2.1.2- Biological Molecules

2.1.2- Biological Molecules

what is the structure of a water molecule

two hydrogen atoms covalently bonded to an oxygen atom

why is water polar

• oxygen has a small negative charge because it has more protons in the nucleus so electrons are more attracted to it; electronegative/ delta neg

• hydrogen has a small positive charge for the opposite reason; electropositive/delta pos

• so has small charges which makes it polar

what is a hydrogen bond

weak interaction between partially negative and partially positive atoms

why are H bonds able to form in water

• water is a polar molecule

• has delta pos H and delta neg O; slightly charged

• these charges attract to one another meaning water has hydrogen bonds

5 properties of water

• high SHC

• high SLH

• ice floats on water; density

• good solvent

• cohesion and adhesion

why does water have a high SHC and why is this good

• lots of H bonds to be broken which requires a lot of energy and so large amount of energy required to change temperature of water

• means can be a stable habitat

• also means stable temperature as a transport medium in animals and plants

why does water have a high SLH and why is this good

• lots of H bonds to break which requires a lot of energy, so lots of energy needed to change state of water

• good as it means we can sweat and cool without losing lots of water

• blood won’t freeze or evaporate, making it a good transport medium

why can ice float on water and why is this good

• H bonds are stable in ice but break and reform in liquid; means that the structure in ice is further apart and so less dense than water and floats

• creates an insulating layer which stops the whole body of water from freezing, making it a stable and good habitat

what is cohesion

• the attraction of water molecules to one another; stick together

what is adhesion

the attraction of water molecules to other polar molecules e.g. carbohydrates

why is cohesion and adhesion of water good

• cohesion creates tension between water molecules and causes capillary action (where water moves up a tube against gravity)

  • makes it a good transport medium in plants and animals

• adhesion also helps with this as it means that it sticks to the walls of the tube and helps to pull it up

• also creates surface tension of water for things like pondskaters; makes the surface of water a habitat too

why is water a good solvent and why is this a good thing

• other polar molecules are able to dissolve in it as its polar

• means it can be a transport medium and transport these substances around the body

elements in carbohydrates

C, H, O

what as monosaccharide

monomer of carbohydrates

monosaccharides

• alpha glucose

• beta glucose

• ribose

• deoxyribose

• galactose

• fructose

molecular formula for glucose

C6H12O6

what type of sugars are alpha and beta glucose

hexose; have six carbons in their ring

are monosaccharides reducing sugars

yes

whats the difference in structure between a and b glucose

alpha H above beta H below

what is the role of a and b glucose

energy sources

what are the equations for ribose and deoxyribose

• ribose= C5H10O5

• deoxyribose= C5H10O4

purposes of ribose and deoxyribose

• ribose= RNA, ATP, NAD

• deoxyribose= DNA

what is the name of the bond that joins two monosaccharides and how does it happen

• glycosidic bond

• bond between carbons 1 and 4

• condensation reaction

• the two OH groups join together, leaving an oxygen to join the two monosaccharides together and leaves a H2O molecule as a byproduct

what is the name for the reverse reaction of condensation

hydrolysis (as it needs water)

examples of disaccharides

• sucrose (glucose + fructose)

• maltose (a glucose + a glucose)

• lactose (glucose + galactose)

are disaccharides reducing or non-reducing sugars?

• all are reducing

• except sucrose which is non-reducing

what do plants store their glucose as

• starch

  • amylose

  • amylopectin

why can plants not store glucose as it is

it is polar and so would cause osmosis and the entering of water into the cell which can cause excessive turgidity

how is starch converted back into glucose when needed

by the use of enzymes

describe amylose

• polymer of a glucose

• only 1,4 glycosidic bonds

• twists into a helix shape in which it is stored; unbranched

• shape is help in place by H bonds

• very compact so can store lots of energy for its size

• insoluble so water does not enter

• too large to diffuse out of cell membrane

describe amylopectin

• a glucose polymer

• same as amylose but every 25-30 molecules, the chain branches and forms 1,6 glycosidic bonds

• heavily branched

• H bonds to stabilise shape

• insoluble

• very compact so can store lots for its size

• too large to diffuse out of cell membrane

describe glycogen

• how animals store their glucose

• primarily found in the liver

• a glucose polymer

• made of 1,4 and 1,6 glycosidic bonds

• more heavily branched than amylopectin so lots of terminal ends

• no H bonds

• insoluble

• cannot diffuse out of the cell

why is having lots of terminal ends important for animals

• animals have a higher metabolic demand from movement, having to flee from predators or catch prey at very short notice etc

• means they need to convert energy at short notice

• having more terminal ends means that more can be converted at once, meaning for faster conversion and more energy for the animal to use

describe the structure of cellulose

• b glucose polymer; means that OH groups don’t align so every other molecule flips 180 degrees to be in line

• insoluble

• unbranched and forms long chains; H bonds between these chains which makes cellulose very strong

• unbranched so can pack close together

what makes cellulose very strong

H bonds between chains

properties of cellulose

• insoluble

• unbranched

• flexible

• high tensile strength

• inert

• gaps to be permeable

what is the role of the cell wall

• keep the cell shape

• permeable to allow substances in

• to stop bursting from turgidity

what elements are in lipids

C, H, O

what forms are lipids found in and at what temperatures

• fats= solid at room temp

• oils= liquid at room temp

functions of lipids

• energy source; eaten or broken down by the body for use

• energy store; long term, compact, insoluble and more energy dense than carbs

• waterproofing e.g. oils that coat feathers of aquatic birds

• protects internal organs against injury

• part of membranes

• insulates the body as fat; helps keep warm in the cold

what are the three key types of lipid

• triglyceride

• phospholipid

• cholesterol

structure of a triglyceride

• one glycerol mol and three fatty acid tails

describe the structure of a glycerol

an alcohol with three OH groups which the fatty acid tails bind to

describe the structure of a fatty acid tail

• carboxylic acid group at the end

• the rest is a hydrocarbon chain

how do fatty acid tails react to form a triglyceride; use name of reaction and bonds formed

• esterfication (condensation) reaction

• ester bond (COO) between the fatty acid and the glycerol

• water is produced as a byproduct

what are the two types of fatty acid and what is the difference between them

• saturated FA= only single bonds between carbon atoms; means they can pack closer together as all straight; fats at room temp

• mono/polyunsaturated FA= means there is at least one double bond between carbon atoms; causes a kink in the chain and so cannot pack as close together

  • oils at room temperature

properties of triglyceride

• non-polar

• hydrophobic

• insoluble

describe the structure of phospholipids

• positively charged phosphate ion head

• glycerol mol

• two fatty acid tails

what charge is phospholipid

• the phosphate ion head is polar and the rest is non-polar

  • this is b/c the phosphate ion head is charged

• makes phospholipids amphipathic (hydrophilic and hydrophobic)

how do phospholipids arrange themselves and why

• arrange with heads facing out and tails inwards; as the tails are hydrophobic and the heads are hydrophilic

• forms a phospholipid bilayer

where is cholesterol made

liver and intestines

what is the structure of a cholesterol mol

• has a hydroxyl group at the end which makes this part polar and hydrophilic and the rest non-polar and hydrophobic

• is an sterol b/c of the OH hydroxyl group

functions of cholesterol

• inserts itself into the bilayer to help control fluidity

• starting molecule for lots of hormones

how many amino acids are there and how many are essential

• 20 total

• 5 non-essential

• 9 essential

• 6 conditionally needed as children

what elements do amino acids contain

C, H, O, N (S)

describe the structure of an amino acid

• amine group (NH2) on left

• carboxyl group (COOH) on the right

• R group on top/bottom (different for every AA)

• H on the opposite side to the R group

• C in the middle

what is the name of a chain of AAs

polypeptide

what is the difference between a polypeptide chain and a protein

protein is the polypeptide folded into its final shape; can also have multiple polypeptides in the protein

name of the reaction of AAs together to form a polypeptide chain and describe what reacts and where this reaction takes place

• carboxyl and amine groups react together

• condensation reaction

• forms a peptide bond (the C of the carboxyl group and the N of the amine group bonded together)

• H2 from the amine group and O from the carboxyl group leave to form a water molecule as a byproduct

• this reaction takes place in the ribosome

describe primary structure of a protein

• specific order of AAs in a polypeptide

• determines the final 3D shape of the molecule

• determined by the DNA sequence of genes

• bonds= peptide

describe the secondary structure of a protein

• twists and folds caused by H bonds (C=O negative and N-H positive)

• alpha helix= polypeptide chain twists into helical shape due to H bonds

• beta pleated sheet= folds into flat, sheet-like structure with folds

• bonds= peptide and H bonds

describe the tertiary structure of proteins

• overall 3D shape of polypeptide chain

• caused by R group interactions

• bonds:

  • disulfide= covalent bonds between two R groups with sulfur

  • ionic= bonding of oppositely charged E groups

  • hydrophobic and hydrophilic interactions=

  • H bonds= electropositive and electronegative charges

  • peptide bonds

describe quaternary structure of proteins

• several polypeptide chains come together

• same bonds as tertiary

what is a conjugated protein

protein with a prosthetic group attached (to help the protein carry out its function; permanent cofactor)

features of a globular protein

• spherical

• soluble in water (hydrophilic R groups are on the outside)

• compact

name three examples of globular proteins

• haemoglobin

• insulin

• catalase

haemoglobin= quaternary structure, where found, function

• four sub-units (2 alpha and 2 beta)

• four haem prosthetic groups, one for each sub-unit (makes it a conjugated protein)

  • contains the Fe2+ ion which binds to O2

• found in RBCs

• function is to bind reversibly with O2 to transport it around the body for respiration

insulin= quat structure, where found/formed and function

• hormone; 2 sub-units, A and B, linked together by disulfide bonds

• formed in the pancreas

• function is to bind to cell receptors; shape has to fit perfectly so the AAs and structure is crucial

• helps to regulate glucose

catalase= quat structure, where found and function

• four polypeptide chains (ABCD)

• four haem prosthetic groups (makes it a conjugated protein)

• Fe2+ in the haem allows catalase to interact with hydrogen peroxide to break it down

  • hydrogen peroxide damaging if it accumulates so significant to remove it

• found in peroxisomes, cytosol (cytoplasm)

properties of fibrous proteins

• strong

• insoluble

• impermeable

• often contain few different AAs; lots of repeats

three examples of fibrous proteins

• keratin

• collagen

• elastin

keratin- properties, where found, structure, function

• strong, inflexible, insoluble, impermeable

• high proportion of cysteine AA; contains sulfur so lots of disulfide bonds which are very strong as they are covalent

• H bonds between strands to increase strength

• found in hair, fingernails, outer surface of skin

• structural protein

collagen= where found, properties, functions, structure

• found in tendonds, ligaments and skin to provide mechanical strength

• properties= strong, flexible, stable

• function is to allow movement and bending without breaking; structural protein

• structure:

  • polypeptide chains wrap together to form a triple helix

  • every third AA is glycine, which has an R group of only glycine so very small and can be very close together

  • staggered ends so no weak spots to increase strength

  • joined by strong crosslinks to form microfibrils and fibrils

elastin= where found, properties, function, structure

• found in skin, artery and alveoli walls, lungs and bladder

• properties= flexible, insoluble, stable, extendable

• function is to allow expansion and recoil, able to return to original shape with no damage

• stretchy fibres due to tropoelastin and are linked by crosslinks so still connected when stretched and return to original shape afterwards