Biology Topic 2: Nucleic acids and proteins

• The DNA within the nucleus carries the instructions for the cell's structure and function. This involves producing proteins.
• Ribosomes are made in the nucleolus (a dense region within the nucleus.)
• Proteins are made out side the nucleus by ribosomes. These may be free in the cytoplasm or associated with the rough endoplasmic reticulum.
• Internal defense: Antibodies (immunoglobins) are Y shaped proteins that protect the body by identifying and killing disease-causing organisms like bacteria and viruses. Example: IgA is found in the gut and airways to destroy disease-causing organisms
• Catalytic: chemical reactions that require a catalyst to proceed at a faster rate. Ending 'ase' indicates an enzyme. For example, Amylase is an enzyme that breaks down starch into sugars in the first stage of digestion.
• Regulation: Regulatory proteins such as hormones act as signal molecules to control biological processes and coordinate responses in cells, tissues, and organs. For example, Oestrogen is a hormone that is critical for reproduction in females, this hormone increases during pregnancy to maintain a healthy pregnancy.
• Transport: proteins can carry substances across membranes or around the body. In blood (haemoglobin), they transport and store oxygen.
• Structural: structural proteins form fibers which give strength and support to tissues. Collagen is a protein that forms strong fibres in connective tissue. It provides structure and strength to skin, bones, tendons, ligaments, cartilage, and teeth.
• Movement: contractile proteins are involved in movement of muscles and form the internal supporting structures of the cell. Example: Actin and Myosin are two proteins that work together to bring about contraction (movement) in all the muscles.
• The four structural levels of proteins are: Primary structure, Secondary structure, Tertiary structure, and Quaternary structure.
• Primary structure is the most basic level and it describes the sequence of amino acids that make up the protein.
• Secondary structure is the very basic fold the polymer makes through hydrogen bonding between amino acids.
• Two structures can be formed depending on their shape: a-helices and B-sheets.
• Tertiary structure is when the protein starts to fold up due to ionic bonding, hydrogen bonding, covalent bonding, or hydrophobic interactions between R groups on the amino acids.
• Quaternary structure occurs when more than one polypeptide chain comes together to make a bigger protein.
• Amino acid structure

  A) amino

  B) side chain

  C) carboxyl

  
• • The reaction that joins amino acids to form a polypeptide is a Condensation Polymerisation reaction. 
  • The carboxyl group of one amino acid is joined to the amino group of another forming a peptide bond
  • This process releases water (condensation)
  • This process requires an input of energy (anabolic)
• Condensation polymerisation diagram

  A) OH

  B) H

  C) H2O

  
• Nucleotide structure

  A) phosphate group

  B) pentose sugar

  C) nitrogenous base

  
• • DNA – deoxyribonucleic acid (double helix)
  • RNA – ribonucleic acid (single stranded)
  • These structures are large, linear polymers.
  • The monomer (building blocks) of these strands are called nucleotides
  • The joining of nucleotides to form nucleic acids is another example of a condensation polymerisation reaction.
• • mRNA: messenger strand made in the nucleus that carries the information for protein synthesis to the ribosomes
  • rRNA: strand of RNA which is synthesised in the nucleolus and binds to protein within the cell to form Ribosomes
  • tRNA: attached to specific amino acids and is involved in transporting them to the ribosome during protein synthesis
• Upstream and downstream are used to describe the positions of regions in the DNA strand

  Upstream refers to anything that is positioned before a region of the DNA

  Downstream refers to anything that is positioned after a region of the DNA
• Transcription

  • Creates a complementary strand of mRNA from the DNA template strand.
  • RNA polymerase binds to the promoter region and travels along the DNA unwinding sections, exposing the bases.
  • RNA polymerase joins RNA nucleotides in a chain, complimentary to the template strand of DNA, using Uracil instead of Thymine.
  • RNA polymerase travels along the DNA until it reaches the termination sequence.
• VCAA expectation: Transcription

  • DNA unwinds/unzips
  • RNA polymerase catalyses transcription through the joining of complementary RNA molecules
  • transcription of the DNA template strand into pre-mRNA occurs
  • in the pre-mRNA, adenine (A) pairs with uracil (U), not thymine (T)
• mRNA editing

  • The single-stranded mRNA made during transcription is called “pre-mRNA”
  • Before mRNA leaves the nucleus it is modified  - a methyl cap is added to the 5’ (phosphate) end and a poly-A tail (stack of adenine nucleotides) is added at the 3’ end. 
  • Sections of the mRNA called introns are removed. 
  • Exons are spliced together to form mature mRNA.
  • mRNA passes through nuclear envelope via active transport.
• Translation

  • Translation is the process that uses mRNA to make a polypeptide chain. 
  • Occurs at ribosomes (either free or attached to ER).
  • mRNA molecule has the instructions for which amino acid is added to the polypeptide chain. The codon (3 base sequence) on the mRNA signals which amino acid is needed.
  • Transfer RNA molecules(tRNA) carry specific amino acids to the ribosomes 
• VCAA expectation: translation

  • ribosome binds to and reads the mrna molecule
  • trna anticodons are complementary to the mrna codons
  • trna brings the corresponding amino acid to the ribosome
  • adjacent amino acids are joined together into a polypeptide chain via condensation reaction
• To create protein from genetic information, a cell must undergo a series of steps. The first is transcription, where the DNA template strand is read and transcribed into pre-mrna. However, it must be processed before translation by splicing introns and the addition of a 5’ methyl-G cap and a 3' poly-A tail. The mRNA can now be translated. This is possible due to its sequences of three nucleotides in the mRNA known as codons. At the ribosome, mRNA is used to create a protein.
• Translation occurs at a ribosome, where the ribosome binds to the mRNA strand and reads it. The process is facilitated by tRNA molecules and their tri-nucleotide sequences known as anticodons. Amino acids delivered by tRNA molecules are linked into a polypeptide chain until a Stop codon is reached and translation is terminated.
• The are two types of genes involved in gene regulation

  • Structural genes: part of the DNA that codes for proteins needed by the organism to function

  Regulatory genes: part of the DNA that produces proteins that control the expression of other genes.  Regulatory proteins include repressor proteins which stop or slow down gene expression, or activator proteins that increase gene expression
• An operon is defined as a set of adjacent genes and the nearby regulatory sequences that affect transcription of the genes.

  Promoter: section of DNA where RNA polymerase binds and transcription begins

  Operator: section of DNA where proteins that control transcription bind (transcription factors)
• • The trp operon, found in E. coli bacteria, is a group of genes that code for enzymes that make the amino acid tryptophan and the regulatory sequences that control their expression.
  • The trp operon is expressed (turned "on") when tryptophan levels are low and repressed (turned "off") when they are high.
  • The trp operon is regulated by the trp repressor protein. When bound to tryptophan, the trp repressor blocks expression of the operon.
• The protein secretory pathway involves various different organelles that produce, fold, modify, and package proteins, eventually exporting them from the cell via the process of exocytosis.
• Proteins are produced at ribosomes, folded in the rough endoplasmic reticulum, transported via transport vesicles to the Golgi apparatus, where they are modified and packaged into secretory vesicles, and then subsequently exported from the cell via the process of exocytosis. Exocytosis is a form of bulk transport, involving the fusion of a secretory vesicle with the plasma membrane, releasing its contents into the extracellular environment.
• Nucleic acid

  • unbranched polymers composed of nucleotide monomers
  • DNA - double helix structure, twisted latter shape of two nucleic strands (Adenine, Thymine, Cytosine, Guanine)
  • RNA - single nucleic strand (Adenine, Uracil, Cytosine, Guanine)
• The region where enzymes bind to on the operon, during gene regulation

  A promoter, as related to genomics, is a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene. The resulting transcription produces an RNA molecule (such as mRNA).
• Introns: non-coding sections of a gene that do not remain in the mature-mRNA sequence as they are removed during RNA processing.

  Exons: coding sections of a gene that are spliced together to form a mature-mRNA sequence that is ready for translation.
• Proteins that catalyse reactions/makes them occur at a faster rate. Enzymes lower the activation energy (the energy required to initiate a reaction) in a chemical reaction. However enzymes do not participate in the reaction (they do not occur at reactants or products). 

  Enzymes are reusable, specific, reversible, speed-up not create, have an active site, are proteins, are a subset of catalyst, act on entire biochemical pathways, end in ‘ase’, and are shown above the arrow in a chemical reaction.
• Catabolic reactions release energy while breaking down larger molecules into smaller ones.

  Anabolic reactions use energy to synthesise larger molecules from smaller units.
• Structural genes are responsible for producing proteins that are involved in the structure or function of a cell. For example, they may code for enzymes, transport proteins, receptors, or peptide hormones. These genes are often found downstream (towards the 3’ end of the coding strand) of the regulatory gene that controls them.