Biology Unit 3 AOS 1 Notes

Bioethics

Bioethics is the application of ethics (our own personal understanding of right and wrong), in biology.

Approaches to Bioethics

. There are 3 key bioethical approaches: · Consequence-based . The individual should be driven by the consequences that are likely to result. The aim is to maximise positive outcomes whilst minimizing negative outcomes, emphasising the surrounding circumstances. · Duty/rule-based . The individual should be driven by the fundamental duty to act in a certain way, following set rules and responsibilities with disregard for the underlying consequences. It is often arguing that actions cannot be justified regardless of the result. • Virtues-based . The individual should be driven by their character rather than fundamental rules or consequences, aiming for emphasis on nature of individuals.

Ethical Concepts

. Integrity - encourages individuals to act honestly and truthfully, especially when presenting results and findings. · Justice - encourages consideration of different people's positions and opinions. . Beneficence - encourages individuals to act in a way that benefits others. . Non-maleficence - encourages individuals to act in a way that removes as much harm as possible. . Respect - encourages individuals to consider values of others including their welfare, beliefs, values, and freedom.

Nucleic Acids & Proteins

Nucleic Acids

· Class of macromolecule that includes both DNA (deoxyribose nucleic acid), and RNA (ribose nucleic acid).

Structure of Nucleic Acids

• Nucleic acids are made of monomers (nucleotides). . DNA and RNA differ on the structure of their nucleotides.

Structure of DNA

· Contains a deoxyribose sugar, a negatively charged phosphate group and a nitrogen containing base (adenine, thymine, cytosine, or guanine for DNA). . The base is attached to the 1' carbon and the phosphate group is attached to the 5' carbon. · Individual nucleotides are bonded through phosphodiester bonds (covalent) through a condensation polymerisation (or condensation reaction). . The phosphate group on the 5' carbon binds onto the carboxyl group, the 3' nucleotide on the next nucleotides. . The two ends of the DNA strand are always different. . The phosphate group is always on the 5' end. . The hydroxyl group is always on the 3' end. . Nucleic acids are always synthesised from the 5' to the 3' end, resulting in enzymes that synthesise them going in the 3' to 5' direction due to them being anti parallel to the template strand. · Hydrogen bonds form complementary bases. · Cytosine + Guanine - 3 Hydrogen Bonds · Adenine + Thymine - 2 Hydrogen Bonds . Two strands are always anti parallel; if one strand were to run in a 5' to 3' direction, the complementary strand would run in a 3' to 5' direction.

Structure of RNA

. Contains a ribose sugar which contains an additional oxygen at the 2' carbon. . Thymine replaced with Uracil. · RNA is single-stranded in comparison to the double helix structure of DNA, is single-stranded. · RNA reads from 5' to 3' and the protein is synthesised in the phosphate to carboxyl direction.

Phosphate Group CH2 5 .O 4 1 3 2 Nitrogenous Base (A, C, G, U) OH Pentose Sugar (Ribose) RNA Nucleotide Phosphate Group CH2 O 5 4 1 3 2 Nitrogenous Base (A, C, G, T) H Pentose Sugar (Deoxyribose) DNA Nucleotide

Structure of Polynucleotides

. Polynucleotides are nucleotides linked to form a single nucleotide strand via condensation reactions. . Nucleotide strands read from 5' to 3'. . The 5' phosphate group of one nucleotide attaches to the sugar of another nucleotide. . The bond between two nucleotides is a covalent phosphodiester bond.

Functions of Nucleic Acids

Function of DNA

· Storage of genetic material. · Prokaryotes have singular circular chromosomes whereas eukaryotes have linear chromosomes. . The sequence of nucleotides decides the sequence of amino acids which decides the protein. · Not all DNA codes for polypeptides, only the genes. · When DNA is copied, the two strands separate, and base pairing occurs to exposed nucleotides. . DNA replication is semi-conservative which means every new DNA double helix consists of one strand of the original DNA, bound to one strand of newly synthesised DNA. . New strand is built 5' to 3'.

Function of RNA

· There are 3 main types of RNA which are: · Messenger RNA A transcript copy of a gene which encodes a specific polypeptide. TL; DR - Brings the DNA blueprint to rRNA. · Transfer RNA Carries the polypeptide subunits (amino acid) to the organelle responsible for synthesis (ribosome). TL; DR - Transports amino acids (needed for proteins) to the ribosome. · Ribosomal RNA A primary component of the ribosome and is responsible for its catalytic activity. TL; DR - Building block of the ribosome (protein factory).

Proteins

· Proteins, also known as polypeptides, are made of monomers known as amino acid chains. · Amino acids are linked together by peptide bonds (to form polypeptides) - polypeptides are linked amino acids. . Polypeptides are synthesised on ribosomes via the process of translation. · Formed by condensation reactions (produces water). . There are 20 different amino acids which are universal to all living organisms. . There are two kinds of amino acids: · Essential: you cannot produce this; can only be acquired through diet. • Non-Essential: can be made by you.

Structure of Proteins

. Polypeptides fold into unique shapes depending on their individual function and needs. · 4 levels of protein structure which are: · Primary - 1º . Describes the order of amino acids in a polypeptide chain. · Formed by covalent peptide bonds between adjacent amino acids. · Controls all subsequent levels of protein structure. · Secondary - 2° . Describes the folding of a chain into repeating arrangements. . Formed by stabilising hydrogen bonds between non-adjacent amino acids. · Sequences may form alpha helices, or beta pleated sheets. . If the above sequences cannot be identified, it is likely to be a random coil. · Tertiary - 3º . Describes the way a chain folds into a 3D shape. · Formed by interactions between variable groups (ionic bonds, H bonds, etc). · Affinity and repulsion between different side chains will affect overall flooding. · Quaternary - 4° · Described the presence of more than one polypeptide chain. . Not all proteins will possess a quaternary structure.

Protein Synthesis

Transcription Process

1. Transcription . The purpose is to synthesise an RNA sequence from a DNA template. . DNA unwinds and unzips with the help of enzymes. . One strand is the template strand, one strand is the complementary. . RNA polymerase binds to the template strand. . The complementary strand is identical to the pre-mRNA that will be formed (exception of thymine and uracil). . RNA polymerase binds to the promoter region with the help of transcription factors. . A promoter, known as the TATA box, signals the start of a gene to transcribe. . Gene sequences exist on both strands, but only the appropriate nucleotide sequence will be transcribed. · The template strand is transcribed. . The complementary strand is not transcribed. TEMPLATE: TAC GGT CAC TGA AGT CCC COMPLEMENTARY: ATG CCA GTG ACT TCA GGG TRANSCRIPT: AUG CCA GUG ACU UGA GGG . The enzyme RNA polymerase is progressively building a complementary RNA strand to the template (reads DNA in a 3' to 5' direction to synthesise it in a 5' to 3' direction - additional note thymine replaced with uracil). . DNA is arranged in an antiparallel direction ensuring the correct strand will be used. . A termination sequence will signal the transcription to stop.

Pre-mRNA Modification

2. Pre-mRNA Modification/RNA Processing . Introns are removed, exons are spliced together. · Done by the process of RNA splicing. . A methyl cap is added to the 5' end and a poly-A tail is added to the 3' end. This is to protect the mRNA from degradation. . Following, pre-mRNA becomes fully mature mRNA. . Then the tail and cap are removed, mRNA can be digested, and the nucleotides can be recycled. . Alternative splicing involves the select removal of exons (in addition to normal removal of introns) and allows for more than one protein to be produced from the same gene. . A single gene can code for more than one polypeptide depending on what exons are kept in, as well as what order the exons are spliced up. . Different combinations form different polypeptides.

Translation Process

3. Translation . The process of translating is producing proteins at the ribosome. · Translation involves a polypeptide synthesis by the ribosomes (i.e., protein production).

Genetic Code

Genes

Gene Expression

Breaking Down RNA Polymerase

Reading Frames

Protein Destinations

Polysomes

Gene Regulation

Gene Loci

Alleles

Mutations

Types of Mutations

Mutagens

Genomes & Proteomes

Coding Versus Non-Coding DNA

Transcription Factors

Nucleosomes

DNA Methylation

Epigenetics

Operons

Trp Operon

2 Scenarios of the Trp Operon

The Leader (trpL)

Attenuation

Lac Operon

Protein Secretory Pathway

Exocytosis

Responsibility and Importance of Organelles

Enzymes

Catalysis

Types of Reactions

Exergonic Reactions

Endergonic Reactions

Substrate-Enzyme Interactions

Specificity

Particle Collision Theory

Factors Affecting Enzyme Activity

Endonucleases

DNA Manipulation

Polymerase Chain Reaction

Gel Electrophoresis

CRISPR-Cas9

Recombination & Transformation

Transforming Bacteria