Biochemistry and Cell Biology

Abu Bakr al-Razi?

A Persian physician, chemist and scholar who lived approximately 865–925 CE. He was a major figure in medieval medicine and chemistry.

What age was Al-Razi in

Islamic golden age

Why is al-Razi relevant to modern biology?

His emphasis on systematic observation and experimentation helped develop the evidence-based approach fundamental to modern science.

Who was Robert Hooke?

An English scientist who lived from 1635–1703 and worked across biology, physics and microscopy.

Hooke

He was the first person to use the term "cell" to describe microscopic structures he observed. 1665

What book did Hooke publish in 1665?

Micrographia, containing detailed observations and drawings made using microscopes.

Hooke

It introduced the concept of cells and helped establish microscopy as an important tool for studying biological structures.

Who was Ross Harrison?

An American embryologist who lived from 1870–1959 and studied development and nervous-system formation.

What major technique did Harrison pioneer?

Tissue culture, allowing living cells or tissues to be maintained and studied outside the organism. 1907

Harrison

Modern cell and tissue culture techniques.

Marie Manyard

An American biochemist, born in 1921 and died in 2003.

What was historically significant about Daly's career?

In 1947, she became the first African-American woman in the United States to earn a PhD in chemistry.

What diseases or health conditions did Daly research?

Her later research included cholesterol and hypertension, particularly their relationship to cardiovascular disease.

Shinya Yamanaka

A Japanese physician and stem-cell researcher, born in 1962.

Yamanaka

He demonstrated that mature, differentiated cells could be reprogrammed into pluripotent stem cells.

Özlem Türeci?

A Turkish-German physician, scientist and entrepreneur, born in 1967.

What is BioNTech known for?

Developing medical technologies including mRNA-based therapies and vaccines, alongside extensive cancer research.

Turechi

Her work demonstrates how understanding mRNA, protein production, cells and the immune system can lead to modern medical applications.

Bohr model

Atoms contain protons neurons and electrons

Elemental isotopes

Different number of neurons, so atomic mass changes but does not drastically change the chemical charaterstics.

Isotopes in Anti-Doping

Used to distinguish steroids that have been naturally produced by the body from steroids that have been externally administrated

Why Can isotopes be used for antidoping

C12/C13 differences in androsterone after testosterones or DHEA administration

What could give a false result

Differences in diet can lead to different endogenous isotope ratios

Breakdown of testosterone or DHEA

What are radioactive isotopes called

Radioisotopes

Fixed half life of 14C

5730

What is tc-99

Tc-99m is a radioisotope used as a radioactive tracer in nuclear medicine.

Why does it say Tc-99 is "tagged" to a pharmaceutical?

Tc-99m on its own doesn't necessarily go exactly where clinicians want to investigate, so Tc-99m can be combined with an appropriate pharmaceutical molecule allowing it to be delivered to target site.

Different types of carbohydrates

Functions of monosaccharides

Cellular energy, Building nucleic acids

General formula of monosacchraides

(CH2O)n

Glycosidic bond

Lipid functions

1)Protection and insulation

2)Neuron myelination

3)Absorption of fat-soluble vitamins

4)Hormone production

5)Cell membranes- lipid bilayers

Lipids

Lipid classifications/sub-groups

1)Triglycerides 2)Phosopholipids 3)Sterols.

Properties of Lipids

Fatty, waxy or oily in compostion

Triglycerides

Main constitute of body fat. Can be Saturated (c-c) or unsaturated. Double bonds can be cis or trans in geomery

Phospholipids

AMPHIPATHIC

has both a hydrophilic and hydrophobic region

Which part of a phospholipid is hydrophilic?

The polar phosphate-containing head.

Sterols

Cyclic organic compounds found in grains, nuts, seeds, fruits and vegetables. A sub-group of steroids

Steroid vs Sterol

Both 4-ring structure but a sterol has a OH- group

What sterol is important in fungi?

Ergosterol

Why is cholesterol described as amphipathic?

Cholesterol has a small polar hydroxyl (-OH) region and a much larger hydrophobic region.

How does Cholesterol affect fluidity

At higher temperatures:
Cholesterol restricts phospholipid movement
→ prevents the membrane becoming too fluid

At lower temperatures:
Cholesterol prevents fatty-acid chains packing too closely
→ prevents the membrane becoming too rigid.

Roles of cholestrol

Role in heart disease.

Synthesis of eg vitamin D, bile, sex hormones

Important part of cell membrane structure

Amino acid

In which direction are protein sequences written?

N-terminus → C-terminus

What is the N-terminus?

The end of a polypeptide containing the free amino group.

What is the C-terminus?

The end containing the free carboxyl group.

What are proteinogenic amino acids?

Amino acids that are incorporated into proteins.

Amino acids encoded in human DNA

Only 20 are genetically encoded in human DNA, these are known as the proteinogenic amino acids

Peptide bond

Formed via a condensation reaction between the carboxyl and amine group

Peptide bond formation

20 proteinogenic amino acids

Angiotensin I

Peptide hormone

Vasoconstriction

Increases blood pressure

Primary structure

The amino acid sequence from N- to C- terminus

Secondary strcture

Logical structural features- number of commonly observedmotifs

Tertiary structure

The overall protein conformation caused by side chain interactions- folding of a polypeptide into a particular 3D shape

What are electrostatic interactions in proteins?

Attractions or repulsions involving charged or polar groups in a protein. Oppositely charged side chains can attract and form ion pairs/salt bridges

What is π-π (pi-pi) stacking?

A non-covalent interaction involving π systems, commonly associated with aromatic groups positioned close to one another. π-π contacts contribute to protein folding and structure.

aromatic ring ⇄ aromatic ring

hydrophobic interactions in proteins?

In an aqueous environment, non-polar/hydrophobic groups tend to associate away from water. The hydrophobic effect contributes importantly to protein folding.

What’s the main bond in secondary structure

Hydrogen bonding

Alpha helix

What holds an alpha helix together

The α-helix is stabilised by hydrogen bonds within the polypeptide backbone.

• C=O of one peptide group acts as a hydrogen-bond acceptor.

• N-H of another peptide group acts as a hydrogen-bond donor

What does "residue" mean?

An amino-acid residue is an amino acid once incorporated into a peptide/protein chain.

What does i+4 mean?

Four residues further along the amino-acid sequence.

Is an α-helix right- or left-handed?

Right handed

How many residues are there per turn of an α-helix?

Approximately 3.6 residues per turn

How does alpha helix form

Hydrogen bonds formed between carboxyl and amino groups. Then the helix turns right-handed (clockwise when vweid from the N-Terminus). The upper and lower ends of the ploypeptide are not involved in this bonding

Beta plated sheet

Build of beta plated sheet

• A β-strand is an extended section of polypeptide backbone.

• Multiple β-strands positioned alongside each other and connected by hydrogen bonds form a β-sheet, also called a β-pleated sheet

Shape of beta plated sheet

Zig-zag. The angular conformation of the peptide chain causes the zig-zag shape.

What bonds hold beta plated sheet togther

Hydrogen bonds in the backbone forms between each segment, as Adjacent β-strands are stabilised by hydrogen bonds between the peptide backbones.

Parallel beta plated sheet

The neighboring β-strands run in the same N → C direction

Antiparallel beta plated sheet

Neighbouring strands run in opposite directions.

Tertiary structure

Consist of many alpha helices and beta sheets twisted around each other. This 3D shape of the protein is influenced by intermolecular forces as well as hydrophobicity.

Restrict the shape of a protein to one or a few conformations

Noncovalent bonds

Under which one of the following conditions is the complete structure of a protein designated as its quaternary structure?

The protein contains more than one protein subunit.

It is estimated that about 30% of the proteins encoded in an animal's genome are membrane proteins that are required for a cell to function and interact with its environment. 

True

What is the name of the linkage which bonds monosaccharides to form oligosaccharides and polysaccharides. 

Glycosidic linkage

1^st Law of Thermodynamics

The total amount of energy within a system and its surroundings is constant OR energy can neither be created nor destroyed, only interconverted between forms.

2^nd Law of Thermodynamics

The total entropy (the level of disorder) of a system and its surroundings always increases.

3rd law of thermodynamics

The entropy of a system approaches a constant value when its temperature approaches absolute zero.

Closed system

cannot exchange matter across boundaries.

Open system

can pass matter back and forth across boundaries.

systems

Enthalpy

Heat Storage Capacity of A System

Formula for enthalpy

Enthalpy  = Internal Energy + (Pressure x Volume)

H (J (or J/mol)) = E (J) + (P (Pa) x V (m³))

Similarities in enthalpy

∆H (enthalpy) and ∆E (energy) are very similar in liquids and solids because there is little change in volume

entopy

refers to the level of disorder in a system (e.g. how energy is distributed in a system)

Key rule of entropy

Entropy increases spontaneously

Gibbs free energy

∆G = ∆H - T∆S

∆G = Change in Gibbs Free Energy (kJ/mol)

 ∆H = Change in Enthalpy (J)

T = Temperature (K)

∆S = Change in Entropy (J/K)

∆G < 0

Reaction occurs spontaneously

∆G > 0

Reaction does not occur spontaneously

∆G°

Under Standard Conditions (298K or 25°C), 1 bar pressure, all reactants and products at 1M.

∆G°’

37°C i.e. 310K, and pH of 7 = 10^-7M [H⁺]

∆H < 0 and ∆S > 0

-∆G

Spontaneous

Exergonic

Energetically Favourable

Loss of available energy

∆H < 0 and ∆S < 0

∆G

Spontaneous

At low temperatures

∆H > 0 and ∆S < 0

∆G

Non-Spontaneous

Endergonic

Energetically unfavourable

Gain in available energy