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---
category:
- "[[Note]]"
type: "[[MOC]]"
topic:
- "[[Access to HE Diploma Applied Biochemistry|Applied Biochemistry]]"
project:
- "[[Access to HE Diploma Applied Biochemistry]]"
title: Applied Biochemistry study and SAQs
created: 2025-12-25T23:22:44.272+00:00
tags:
---
[Working folder](file:///C:%5CUsers%5CBobbie%5COneDrive%5C_Sprint%5CMed%20School%5CAccess%20to%20HE%20Diploma%5C4%20Applied%20Biochemistry)
[[Med_Biochem_SAQ_learning_material_questions.pdf]]
## Introduction
Key words:
- [[Mono|Mono]] : one part or unit
- [[Oligo|Oligo]]: several units
- [[Poly|Poly]]: a lot of units.
- [[Macro|Macro]]: large
- [[Monomer|Monomer]]: a [[Macromolecule|macromolecule]] that's is able to bond in long chains.
- [[Oligomers|Oligomers]]: generally between 2-100 monomers in a chain
- [[Dimer|Dimer]]: two chemically bonded monomers.
- [[Trimer|Trimer]]: three chemically bonded monomers.
- [[Tetramer|Tetramer]]: four chemically bonded monomers.
- [[Polymer|Polymer]]: generally a chain, or network (chain with branches), of a lot of chemically bonded monomers.
## Anabolic and catabolic reactions
- [[Anabolic|Anabolic]] reactions combine molecules into larger more complex ones, consuming energy during the reaction.
- [[Catabolic|Catabolic]] reactions break down molecules into smaller simpler ones, releasing energy during the reaction.
## Carbohydrates
In a nut shell: carbon + hydrogen + oxygen (in differing amounts) make up a [[carbohydrate|carbohydrate]].
- Simple carbohydrates
- **[[Monosaccharide|Monosaccharide]]** a single carbohydrate molecule (monomer).
- [[Glucose|Glucose]]
- [[Galactose|Galactose]]
- [[Fructose|Fructose]]
- **[[Disaccharide|Disaccharide]]**: two chemically bonded carbohydrate molecules (dimer).
- [[Sucrose|Sucrose]]
- [[Lactose|Lactose]]
- [[Maltose|Maltose]]
- Complex carbohydrates
- **[[Polysaccharide|Polysaccharide]]**: a chain of chemically bonded molecules (polymer).
- [[Fibre|Fibre]]
- [[Glycogen|Glycogen]]
- [[Starch|Starch]]
### Carbohydrate chemical reactions
**[[Condensation reaction|Condensation]]**: where two molecules are bonded together through $\ce{HO}$ atoms on either side bonding to create one free $\ce{H2O}$ molecule (water), and leaving one oxygen joining two carbon atoms from each side
![[Pasted image 20260114212012.png|500]]
**[[Hydrolysis reaction|Hydrolysis]]** the reverse of the condensation reaction, breaking the bonding between two molecules by the addition of a water molecule.
![[Pasted image 20260114212135.png|500]]
Polysaccharide are useful in cells as they don't us up all of the water, which would lead to [[cell|cell]] death, Multiple monosaccharides or disaccharide would (due hydrolysis reactions)--here's only two ends for the reactions to occur, where as multiple molecules mean more sites and more water used for hydrolysis.
### SAQ 1
1. Explain the difference between a disaccharide and a polysaccharide.
- A disaccharide is a simple carbohydrate composing of two carbohydrate molecules chemically bonded by a [[glycosidic linkage|glycosidic linkage]]--a single [[oxygen|oxygen]] [[atom|atom]]. A polysaccharide is multiple carbohydrate particles joined in a chain, which forms a complex carbohydrate.
2. What biomolecule is required as a reactant in a Hydrolysis reaction, and forms a by-product in a condensation reaction?
- $\ce{H_2O}$, but I'm not sure that water is a biomolecule, so possibly the answer is enzymes.
## Lipids
[[Lipids|Lipids]] are a a group of molecules made up of [[carbon|carbon]], [[hydrogen|hydrogen]] and [[oxygen|oxygen]].
### Triglycerides (Fats)
[[Triglycerides|Triglycerides]] consist of a [[Glycerol|Glycerol]] molecule with three [[fatty acid chain|fatty acid chain]] attached.
![[Pasted image 20260114212419.png]]
These chains are joined and broken through the condensation and hydrolysis, enabling the body to both store energy and release when required.
![[Pasted image 20260114212659.png|500]]
In the body, the enzyme [[lipase|lipase]]--after being mobilised by the release of [[adrenaline|adrenaline]] or glucagon--[[catabolises|catabolises]] the triglyceride through via hydrolysis, releasing the 3 fatty acid chains from the Glycerol molecule.
The glycerol is transported via the blood stream to the [[liver|liver]] where is is turned into glucose.
To enable transportation through the blood stream, the protein [[albumin|albumin]] binds to the fatty acids. They are then utilised in various parts of the body where they're transformed into glucose via the [[Kerbs cycle|Kerbs cycle]].
### Phospholipids
[[Phospholipids|Phospholipids]], the clue is in the name Phosho-lipid, is a sub-type of lipid. Where as triglycerides have three fatty acid chains connected to a glycerol molecule, here one of those chain is replaced by a phosphate molecule. The phosphate 'head' region being [[hydrophilic|hydrophilic]], and the two fatty acid chain 'tail' regions being [[hydrophobic|hydrophobic]].
![[Pasted image 20260114221926.png|250]]
In water phospholipids have a tendency to create sphere structures called [[micelle|micelle]]. They can also construct a double layer call a [[phospholipid bilayer|phospholipid bilayer]], which is a
![[Pasted image 20260114222503.png]]
### Steroids
A [[steroid|steroid]] is four fused carbon rings. [[Cholesterol|Cholesterol]], shown below, is a type of [[Steroid|steroid]]. Note the four carbon rings.
![[Pasted image 20260121201311.png|300]]
### Amino acids
[[Amino acids|Amino acids]], usually written as $\ce{H2NCHRCOOH}$, the structural form is below shows the generalised amino acid structure.
![[Pasted image 20260121202416.png|400]]
There are only 20 types of amino acids. The [[Variable R Group|Variable R Group]] is what makes each amino acid distinct.
Amino acids can form [[peptide bonds|peptide bonds]] with each other via the [[amino group|amino group]] ($\ce{NH2}$) and/or the [[carboxylic acid group|carboxylic acid group]] ($\ce{COOH}$) to form chains.
- [[dipeptide|dipeptide]] (double amino acid)
- [[polypeptide|polypeptide]] (many amino acids)
The figure below shows the condensation reaction that joins two amino acids via a peptide bond, resulting in a dipeptide.
![[Pasted image 20260121205113.png]]
### Protein
[[Protein|Proteins]] are long chains of amino acids, joined via peptide bonds. There structure is described in four layers of hierarchy
![[Pasted image 20260121210351.png|600]]
- [[Protein primary structure|Primary structure]]:
- The precise sequence of amino acids in a polypeptide--the structure created by the initial bonding between amino acids
- Scope
- A single polypeptide
- Peptide bonds, the initial strong covalent C-N bonds.
- [[Protein secondary structure|Secondary structure]]:
- The folding of a polypeptide into a regular, repetitive pattern. The folding being held together by hydrogen bonds between the N-H and C=O--the remaining free parts of the amino and carboxyl group following the initial peptide bonds.
- Scope
- A single polypeptide
- Hydrogen bonds between the N-H and C=O--the remaining free parts of the amino and carboxyl group. This structure level does not involve R-group bonding.
- Loose flexible loops and random bonding are generally not considered a secondary structure.
- Typical secondary structures
- [[Alpha-helix|Alpha-helix]]
- The chain forms into a helix structure with when each amino acids N-H group forms a hydrogen bond with the C=O group of an amino acid 4 places back in the chain.
- ![[Pasted image 20260126161051.png|300]]
- [[Beta sheet|Beta sheet]]
- A polypeptide chain forms hydrogen bonds with itself to form a sheet
- ![[Alpha_beta_structure_(1).png|250]]
- [[Beta turns|Beta turns]]
- [[Omega loops|Omega loops]]
- [[Supersecondary Structure (Motifs)|Supersecondary Structure (Motifs)]]
- Scope
- A single polypeptide
- Peptide bonds, the initial strong covalent C-N bonds.
- Multiple secondary structures
- Examples:
- [[Beta-Alpha-Beta|Beta-Alpha-Beta]]
- [[Greek Key|Greek Key]]
- [[Helix-Turn-Helix|Helix-Turn-Helix]]
- [[Zinc Finger|Zinc Finger]]
- [[Protein tertiary structure|Tertiary structure]]
- The final 3D shape of a folded polypeptide, where the folds are stabilised by R group bonds (e.g. hydroponic interactions, disulfide bridge, hydrogen bonds, hydrophilic interactions, ionic bonds)
- Scope:
- A single polypeptide
- R group bonds
- [[Protein quaternary structure|Quaternary structure]]
- The final 3D shape of multiple folded polypeptide structures, where the R group bonds are between the individual tertiary structure or other tertiary structures
- Scope:
- Multiple polypeptides
- R group bonds
![[Pasted image 20260126150058.png|300]]
The structure of a protein can be changed by the influence of another substance, which can change the bonds within the structure of the protein. This is referred to a [[denaturing|denaturing]]. Some protein can reform/repair and for some this ends the function of the protein.
### Reagent Tests Used to Identify Biomolecules
#### Benedict's reagent
[[Benedict's reagent|Benedict's reagent]] tests for [[reducing sugars|reducing sugars]], reducing sugars being monosaccharides that possess a free [[aldehyde|aldehyde]] ($\ce{-CHO}$) or [[ketone|ketone]] ($\ce{-C=O}$) groups. The reagent contains [[cupric ion complexes|cupric (copper) ion complexes]] with [[citrate|citrate]] (a salt of citric acid) in an alkaline solution. The reducing sugars reduce the cupric ion to [[cuprous oxide|cuprous oxide]] at basic (high) pH.
![[Pasted image 20260121220129.png|350]]
#### Iodine solution
[[Iodine-potassium iodide|Iodine (iodine-potassium iodide) solution]] tests for starch by staining. Starch, unlike monosaccharides, disaccharides, and other polysaccharides saccharides, is coiled polysaccharides (polymer) of glucose which iodine interacts with, becoming bluish black, otherwise it remains yellowish brown.
![[Pasted image 20260121220910.png|175]]
#### Biuret reagent
[[Biuret reagent|Biuret reagent]] is a 1% solution of [[copper sulphate|copper sulphate]] ($\ce{CuSO4}$) which test for proteins with at least two peptide bonds--proteins composed of at least 3 amino acids. A copper ion ($\ce{Cu2+}$) reacts with the peptide bonds producing a violet colour. The intensity of the violet is proportional to the number of peptides bonds. Free amino acids and dipeptides show no reaction, or result in a pinkish colour, and long-chain polypeptides (proteins) produce a strong positive result.
![[Pasted image 20260121230137.png]]
#### Emulsion (ethanol) test for Lipids
The primary component of lipid is the fatty acid, a free fatty acid is a single fatty acid, which is composed of an even number of carbon atoms terminated in a carboxyl group ($\ce{-COOH}$). A variety of Lipids dissolve in solvents, such as [[ethanol|ethanol]], but not in polar solvent such as water. The test involves first dissolving the substance in ethanol, and the resulting solution then dissolved in water, if lipids are present, they will precipitate and form an emulsion.
![[Pasted image 20260121231406.png|300]]
## Enzymes
[[Enzymes|Enzymes]] are globular proteins that can speed up the rate of [[intracellular|intracellular]] and [[extracellular|extracellular]] chemical reactions, without being used up during the reaction.
### Enzyme Specificity
[[Enzyme specificity|Enzyme specificity]] refers to the shape of an enzyme, or more specifically the shape and chemical properties of the enzyme's [[active site|active site]]--an indentation in it's tertiary structure--where a substrate can bind.
The [[induced fit theory|induced fit theory]] shows us that the shape of an enzyme's active site is not initially a complementary fit for it's particular substrate, but the precise arrangement of R-groups within the active site of the enzyme align with chemical groups of an opposite charge in the substrate. These opposite charges create attractive forces which elastically deform the enzyme, changing the shape of the active site, enabling an [[enzyme-substrate complex|enzyme-substrate complex]] to form. Through this bonding and elastic deformation, the enzyme induces tension into the maltose substrate, lowering the reaction activation energy and catabolising the reaction.
Following the reaction the resultant [[enzyme-product complex|enzyme-product complex]] no longer complements the enzymes active site, allowing the enzyme to return to its original form and the product is released.
### Catalytic power
A [[catalyst|catalyst]] is a substance that speeds up a reaction but it not consumed or changed by it. Enzymes are biological catalysts that reduce the activation energy required to for a reaction. If the reaction is releasing energy, enzymes can reduce the overall energy required to access the stored energy.
![[Pasted image 20260125192726.png|400]]
### Temperature and enzyme activity
- ideal balance of kinetic energy and structural stability
Enzymes have an optimum temperature and pH for their biological function. Heat, or thermal energy, is the movement of molecules within a system. As the thermal energy increases, so do the interactions between molecules. This increases enzyme reaction as the likelihood of a substrate interacting with an enzyme site becomes more likely, but only up to a point. The collation of molecules with greater force, or just the increased vibration of the atoms themselves, can break the hydrogen bonds and hydrophobic interactions (both backbone and R-group), changing the shape of the protein in the process. Any changes to an enzymes active site will render it [[denature|denatured]] and unable to perform for it original function.
The optimum temperature for enzymes found in the human body is around 37c, below this the molecules interact less and therefore less reactions happen, above this the enzymes start to denature and enzyme activity drops off quickly. 37c is a temperature at which there's an ideal balance of kinetic energy and structural stability.
![[Pasted image 20260125201100.png|300]]
Temperature Co-efficient:
$$Q_{10}=\frac{\text{Rate of reaction at T+10°c}}{\text{Rate of reaction at T°c}}$$
### pH and enzyme activity
- -/+ changes in pH effect hydrogen bonds and ionic bonds between the R-groups of amino acids in a proteins
- extreme changes in pH can cause coagulation of proteins--an insoluble clump as the proteins to unravels and become entangled around each other
![[Pasted image 20260127183436.png|300]]
### Enzyme inhibition
- an enzyme active site is very sensitive to any changes in the shape of the protein.
- [[non-competitive inhibitor|non-competitive inhibitor]]
- does not embed in active site
- a molecule that embeds in an [[allosteric site|allosteric site]]
- deforms active site
- can stop a substrate from binding, but not always
- stops or inhibits normal enzyme activity
- [[competitive inhibitor|competitive inhibitor]]
- embeds in the active site
- similar in shape to an enzymes substrate
- binds strongly with enzyme
- prevents binding of substrate at active site
- can be overcome by increasing substrate levels
## Nucleic acids
[[Nucleic acid|Nucleic acid]]
- [[Deoxyribonucleic (DNA)|Deoxyribonucleic (DNA)]]
- [[Ribonucleic (RNA)|Ribonucleic (RNA)]]
### Structure of DNA Heading
DNA
- held within the [[nucleus|nucleus]] of almost every cell
- [[Erythrocytes|Erythrocytes]] (red blood cells) are one exception
- they loose nucleus to maximise space to carry [[haemoglobin|haemoglobin]]
- DNA is a polymer of nucleotides
- [[nucleotides|nucleotides]] are made up of:
- 1x [[phosphate|phosphate]]
- 1x [[deoxyribose|deoxyribose]] (sugar)
- 1x [[nitrogenous base|nitrogenous base]]
- ![[Pasted image 20260128194413.png|250]]
- Phosphate and sugar bond to form the DNA [[sugar-phosphate backbone|sugar-phosphate backbone]]
- DNA 'backbone' has directionality
- 5' (prime) end has the free phosphate
- 3' (prime) end has the free -OH
- ![[Pasted image 20260128204406.png|200]]
- ![[Pasted image 20260128204422.png|200]]
- nitrogenous base unit varies
- [[Adenine|Adenine]]
- [[Thymine|Thymine]]
- [[Guanine|Guanine]]
- [[Cytosine|Cytosine]]
- nucleotides are arrange in two chains which spiral into a [[double helix|double helix]]
- ![[Pasted image 20260128195056.png|150]]
- found in homologous pairs of [[chromosomes|chromosomes]]
- ![[Pasted image 20260128194021.png|150]]
- 23 chromosomes pairs in almost every human body cell
- each chromosomes pair is two identical chromatids connected by a centromere
- 46 chromatids in total
- only 23 are individual/unique, as they are duplicated
- size or complexity of organism is not related to number of chromosomes
- total number of base pairs do correlate with complexity
- chromosomes contain genes
- genes are a collection of base paris that make a cell/protein/item/thing
- chromosomes are formed by super-coiling of DNA double helix
- aided by histones (proteins)
### Base units
- four nitrogenous base units found in DNA
- [[Guanine|Guanine]]
- [[Cytosine|Cytosine]]
- [[Adenine|Adenine]]
- [[Thymine|Thymine]]
- these four base units pair up to make only two combinations of [[base pairs|base pairs]]
- Guanine always pairs with Cytosine
- Adenine always pairs with Thymine
- all information to create an organism is encoding within the sequence of these chemicals
- ![[Pasted image 20260128200458.png|500]]
- replication (such as cell division)
- the two strands unzip, by breaking the hydrogen bonds between the base pair
- enzymes add new identical DNA strands, always pairing G-C and A-T
- ![[Pasted image 20260128200936.png|400]]
something more about nucleosome, chromatin, octamer, that didn't make sense.
## Structure of RNA
![[Pasted image 20260128202057.png|500]]
- RNA is single stranded helix, as oppose to DNA double stranded helix
- RNA is a more temporary version of it's DNA counterpart
- RNA sugar is ribose (DNA is deoxyribose)
- ribose sugar possess one more oxygen atom than deoxyribose
- RNA has nucleotide base Uracil instead of thymine
- 3 main types of RNA
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- one version of tRNA for each 20 different amino acids that make proteins
- rRNA transports the amino acids to the ribosomes for building polypeptides
- mRNA strands serve as templates, or [[codon|codon]]
- Ribosomal RNA (rRNA)
- catalyst for protein production
- major component of the ribosome
## DNA replication
DNA's design facilitates replication. Two complete double helixes are formed from one in a process called [[semi-conservative replication|semi-conservative replication]].
- enzyme [[DNA topoisomerase|DNA topoisomerase]] breaks one strand of the DNA, for the helix to start to unravel
- The whole DNA is never unwound in one go
- ![[Pasted image 20260128204533.png|400]]
- the start of the replication fork by the [[DNA helicase|DNA helicase]]
- [[DNA polymerase|DNA polymerase]] enzymes do the replication process, adding the correct base pairs
- [Short video showing DNA polymerase in action](https://www.youtube.com/watch?v=7zQC6BEq1i0)
- DNA polymerase only add base pairs onto the 3' end of backbone
- it's moves in 5' to 3' direction on the new DNA
- it's moves in 3' to 5' direction on the original DNA
- 3' end replication (leading strand)
- new pairs attached in one continuous go
- backbone is continuous
- 5' end replication (lagging strand)
- travels in opposite direction
- shifts position multiple times
- these shift leave [[Okazaki fragments|Okazaki fragments]] behind, due to the disconnections in DNA backbone at each shift point
- Okazaki fragments are serval thousand base pairs in length
- enzyme [[DNA ligase|DNA ligase]] then joins the DNA backbone (Okazaki fragments) to create on continuous backbone
- some DNA polymerase have a specific function
- read the replication and error check and repair any errors
## Protein synthesis
- Transcription
- a portion on DNA is unzipped in the region of the gene that codes for a protein
- single strand of messenger RNA (mRNA) is made by pairing with the exposed DNA nucleotide bases by enzyme [[RNA polymerase|RNA polymerase]]
- the mRNA detaches and exits nucleus through a [[nuclear pore|nuclear pore]] and enters the cell [[cytoplasm|cytoplasm]]
- Translation
- in the cytoplasm, ribosomes attach to mRNA
- mRNA is translated into into transfer RNA (tRNA)
- tRNA is transferred into a sequence of amino acids to form a protein
- ![[Pasted image 20260128211333.png|500]]
- each set of 3 mRNA bases (codon) will pair with complimentary tRNA base triplet (anticodon)
- each 3 base pairs (in a line) represents one of 20 amino acids
- each tRNA is specific to one of the 20 amino acids used in human biology
- the tRNA transfers the amino acid into the ribosomal when it matches with the correct base pair
- the tRNA (amino acid carries) are reusable
- the protein is constructed one amino acid at a time until a [[stop-codon|stop-codon]] signals the ribosome to stop construction of the protein
- ![[Pasted image 20260128212641.png|400]]
- what I have just learned is really cool!
- as if the human body (or 'dead' proteins) do all this complex behaviour!
## Basic principles of gene cloning and DNA analysis
- usual process of gene cloning
- ![[Pasted image 20260128213201.png|400]]
- isolation of the gene to reproduce
- insertion of the gene in the DNA of a host cell by a suitable DNA carrier, called a vector
- check to find the host cells which contain the new gene
- multiplying/cloning the organism to reproduce the gene
- the toolkit
- [[Restriction endonucleases|Restriction endonucleases]] (restriction enzymes)
- types
- differentiate by where they cut DNA at specific nucleotide sequence
- some cut DNA straight across
- some produce staggered cut
- Type 1
- Type 2
- Type 3
- Type 4
- Type 5
- part of the natural defence system of bacteria against bacterial viruses
- they stop infection process by cutting virus DNA into fragments
- cut piece have unpaired bases called '[[sticky ends|sticky ends]]'
- sticky ends can join with complementary sticky ends
- ![[Pasted image 20260128215608.png|300]]
- [[Ligase|Ligase]]
- an enzyme that can join two pieces of DNA
- ligase is used to create [[recombinant DNA|recombinant DNA]] (DNA from different sources)
- [[Reverse transcriptase|Reverse transcriptase]]
- an enzyme that catalyses the construction of a single chain of DNA from mRNA
- this single chain synthetic DNA is called cDNA (complementary DNA)
- [[cDNA|cDNA]] is a synthetic single-stranded or double-stranded DNA that only contains expressed genes and lacks any non-coding introns
- the genetic code, or gene, in one organism will make the protein in another
- the genetic code is universal
- ![[Pasted image 20260128220610.png|300]]
- Isolating the gene
-
### Process for producing synthetic insulin using recombinant DNA technology
## Errors in the course study materials
### 3.5.1
- The material gives the impression that 37c is the optimum temperature for all enzymes, it does not make the distinction that 37c is optimum temperature for enzymes in the human body.
- Figures 34 & 35: y axis incorrectly labelled, should read 'Reaction rate', or the chart should show an inverse U
### 3.5.2
- Incorrect statement: "This is because the molecule does not stop the substrate from binding with the enzyme". Non-competitive inhibition can stop a substate from binding with the active site. It isn't made clear that with non-competitive inhibition the inhibitor embeds in the allosteric site, which is distinct from the active site binding (competitive inhibition).
- Figure 37 incorrectly labels the location of a competitive inhibiter as the 'Allosteric site'.