T1

1. monosaccharide
2. disaccharide
3. polysaccharide

1. monosaccharide
2. disaccharide
3. polysaccharide

1. mono: individual sugar monomer
2. di: molecules formed by condensation of 2 mono --> glycosidic bonds
3. poly: polymers formed by condensation of many mono- (repeating mono- unit)

explain how monosaccharides join to form dis. or polys.

through condensation reactions and forming glycosidic bonds

oligosaccharides

poysaccharides w/ 3-10 sugar units

saccharides levels

hexose glucose

explain how the structure of GLUCOSE is related to its function

six-carbon sugar: high energy content, easily metabolized through glycolysis

hydroxyl groups: make it highly soluble in water, facilitating its transport in the bloodstream to various cells in the body

explain how the structure of STARCH is related to its funciton

F: energy storage - plants
· mixture of amylose + amylopectin - α glucose poly.

1. large molecules --> too large to diffuse out of cell
2. no distinct polarity --> unreactive
3. insoluble --> no osmotic effect

ribose

explain how GLYCOGEN structure related to its functio

F: energy storage - animals + fungi
· 1,4 + 1,6 glyc bonds --> α glucose monomers

1. compact: +in - vol
2. unreactive: no polarity
3. low solubility: no osmotic effect
4. large ≠ diffuse out of cell
5. more branches, more terminal glucose molecules, hydrolysed faster and supply of energy
animals = more active

types of glycosidic bond

1,4: results in linear polymer
1,6: results in branched polymer

glycosidic bond

between OH group + H
glycosidic bonds asily broken down
rapid release of glucose (mono) for cellular respiration
1,4 - non branched
1,6 - branched

structure cellulose

contain only beta glucose
unbranched, linear chains
alternate monomers rotated through 180 º
contain only 1,4 glycosidic bonds
cellulose molecules are bonded to each other by H bonds
polysaccharide of beta glucose
every other glucose is inverted
cellulose molecules arranged parallel/ as microfibrils
joined by H bonds

how structure of CELLULOSE relates to its function

plant cell walls
1. cellulose molecules are straight
2. many H bonds hold molecules/ chains together (microfibrils)
3. results: strong to prevent cell lysis, matiain turgidity, resist turgor pressure
4. polar nature of glucose allows water molecules to diffuse through

condensation reaction

water molecule removed from rectants and bond fromed

covalent bonds formed

· protein: peptide bond
· lipids: ester bond
· carbohydrates: glycosidic bond

hydrolysis

water molecule used + bond broken

properties of saturated vs unsaturated fatty acids

tryglyceride formation

(1) CONDENSATION reaction
(2) 1 glycerol + 3 fatty acids
(3) hydroxyl group + carboxyl group
(4) ester bond
(5) + 3 H2O

relate the structure of lipids to their function

1. high energy: to mass ratio
energy storage, high calorific value from oxidation
2. insoluble - non polar
no osmotic effect
used for water proofing - hydrophobic fatty
3. thermal insluation
slow conductor of heat
4. buoyancy
less dense than water

describe structure & function of phospholipids

amphipathc
glycerol backbone
- attached to 2 hydrophobic FA tails
- & 1 hydrophilic -vely charged phosphate head (PO3)⁻
= POLAR molecule

F: forms phospholipid bilayer: component of membranes
+ tails can splay outwards: waterproofing

phospholipid structures

structure amino acid

peptide bond

H amino group + OH carboxyl group
amino acid monomers --> form di peptides --> polypeptides
linked by peptide bonds formed in condensation reactions

primary structure of protein

the exact sequence and number of amino acids in polypeptide chains
determined by sequence of codons on mRNA
+ only peptide bonds

secondary structure of protein

a polypeptide chain folding
into alpha helix or beta pleated sheet
due to H bonds between different regions of polypeptide chains
H bonds between C(O)OH & NH2

describe 2 types of secondary protein structure

alpha helix:
all NH bonds on same side of protein shape
H bonds parallel to helical axis
beta pleated sheet:
NH and C=O groups alternate sides

tertiary structure of protein

3D further folding of proteins - supercoiling
complex 3D structures
held together by bonds between R groups of AA along chain
1. hydrogen bonds (numerous and easily broken)
2. ionic bonds (2nd strongest, between charged R groups, change pH interrupts them)
3. disulphide bridges (strong covalent S-S) - CYSTINES

quarternary structure of protein

more than 1 polypep chain
same bonding as 3tiary
- between R groups of diff chains
can have a prosthetic group - non-protein compontnet
--> result in conjugated molecules

explain how the sequence of amino acids determines the shape/properties of a protein

primary structure: seq of aa that determines 3tiary structure
because aa/ R groups determine position bonds (hydrogen, disulphide, ionic)
polar aa/ R groups need to be on outside so it can dissolve into plasma
final structure of molecule has to be specific shape to be complementary/bind to the receptor molecules
or have active site

describe funtion and structure of globular proteins

· spherical and compact
· usually (semi) water soluble - form colloids in water
· involved in metabolic processes eg. enzymes, heamoglobin, hormones
· complex 3tiary/ 4arternay structures held together by (our 3) bonds

explain why globular proteins are soluble in water (4)

protein folded so hydrophilic R groups face outwards, hydrophobic R grps in
these exposed R groups are charged: polar / ionic
therefore they form H bonds with water
because water is a polar solvent / dipole nature

describe funtion and structure of fibrous proteins

· form long parallel chains/ fibres
· very little or no 3/4 structure - mainly 2dary
· occasional cross-linkages which form microfibriles for tensile strength
· sequences of aa repeat
· insoluble in water
· useful for structure and support. eg: collagen

function collagen

structure: component of bones, cartilage, connective tissue, tendons

structure collagen

fibrous protein:
· 3 polypeptide chains
· that form a triple helix
· helices held toegether by hydrogen bonds
· many tropocollagen molecules (triple helices) joined together
· form long parallel chains/ fibres
· very little 3/4 structure - mainly 2dary
· STABLE alpha triple gamma helix - repeating aa seq: glycine-proline-other
· insoluble in water
· cross-linkages: H bonds and staggered covalent bonds between fibres form microfibriles and = high tensile strength

explain significance of repeating amino acid sequences in formation of tropocollagen

glycine is very small so collagen fibres close together

R group = single H

allows formation of hydrogen bonds to hold polypep. chains together

funtion haemoglobin

binds to O2 with variable affinity to transport it around the body in bloodstream

structure heamoglobin

globular protein:
· spherical and compact
· 2 alpha and 2 beta chains, 4 prosthetic haem groups: conjugated
· hydrophilic R groups face outwards, hydrophobic R grps in
--> water soluble - dissolves in plasma
· Fe2+ haem groups forms dative bond with O2
· 3tiary structure changes so it is easier for subsequent O2 molecules to bind

role in plants of 4 inorganic ions

1. phosphate ions - to make ADP & ATP
2. magnesium ions - produce chlorophyll
3. nitrate ions - DNA and amino acids
4. calcium ions - to form calcium pectate for middle lamella

calcium pectate

sticks cell walls together
found in middle lamella

explain how dipolar nature of H2O is essential dor living organisms

hygrogen bonds, polar
1. water is a polar solvent - used for transport medium
2. has high surface tension - allows pond-skaters
3. high specific heat cap. - thermoregulation
4. water max dense at 4ºC
5. incompressible - used for hydraulics & structural support (turgor changes)

nucleic acids

polymers of nucleotides
RNA (ribonucleic acid) & DNA (deoxyribonucleic acid)

structure of nucleotides

nucleotides definition

individual monomers that make up polynucleotides which are compsed of a phosphate group, a pentose sugar and a nitrogen containing base

structure of DNA

phosphodiester bonds

two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds
found in DNA and RNA backbone
2 in phosphodiester bonds, 1 loses H to gain -1 charge

pentose sugar in nucleotide in DNA and RNA

deoxyribose
ribose

organic bases in DNA

Adenine
Cystosine
Guanine
Thymine

purine bases

have 2 nitrogen containing rings
Adenine and Guanine

organic bases in RNA

Adenine
Cystosine
Guanine
Uracil

pyramidines

contian 1 nitrogen containing ring, single ring structure
pyramidines - Thymine, Cystosine, Uracil

ribose and deoxyribose structure

base pairing

A-T: 2 H bonds
C-G: · H bonds

RNA

single stranded
can form complex shapes through H bonds
comes in multiple different forms
made of nucleotides (AGCU)

mRNA - messenger: sugar phospate backbone
tRNA - transfer
rRNA - ribosomal
which are involved in protein synthesis

DNA replication

semiconservative

1. DNA double helix unwinds forming a replication fork
· H bonds compl. bases broken
· catalyst: DNA helicase
2. both free strands used as templates
· free nucleotides line up
· complementary base pairing occurs between template & free nucleotides
3. adjacent nuclotides (which contain the bases) joined
· condensation reaction
· phosphodiester bonds
· catalyst: DNA polymerase
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DNA polymerase only works in 5' to 3' direction
strands run in opposite directions
leading strand: in 5' --> 3' direction: made continuously by DNA polymerase
lagging strand: in 3' --> 3' direction
made as a series of small chunks at a time in 5' to 3' direction between primers forming okazaki fragments

ligase seals fragments in both strands w ph.diester bonds
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4. 2 identical new DNA molecules automatically fold: double helices
· H bonds within molecules

enzymes involved in DNA replication and function

DNA helicase - unwinds DNA helix by breaking H bonds between bases

DNA polymerase - catalyses formation of phosphodiester bonds between nucleotides during the synth of a new DNA strand

ligase - enzyme which joins Okazaki fragments on lagging strand together or any other fragments by forming phosphodiester bonds between them

semi-conservative replication definition

new DNA molecules contain 1 original strand and 1 newly synthesised strand
· ensures genetic continuity between generations of cells
· genetic info passed from one gen to the next

gene definition

sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain

(explain) nature of genetic code

· consist of triplets of bases: codons, which each code for 1 amino acid
· contains (1) start and (3) stop codons: maks start/stop protein synth, establish reading frame
· degenerate: more than one triplet codes for the same amino acid
this reduces the effect of mutations
· non-overlapping: each triplet only read once, triplets don't share bases
· not all of the genome codes for proteins: non-coding regions (introns)
coding regions = exons
· universal: same in all organisms + species

degenerate nature of genetic code effect

mutations have less effect:

• more triplet codes than amino acids

• some mutations have no effect on protein made as new triplet may still code for same amino acid

• helps mantain same structure + function of protein

• deletion/ insertion: more likely harmful, causes ‘frameshift’

• all codons ‘downstream’ of the mutation are read differently

gene mutations

changes to base sequence:

1. deletions: nucleotides not incorporated into chain

2. insertions: extra nucleotide(s) incorporated into growing DNA chain

3. substitutions: incorrect nucleotide incorporated into chain

frame shift: (1st two)

• more harmful

• all codons downstream of mutation are read diff and likely produce diff aa

start and stop codons

start: TAC
stop: ATT, ATC, ACT

enzymes def

• biological catalysts 

  1. bio: globular proteins: synthesised by ribosomes from mRNA.

  2. catalysts, lower activation energy: minimum amount of energy particles must collide with in order to react.

• control RoR of metabolic R

  • anabolic: build new chemicals

  • catabolic: break subs down

• place of actions of enzymes: intra and extracellularly 

how do enzymes lower activation energy

form enzyme/substrate complex: 

• active site affects bonds in substrate, less energy req to break them

• reacting substances are brought close together, easier for bonds to form between them

once ration complete, product no longer fits active site and leaves

induced fit hypothesis

active site: still has specific shape but is flexible

• substrate enters active site 

• AS undergoes small conformational changes to fit substrate better

  / shape of active site is modified around it to form the active complex

• this puts strain on substrate bonds, lowering activation energy

• once products left complex, enzyme reverts to inactive form 

specificity of enzymes

• result of very specific active site shapes arising from seqs of aa folded in a particular way: 1/2/3/4 structure/ folding

• .: each enzyme only compl to one type of substrate and will only cat that reaction

types of inhibition of enzyme activity

1. reversible: enzyme not permanently damaged. once inhibitor removed, enzyme activity functions normally

   1. competitive inhibition

   2. non-competitive inhibition

2. irreversible:

   inhibitor combines w enzyme by permanent covalent bonding, impeding catalysis 

   never “natural”: not used as a means to control metabolism

   slower, but much more damaging effects 

3. end-product inhibition

how enzymes are affected by competitive inhibition

1. inhibitor molecule similar in shape to substrate molecule, binds to active site, forms enzyme-inhibitor complex

2. temporarily prevents ES complexes forming until released, decr RoR

3. competes w substrate for binding at active sites: the more inhibitor mols there are, less likely substrate will bind to enzyme

   level of inhibition depends on levels of substrate and inhibitor (game of probability/ numbers)

how enzymes are affected by non-competitive inhibition

1. inhibitor binds to enzyme/ forms complex w enzyme or ES complex

   → forms bonds w enzyme at allosteric site 

2. trigger conformational change/ change of shape of active site

   → prevents substrate binding, can no longer catalyse reaction

3. not on the active site: inhibitor not competing for the active site

   → only level of inhibitor affects level of inhibition. concentration of substrate does not affect level of inhibition

how enzymes are affected by end-product inhibition

an (end) products of the reaction (pathway) acts as competitive or non-comp inhibitor for an enzyme involved in (beginning of) pathway

prevents further formation of products: feedback control
—> if levels high: inhibits formation of more product, if low, no enzyme inhibition

regulatory enzymes: can have molecules can bind to them and bring about non-competitive inhibition (not active site)

how to compare effect of an enzyme

measure initial RoR 

1. bc RoR decreases over time, initial is fastest rate

2. bc as R progresses substrate is used up/ broken down, conc decrs

3. so less substrate can collide w enzyme + form complexes 

4. initial: substrate is in excess, not limiting, subs conc should not limit RoR

5. subs conc is no longer controlled

6. before end prodcut inhibition can occur

how to measure initial RoR

calc initial rate: tangent to graph at t=0

factors affecting rate of enzyme controlled reactions

stages of protein synthesis

1. transcription

2. mRNA leaves thru nuclear pores, travels to ribosomes/ RER

3. translation (protein synth)

4. modified (4º structure produced) and packaged into vesicles: golgi apparatus

5. exocytosis releases protein

   

Describe the process of transcription (4)

• in nucleus

• DNA strands separate

• antisense strand used as template for mRNA

  • mRNA forms on antisense strand in order to code for a peptide 

  • coding strand of DNA= sense strand

  • is identical to coding strand of DNA

• RNA polymerase binds to open DNA and synthesizes mRNA

tRNA structure

role of ribosomes in protein synthesis

• translation 

• to hold the tRNA on mRNA

• whilst peptide bonds form to join adj amino acids together 

describe the process of translation

1. in cytoplasm/RER, in ribosomes

2. mRNA attached to ribosome 

3. tRNA is attached to a specific amino acid, brings aa

4. tRNA anticodon binds to mRNA codon. compl ase pairing (H) ➰ tRNA +mRNA

5. peptide bond form ➰ amino acids

6. process involves start/ stop codons

Describe how monomers are bonded to a polypeptide chain during the synthesis of a protein

• formation of peptide bond

• between amino acids and carboxyl gr

• by condensation R

effect of point mutations on amino acid sequences:

changes triplet/ codon, may change amino acid coded for
if affects protein produced, can change phenotype 

eg. sickle cell anemia: gen disease, produces sickle shaped RBCs due to point mutation that causes a change in a single amino acid in the polypeptide sequence

• hemoglobin formed forms rods, gives RBC that shape

• oxygen not carried efficiently

• cannot reach narrow blood vessels