F cell I- Introduction to the living cell, amino acids and protein

Question 1

What is the definition of a cell?

Answer 1

The fundamental unit of all living things on Earth. They take nutrients and free energy from their surroundings and duplicate themselves

Question 2

What is the concept of life as a ‘pattern in flux’?

Answer 2

Constituents of living matter, whether functional, structural, simple or complex, are in a steady state of rapid flux, meaning the molecules are constantly being replaced.

Cells divide, die and are replaced

Question 3

What is the smallest cell?

Answer 3

Mycoplasma genitalium (0.3 micrometers)

Question 4

What is the largest cell?

Answer 4

On Earth, an ostrich egg cell, which are 20cm

Question 5

Who is termed the father of microbiology?

Answer 5

Antonie van Leeuwenhoek

Question 6

Describe Germ theory and who discovered this

Answer 6

Robert Koch:
(not all of these points are correct as of today, but this revolutionised ideas about infectious diseases)
- Microorganism must be found in abundance in all organisms suffering from disease, but not in healthy organisms
- Microorganism must be isolated from a diseased organism and grown in pure culture
- Cultured microorganism should cause disease when introduced into a healthy organism
- Microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent

Question 7

Describe the universal features of cells

Answer 7

• Plasma membrane - all cells surrounded by this, made of lipid molecules with hydrophilic head, hydrophobic tail, arranged in bilayer, bilayer attached to proteins + sugar molecules which are attached to each other
• Exchange of molecules with surroundings - Cells exchange molecules with surrounding e.g. sugars, amino acids, peptides, amines can enter cells, ions, sugars etc also leave cels
• Cells communicate - Extracellular signal molecule secreted by one cell binds to receptor proteins in plasma membrane of target cell, transmit that signal to intracellular signalling proteins and effector proteins, altering metabolism, gene expression, movement, cell shape
• Genetic information stored as DNA - All cells store hereditary info as DNA, DNA made of phosphate, sugar and base, base pairs bonded by H bonds
• Gene expression - 1 proton is coded for by a gene, genetic code shows which codons produce which proteins
• Protein synthesis - DNA fragment corresponding to one protein is one gene, DNA synthesis (replication), RNA synthesis (transcription), protein synthesis (translation). Cells translate RNA into protein, growing polypeptide chain, incoming tRNA loaded with amino acid.

Question 8

What are the major organelles and cellular structures within most cells?

Answer 8

• Nucleolus
• Nucleus
• Ribosome
• Vesicle
• rER
• Golgi apparatus
• Cytoskeleton
• sER
• Mitochondria
• Vacuole
• Cytosol
• Lysosome
• Centriole

Question 9

What do sugars in cells produce?

Answer 9

Polysaccharides

Question 10

What do fatty acids in cells produce?

Answer 10

Fats, lipids, membranes

Question 11

What do amino acids in cells produce?

Answer 11

• Proteins

Question 12

What do nucleotides in cells produce?

Answer 12

• Nucleic acid

Question 13

Describe the chemical structure of an amino acid

Answer 13

A central C atom attached to an amine group (NH2), a carboxyl group (COOH), a H and a ‘R’ group side chain. R group varies

Question 14

Describe the chemical structure of a peptide bond

Answer 14

Peptides have 2 different ends, 1 amino-terminal end and 1 carboxyl-terminal end

Question 15

How do amino acids form peptide bonds?

Answer 15

Via condensation reaction, carboxyl group reacts with amine group

Question 16

What happens to amino acids at a low pH?

Answer 16

• Proton (H+) concentrations are very high, so amino acids protonated

Question 17

What happens to amino acids at a high pH?

Answer 17

• Proton concentrations (H+) are low, so amino acid is deprotonated

Question 18

Describe primary structure of a protein

Answer 18

The primary structure of an amino acid is the sequence of amino acids in the amino acid chain connected by peptide bonds

Question 19

Describe the secondary structure of a protein

Answer 19

Proteins form alpha helix or beta pleated sheets

Question 20

Describe alpha helix

Answer 20

Hydrogen bonds formed between peptide bonds within single strand of protein structure, right handed helix (twists in direction of fingers when you make fist in Right hand) stabilised by H-bonds between the amide H of one amino acid and the carbonyl (C=O) group 4 residues along the chain.

Side chains (R groups) protrude from sides of the helix where they’re free to interact, and in some cases the residues (amino acids) are hydrophilic on one side of the helix, and hydrophobic on the other.

Question 21

Describe beta pleated sheets

Answer 21

2 or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held by hydrogen bonds. H bonds form between carbonyl and amino groups of backbone, while R groups extend above and below plane of sheet

Question 22

What is a parallel Beta pleated sheet?

Answer 22

The strands all point in the same direction, meaning the N- and C-terminals all match up at the same points

Question 23

What is an anti-parallel Beta pleated sheet?

Answer 23

The strands alternate to point in opposite directions (meaning that the N-terminal of one strand is positions next to the C-terminal of the other strand)

Question 24

Describe the tertiary structure of a protein

Answer 24

• Folding of protein chains that have formed secondary structures
• Helices and sheets folded up into more densely packed globular structures
• Formation of these structures depends on weak chemical bonds between side chains
• These structures may be stabilised by covalent disulphide bonds between cysteine molecules

Question 25

Describe the quaternary structure of a protein

Answer 25

Proteins made of several polypeptide chains, e.g. haemoglobin

Question 26

What are the principal non-covalent bonds that contribute to protein structure?

Answer 26

• Ionic bonds- electrostatic attraction between oppositely charged ions
• Hydrogen bonds- Proton shared by 2 different atoms with relatively high electronegativity (N, O, F). Could form between 2 different oxygen atoms, a carbonyl group and an amide group
• Van der Waals- When atoms come into very close distance, causes weak intermolecular forces

Question 27

What are hydrophobic interactions?

Answer 27

Hydrophobic side chains push away from surface of protein, often form at centre of globular proteins

It is also the tendency of non-polar substances to aggregate in aqueous solutions and be excluded by water

Question 28

How are covalent crosslinks formed within and between polypeptides?

Answer 28

Disulphide bonds (these are a type of covalent bonding) form between cysteine molecules in polypeptide chains, which combine in an oxidation reaction to form the disulphide bond

In tertiary structure, they may crosslink on a single polypeptide chain

In quaternary structure, the crosslink forms between two separate molecules

Question 29

How does protein sequence determine its structure and function

Answer 29

• Each protein has a unique sequence of amino acids, specified by a gene
• The primary sequence determines the folding of the polypeptide into the functional protein structure
• Changes in the sequence caused by mutations result in altered structures and this can cause alterations in function, e.g. sickle-cell anaemia

Question 30

What causes sickle cell anaemia?

Answer 30

• Beta subunit of haemoglobin, mutation occurs that changes hydrophilic glutamic acid (glutamine), which is negatively charged amino acid, to valine, which is hydrophobic at position 6.
• Mutation is a point mutation, causing change in amino acid chain, producing different protein (valine instead of glutamine)
• As valine hydrophobic, causes a hydrophobic interaction.

Question 31

What happens to the haemoglobin in sickle cells in the deoxygenated state?

Answer 31

• Mutant haemoglobin (HbS) form insoluble fibres with other HbS molecules, resulting in the precipitation of the protein.

This precipitation distorts the normal disc shape to create the ‘sickle’ shape, and these block capillaries.

Breakage of the cells causes anaemia

Question 32

Define homeostasis

Answer 32

The ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes