysaccharides and examples

• large, non-sweet, insoluble

• e.g. starch, glycogen, cellulose

how are monosaccharides grouped (+general group names)

• grouped by number of carbon atoms:

  • 3→ triose

  • 5→ pentose

  • 6→ hexose

alpha (α) glucose

-OH group below

beta (β) glucose

-OH group above

other hexose sugars

• fructose- sweeter than glucose, main sugar found in fruit and nectar, very soluble

• galactose- not as soluble as glucose, has important role in production of glycoprotein and glycolipids

ribose

-OH attached to carbon 2

deoxyribose

-no OH attached to carbon 2

what is a reducing sugar

• can donate electrons (oxidises carbonyl group)

• detected using Benedict’s test

  • reduces copper sulfate into copper oxide

what is a non-reducing sugar

• cannot donate electrons

  • must be hydrolysed to break disaccharide into 2 monosaccharides

what is a disaccharide

formed from 2 monosaccharides joined together by a glycosidic bond during a condensation reaction

what monosaccharides make maltose

α-glucose+α-glucose

what monosaccharides make sucrose

α-glucose+fructose

what monosaccharides makes lactose

α-glucose+galactose

making disaccharides (e.g. maltose)

C₆H₁₂O₆+C₆H₁₂O₆ → C₁₂ H₂₂ O₁₁ +H₂O

homopolysaccharide

polymer made of identical sugar molecules

heteropolysaccharide

polymer made of more than one type of monosaccharide

what is glucose stored as

• glycogen

• amylose

• amylopectin

what monomer forms glycogen and starch

alpha glucose

structure of amylose

• unbranched

• 1,4 glycosidic bonds

• coils into helix- stabilised by hydrogen bonds

how does the structure of amylose link to its function

• helix → compact

• polysaccharide= large molecule→ cannot leave cell

• large molecule= insoluble→ doesn’t affect water potential

structure of amylopectin

• branched

• 1,4 glycosidic bonds

• 1,6 glycosidic bonds

• coils into helix- held together by hydrogen bonds

how does the structure of amylopectin relate to its function

• helix → compact

• polysaccharide= large molecule→ cannot leave cell

• large molecule= insoluble→ doesn’t affect water potential

• branches → easily hydrolysed by enzymes to release glucose

structure of glycogen

• branched

• 1,4 glycosidic bonds

• 1,6 glycosidic bonds

• coils into helix- held together by hydrogen bonds

how does the structure of glycogen link to its function

• helix → compact

• polysaccharide= large molecule→ cannot leave cell

• large molecule= insoluble→ doesn’t affect water potential

• more branches:

  • more compact

  • more ends=easier to remove monomer units (needed as humans have higher metabolic demand)

structure of cellulose

• β-glucose molecules bonded together by 1,4 glycosidic bonds

• each alternate β-glucose is flipped 180° so it can bond to the adjacent molecule

• makes long chains that are unbranched and straight

• run parallel with hydrogen bonds (due to many OH groups) between the chains

how is the cell wall formed from cellulose

• 60-70 cellulose molecules become crosslinked by hydrogen bonds- form microfibrils

• around 400 microfibrils are bonded together by H-bonds to form macrofibrils:

  • have high tensile strength-reduces bursting- embedded in polysaccharide glue (pectin) to form cell walls

  • macrofibrils run in all directions to increase strength

features of the cell wall

• very strong- thousands of chains linked together

• fully permeable- allow movement of water and substances to and from membrane due to space between fibrous chains

triglycerides

• made up of C, H, O

• non polar- insoluble in water, so doesn’t affect water potential

• soluble in alchohols

structure of triglycerides

• 3 fatty acid chains ester bonded to a glycerol molecule

• formed in condensation reactions

types of triglycerides

• saturated- no C=C double bonds

  • fully saturated with hydrogen

  • stack neatly into layer so are solid

• monounsaturated- 1 C=C double bond

  • liquid-chains pushed further apart by C=C double bond

  • form oils

• polyunsaturated- many C=C double bonds

  • liquid- forms oils

roles of lipids

• Cell membranes- cell membrane formed of phospholipid bilayer

• energy source:

  • triglycerides broken down in respiration to release energy and make ATP

    • ester bonds hydrolysed, then glycerol and broken down into carbon dioxide and water

    • makes more water than respiration of a sugar

• waterproofing:

  • waxes are a type of lipid

  • fatty acids and alcohols larger than glycerol

• insulation:

  • adipose tissue is a storage location for lipids, slow conductors of heat

  • lipids in nerve cells act as electrical insulators

• buoyancy:

  • fat is less dense than water, so it floats

• protection:

  • fat around organs absorbs shock

  • bacteria have peptidoglycan around cells

phospholipids

• polar molecules

• amphipathic- has both hydrophobic and hydrophilic regions

structure of phospholipids

• have 2 fatty acids and a phosphate group

• phosphate head is a hydrophilic head:

  • polar-attracted to water

  • not attracted to fat-orientates towards aqueous solutions

• fatty acids are hydrophobic tail:

  • non-polar→orients away from water

  • mixes with fat- orientates away from aqueous solution

phospholipid bilayer

• plasma membrane separates 2 aqueous environments

• individual phospholipids can move within their layer, but won’t expose hydrophobic tails to water→ provides stability

• selectively permeable → only small non-polar molecules move through

phospholipids in water

• arranged in layer on water with heads in water and tails sticking out

  OR

• form micelles-rings/circles

Glycolipids

• the structure of phospholipids allows them to form glycolipids by combining with carbohydrates within cell surface membrane

• Important for cell recognition

cholesterol

• completely hydrophobic

• made of 4 carbon rings

• made in liver

function of cholesterol

• form steroid hormones e.g. testosterone, oestrogen

• pass directly through lipid bilayer → go to nucleus

• sits between phospholipid hydrocarbon chain

  • strengthens cell membrane and regulates fluidity

lipids in plants

• produce a derivative of cholesterol found in membranes-stigmasterol

• some plant steroids can be converted to animal hormones

roles of proteins

• enzymes

• hormones and receptors

• growth and repair

• structural

• antibodies

amino acids structure

where do amino acids come from

• 20 naturally occurring amino acids

• plants make amino acids using nitrates and products of photosynthesis

• animals can make some amino acids but need to ingest others

  • ingested→ essential amino acids

joining amino acids

condensation reaction

levels of protein structure

• primary

• secondary

• tertiary

• quaternary

primary structure of proteins

• the sequence of amino acids in polypeptides of a protein

• less than 50 amino acids= peptides, more than 50= polypeptides/proteins

• coded from DNA

• consists of peptide bonds between amino acids

secondary structure of proteins

• the way in which proteins are coiled

• hydrogen bonds present due to δ+NH group and δ- -C=O group

tertiary structure of proteins

• describes 3D shape of proteins- can be:

  • fibrous

  • globular

• formed due to bonds between R groups of amino acids- bend polypeptide chains

• determines function of protein

• ionic or disulphide bonds present

Quaternary structure of proteins

• proteins may consist of two or more polypeptides

• e.g. haemoglobin, antibodies

hydrophobic interactions of proteins

• non-polar R groups cluster together in water

  • weak associations = hydrophobic interactions

• when polypeptide chain folds, hydrophobic R-groups tend to be close to each other in interior of folded chain, whereas hydrophilic R-groups tend to be on outside, attracted to water

denaturing proteins

• denaturing→ bonds maintaining protein are broken

  • protein stops functioning properly

    • fibrous- lose structural strength

    • globular- insoluble and inactive

• happens if temp is above optimum or if pH is not optimum

properties of fibrous proteins

• formed of regular and repetitive amino acid sequences- form parallel polypeptide chains held together by crosslinks

• long, rope-like fibres

• high tensile strength

• flexible

• insoluble in water (non polar hydrophobic R groups face outwards)

functions of fibrous proteins

• structure e.g. collagen

• protection e.g. keratin

• elasticity e.g. elastin

• contraction/ mechanical movement e.g. actin and myosin

properties of globular proteins

• spherical shape- tightly folded polypeptide chains

• specific tertiary structure

• chains folded so hydrophilic R group faces outwards→ soluble

• temperature and pH sensitive

functions of globular proteins

• transport proteins e.g. carrier proteins

• transport substances e.g. haemoglobin

• enzymes e.g. pepsin

• hormones e.g. insulin

• antibodies- destroy pathogens through agglutination

prosthetic groups and examples

• a non protein component that forms a permanent part of the functioning protein molecule

• e.g. iron in Haem, Zn ion in carbonic anhydrase

conjugate protein and examples

• a protein containing a prosthetic group

• e.g. haemoglobin carbonic anhydrase

haemoglobin

• oxygen carrying pigment found in erythrocytes

• 4 polypeptide chains in quaternary structure-globins- each has prosthetic haem group:

  • α-globin

  • β-globin

• four globin subunits held together by disulphide bonds

• prosthetic haem group contains Fe²⁺ ion- can reversibly combine with oxygen to form oxyhaemoglobin

• each haemoglobin can carry 4 oxygen molecules, so 8 oxygen atoms

insulin

• 2 polypeptides

• both chains fold into tertiary structure- joined by disulphide links

• hydrophilic R groups face on outside- soluble

• increase glucose uptake into cells

pepsin

• digests protein in stomach

• single polypeptide

• few basic R groups, many acidic R groups- more stable in acidic environment- few basic groups to accept H⁺ ions- little effect on structure.

keratin

• rich in cysteine- many disulphide bridges and hydrogen bonds- strong molecule

• found in nails, hair, skin, claws etc

• provides mechanical strength

• impermeable and waterproof barrier- prevents infection and waterborne pollutants

elastin

• found where stretch is important e.g. skin, alveoli, blood vessels, lungs, bladder

• stretch and recoil due to crosslinks and coils

collagen

• provides mechanical strength:

  • arterial walls

  • tendons connect muscles to bones

  • cartilage and connective tissue

  • bones made of collagen reinforced with calcium phosphate

• 3 chains- H bonds between chains

• forms crosslinks with other collagen molecules to form collagen fibrils

  • lots of fibrils=collagen fibre

cations (5)

• Ca²⁺

• Na⁺

• K⁺

• H⁺

• ^NH₄+

Anions (5)

• NO₃^-

• HCO₃^-

• Cl^-

• PO₄^3-

• OH^-

Calcium ions

• increases rigidity of bones, teeth and cartilage

• component of crustacean exoskeleton

• enzyme activator

• stimulates muscle contraction and regulates nerve transmission

• regulates cell membrane permeability

• important for cell wall development in plants