IB HL Biology Topic D1.1 and 1.2

DNA replication

The process of producing exact copies of DNA with identical base sequences, occurring during the S phase of interphase and necessary for cellular reproduction, organismal growth, and tissue replacement.

DNA Synthesis

The creation of RNA (messenger RNA) as a temporary 'photocopy' of specific genetic instructions, leading to the production of proteins that carry out cellular functions.

Central Dogma of Molecular Biology

Explains the flow of genetic information within a cell, where DNA serves as the master set of instructions, RNA acts as a temporary copy of genetic instructions, and proteins are the products created from these instructions.

DNA

A stable molecule with a conserved sequence throughout a cell's life, replicated only during the S phase of interphase, essential for cellular reproduction, organismal growth, and tissue replacement.

Chromosomes

Discrete structures within cells where a single molecule of DNA is organized, with the number per cell being a characteristic feature of species, and differing in organization between prokaryotic and eukaryotic cells.

Plasmids

Additional DNA molecules found in bacteria that can be transferred between bacterial cells via conjugation using sex pili.

Nucleosomes

DNA wrapped around histone proteins to form a compact structure called chromatin, which can be tightly or loosely packed based on cellular requirements.

Semi-conservative DNA replication

A process where one strand of the new double-stranded DNA molecule is from the original template (conserved), and the other strand is newly synthesized (not conserved).

Complementary base pairing

The accurate pairing of nitrogenous bases during DNA replication, where adenine (A) pairs with thymine (T) via two hydrogen bonds, and cytosine (C) pairs with guanine (G) via three hydrogen bonds.

Helicase

An enzyme that unwinds the double helix and separates the two polynucleotide strands by breaking the hydrogen bonds between complementary base pairs during DNA replication.

DNA Polymerase

An enzyme that synthesizes new DNA strands from parental template strands by aligning free deoxynucleoside triphosphates opposite their complementary bases and linking them to form the new strand.

Polymerase Chain Reaction (PCR)

An artificial method of replicating DNA in the laboratory to amplify large quantities of a specific DNA sequence from a minute sample using temperature variations in a thermal cycler.

Gel Electrophoresis

A technique used to separate DNA fragments based on size and charge by running them through a gel under an electric field, allowing for analysis and comparison of DNA samples.

Elongation

Sample is heated to the optimal temperature for a heat-tolerant polymerase (Taq) to function (~75ºC)

Taq polymerase

Enzyme isolated from the thermophilic bacterium Thermus aquaticus, functions at ~75ºC in PCR without denaturing, extends nucleotide chain from primers

DNA Applications

PCR and gel electrophoresis used in biotechnological applications like DNA profiling, gene cloning, and sequencing via the Sanger method

DNA Profiling

Technique to identify individuals based on unique DNA profiles from short tandem repeats (STRs) in non-coding regions of the genome

Gene Cloning

Isolating and copying a gene of interest to express in a different host organism, involves plasmid vectors and recombinant DNA technology

Genetically Modified Organisms (GMOs)

Organisms created by gene modification, used in agriculture for traits like pest resistance, increased shelf life, and nutrient enhancement

DNA Sequencing

Method using chain-terminating dideoxynucleotides (Sanger method) to determine DNA sequence by fragment length

Directionality of DNA polymerases

DNA polymerases synthesize DNA in a 5' → 3' direction, strands are antiparallel resulting in opposite extension directions

Okazaki Fragments

Short DNA fragments on the lagging strand formed during discontinuous replication, joined by DNA pol I and DNA ligase

DNA Primase

Enzyme that generates RNA primers on template strands for DNA polymerase III to initiate replication

DNA Polymerase I

Enzyme that removes RNA primers from lagging strand and replaces them with DNA nucleotides during replication

DNA Ligase

Enzyme that joins Okazaki fragments by forming phosphodiester bonds between sugar-phosphate backbones

DNA Proofreading

Process by which DNA polymerase III corrects errors during replication by excising incorrect nucleotides and replacing them

Transcription

The synthesis of RNA using a DNA template, mediated by RNA polymerase, where free nucleotides align opposite their exposed complementary base partner and are covalently joined to generate an RNA transcript of the DNA sequence.

Role of hydrogen bonding and complementary base pairing

The segment of double-stranded DNA that codes for an RNA sequence, with the template strand being complementary to the RNA transcript (antisense) and the coding strand being identical to the RNA transcript (sense).

Stability of DNA templates

The conservation of genetic information within a cell, where DNA serves as the master set of instructions, RNA acts as a temporary copy of specific genetic instructions, and proteins are the products created from these instructions.

Gene Expression

The process by which genes are switched on or off through transcription, determining the levels of protein synthesis and controlling cellular activities within a cell.

Translation

The synthesis of polypeptides from mRNA at the ribosomes, where proteins are produced either by cytosolic ribosomes or by ribosomes embedded in the rough endoplasmic reticulum.

Roles of mRNA, ribosomes, and tRNA in translation

Involves three main types of RNA: mRNA (encodes protein sequence), tRNA (carries amino acids to mRNA), and rRNA (provides catalytic activity for combining amino acids).

Complementary Base pairing between tRNA and mRNA

The reading of the base sequence of an mRNA molecule by the ribosome in triplets of bases called codons, with tRNA molecules bringing amino acids to the ribosome based on complementary sequences (anticodons) to the codons.

Features of the genetic code

The genetic code is universal across almost all living organisms, with codons coding for specific amino acids and degeneracy occurring where more than one codon codes for a single amino acid.

Genetic Code

Set of rules converting mRNA sequences into amino acid sequences

Degeneracy

Multiple codons coding for a single amino acid, mainly in the third base

Silent Mutations

DNA sequence changes not altering the polypeptide sequence

Start Codon

Codon (AUG) initiating translation

Stop Codon

Codon terminating translation

Peptide Bond

Bond linking amino acids in a polypeptide chain

Mutations in Protein Structure

Changes in nucleotide sequence altering protein structure

Sickle Cell Anaemia

Genetic disease from a point mutation causing abnormal haemoglobin

Promoter

Upstream non-coding sequence initiating transcription

Coding Sequence

Region of DNA transcribed into RNA by RNA polymerase

Terminator

Sequence signaling the end of transcription

Non-coding DNA

Majority of human genome not encoding polypeptides

Telomeres

Repetitive sequences at the ends of chromosomes that prevent chromosomal deterioration during replication.

Introns

Non-coding sequences within eukaryotic protein-encoding genes that are removed during RNA processing.

Non-coding genes

Genes that produce RNA sequences not coding for proteins, such as tRNA and rRNA genes.

Gene regulatory sequences

Sequences that moderate transcriptional activity, like enhancer and silencer sequences.

Capping

Addition of a methyl group to the 5'-end of transcribed RNA to protect against degradation and aid in recognition by translational machinery.

Polyadenylation

Addition of a poly-A tail (long chain of adenine nucleotides) to the 3'-end of RNA transcript to enhance stability and facilitate nuclear export.

Splicing

Process of removing introns from eukaryotic genes to form mature mRNA by fusing exons together.

Alternative splicing

Process where specific exons are selectively removed, resulting in different polypeptides from a single gene sequence.

Initiation of translation

The start of polypeptide synthesis involving binding of ribosomal subunits, initiator tRNA recognition of start codon, and formation of ribosomal complex.

Elongation

Process where ribosome sequentially adds amino acids to a growing polypeptide chain during translation.

Translocation

Movement of ribosome along mRNA strand by one codon position, involving tRNA movement and peptide chain transfer.

Termination

End of translation where ribosome reaches a stop codon, releasing the polypeptide and disassembling.

Protein Modification

Covalent changes to proteins post-translation, including disulphide bridges, conjugation, chemical modifications, and proteolytic cleavage.

Proteasomes

Protein complexes that degrade unneeded proteins by breaking peptide bonds, helping regulate protein levels and recycle amino acids.

Ubiquitin

Small protein tagging proteins for degradation by proteasomes.

Functional proteome

The totality of cellular proteins sustained by proteasomes through protein breakdown and amino acid recycling.