U3 Chapter 2 Nucleic acids and proteins

Protein

• diverse group of molecules with various functions in a cell

• made up one or more polypeptides that fold into a functional structure

polypeptide

• (polymer)

• large structure made up of amino acids (monomers), bound together via peptide bond

monomers

• small, repeating units that built up large polymers through a process called polymerization

• amino acids —>polypeptides, nucleotides —> nucleic acids, monosaccharides —> polysaccharides

polymers

• large molecules made up of repeating monomers linked together

• eg. proteins (polymer of amino acid), nucleic acids, polymer of nucleotideslarge macromolecules formed by the polymerization of monomers, such as proteins and nucleic acids.

polymerization

• process of linking monomers to form polymers

• eg. amino acids —> polypeptides, nucleotides —> nucleic acidsthe chemical reaction that joins monomers together to create larger macromolecules.

biomacromolecule

• large biological molecules made up of monomers that perform essential functions in living organisms

• eg. proteins, nucleic acids, carbohydrates

nucleotides

• monomers of nucleic acids

  • phosphate group

  • five-carbon sugar

  • nitrogenous base

proteome

all the proteins that are expressed by a cell or organism

proteomics

• study of the structure and function of proteins as well as the way they function and interact with each other

proteomics is used in

• medical diagnosis

• producing monoclonal antibodies to treat cancer or viruses

• design drugs to treat various conditions

diversity of proteins

transport proteins, receptors, enzymes, antibodies, hormones, structural proteins

transport proteins

facilitated diffusion

receptors

signal transduction

enzymes

biological catalysts that speed up chemical reactions

antibodies

defends against foreign pathogens

hormones

signals between different cells or cause stimulation or inhibition

structural proteins

provides strength, support and protection

amino acids

• 20 different types of amino acids - 9 are essentials (not made by the body)

amino acids are made up of:

• carboxyl group (COOH)

• amino group (NH2)

• R group (determines the type of amino acid)

R group

• each R group has unique chemical properties that influence the interactions between amino acids within a protein

• hydrophobic R group: form bonds with other hydrophobic amino acids

• hydrophilic R groups: form bonds with other hydrophilic amino acids

synthesis of proteins

• amino acids are joined together by peptide bonds in a condensation polymerisation reaction which involves the removal of water

• a polypeptide chain forms (primary structure)

primary structure

• polypeptide chains of amino acids held via peptide bonds

• formed when amino acids are joined together through a condensation reaction

• produced in ribosomes through translation

secondary structure

• formed when a polypeptide chain fold and coils forming hydrogen bonds between amino acids

  • alpha helix coils

  • beta pleated sheets

tertiary structure

• functional 3D shape of a protein

• when secondary folds further by forming interactions and bonds between R-groups

• these interactions are:

  • disulfide bonds (strong)

  • weak hydrogen or ionic bonds

  • hydrophobic interactions

quaternary structure

formed when two or more polypeptide chains with tertiary structures join

***not all proteins will have a quaternary structure

changes to protein structure

• The folding of a protein is dependent on the sequence of amino acids in a primary structure

• One change in the amino acid sequence, forms a different protein or may not be functional at all

• Proteins can also be denatured when subject to high temperatures or extreme pH levels.

nucleic acids

organic biomacromolecules composed of repeating units called nucleotides

• DNA (deoxyribonucleic acid)

• RNA (ribonucleic acid)

how are nucleotides linked in a chain

• The phosphate group attaches to the 5' carbon of the sugar, while the nitrogenous base attaches to the 1' carbon. The 3' carbon attaches to the next nucleotide (on its 5’) via a phosphodiester bond.

phosphodiester bond

strong covalent bond that links the phosphate group of one nucleotide to the sugar of the next nucleotide

DNA

• found in the nucleus of eukaryotes

• In humans, DNA is organized into 46 chromosomes, each containing thousands of genes.

• Genes carry the instructions for protein production.

structure of DNA

• Two strands of multiple nucleotide chains running antiparallel (5' to 3' in one direction, 3' to 5' in the other).

• Strands are held together by hydrogen bonds between complementary nitrogenous bases:

  • Adenine (A) pairs with Thymine (T)

  • Cytosine (C) pairs with Guanine (G)

triplet

three bases in DNA read together

RNA

• single-stranded nucleic acid containing ribose sugar

• Thymine (T) is replaced by Uracil (U), which pairs with Adenine (A).

types of RNA

• mRNA (messenger RNA)

• tRNA (transfer RNA)

• rRNA (ribosomal RNA)

mRNA

• Formed in the nucleus through transcription

• Carries genetic information from the nucleus to the ribosomes for translation (protein synthesis)

• Three bases are read together and is known as a codon.

• must always start at 5’

tRNA

• Once an mRNA molecule binds to the ribosomes, it is read, and tRNA delivers individual amino acids to begin forming a polypeptide chain.

• Made up of 3 nucleotides and is known as an anticodon.

rRNA

• Serves as the main structural component of ribosomes within cells.

• rRNA folds into small subunits to make up a ribosome.

transcription

• RNA polymerase to create a pre-mRNA molecule in the nucleus

• thymine is replaced by Uracil

• initiation, elongation and termination

initiation (transcription)

• Transcription factors bind to the promoter region to initiate transcription

• RNA polymerase binds to the promoter region which signals the weak Hydrogen bonds between the nitrogenous bases to break. This unwinds the DNA strand

• Results in bases of the DNA stand to be exposed.

elongation (transcription)

• RNA polymerase moves along the template strand of DNA in a 3’ to 5’ direction

• As it moves along, complementary RNA nucleotides are added to produce a pre-mRNA molecule

termination (transcription)

• Transcription ends when RNA polymerase reaches the termination sequence

• Signals the pre-mRNA molecule to be released for processing

• DNA molecule winds up and hydrogen bonds reform between the strands

processing of pre mRNA into mRNA

• Post transcriptional modifications:

  • Remove introns (non-coding regions)

  • Splicing exons (coding regions) of the mRNA molecule together

  • Adding a methyl cap to the 5’ end of the mRNA molecule, allowing it to bind to the ribosomes during translation

  • Adding a poly A tail to the 3’ end of the mRNA molecule, stabilising the molecule to prevent it from degrading

• Matured mRNA molecule exits the nucleus to the ribosomes for translation

alternative splicing

• 1 gene = multiple proteins

• Involves splicing a pre-MRNA in different ways, resulting in a different protein produced

translation

• reading the mRNA molecule produced in transcription and producing a polypeptide chain of amino acids

• initiation, elongation and termination

initiation (translation)

• 5’ end of mRNA molecule attached to the ribosome

• Start codon (AUG) is read then a tRNA molecule with the complementary anticodon (UAC) binds to the ribosome to deliver the amino acid methionine

elongation (translation)

• Next codon is read, and the complementary TRNA molecule delivers a specific amino acid to the ribosome

• Amino acid will bind to the adjacent amino acid and form a peptide bond

• Process continues and a growing polypeptide chain of amino acids is produced

termination (translation)

• Once the STOP codon is read, this signals the end of translation

• There is no tRNA molecule that corresponds with the STOP codon

• Instead, a release factor binds to release the polypeptide chain of amino acids for modification

organelles related to transcription and translation

RER, Golgi apparatus, Vesicles and Mitochondria

codon chart

• used to determine the amino acid

• stop codon is not an amino acid (only conveys msg to STOP)

• start codon is an amino acid

• all polypeptide chains will have a start and stop codon

features of genetic code

universal, unambiguous, degenerate, non-overlapping

universal

nearly all living organisms use the same codons to code for specific amino acids

unambiguous

each codon is only capable of coding for one specific amino acid

degenerate

multiple codons may code for the same amino acid

• eg. UUA, UUG, CUU, CUC all code for leucine

• means that if a mutation occurs in the genetic code, the protein may not change

non-overlapping

each triplet or codon is read independently without overlapping from adjacent triplets or codons

promoter region

• starting position and decides direction of transcription

  • must be where the 3’ is and hold the start triplet

• RNA polymerase binds to it and starts copying after the TATA box allowing for transcription

• sequence of DNA to which RNA polymerase binds

TATA box

• series of TATATATA before a G

  • message to signal that it is the starting region

operator region

a short region of DNA that is the binding site of repressor proteins which can then inhibit gene expression

• found in prokaryotes

RNA polymerase

enzyme - reads in 3’ to 5’ direction (can be read left to right or right to left)

start triplet

• TAC

• where RNA polymerase begins copying the gene into an mRNA molecule

template strand

the strand to be copied

exons

• coding region of a mRNA

  • transcribed and translated into the final protein

• they go out of the nucleus

introns

non-coding regions of a gene (don’t contribute to final protein) that must be removed but stay in the nucleus

• only in eukaryotes

leader region

critical role in regulation of gene expression in prokaryotes

• found upstream of exons and downstream of Promoter and operator regions

termination sequence

sequence of DNA that codes for the termination of transcription

exocytosis

• a form of bulk transport. ATP is required - active transport (mitochondria)

  • Vesicle containing secretory products is transported to the plasma membrane.

  • Membrane of the vesicle fuses with the plasma membrane.

  • secretory products are released from the cell into the extracellular environment

key organelles in the protein secretory pathway

ribosome, rough endoplasmic reticulum, transport vesicle, golgi apparatus, secretory vesicle

ribosome

• site of protein synthesis

• assemble polypeptide chains from amino acids by translating mRNA

rough endoplasmic reticulum

processes, folds and transports proteins

transport vesicle

contains the proteins and buds off the rough er and travels to the golgi apparatus. It fuses with the Golgi membrane and releases the protein

golgi apparatus

modifies and packages proteins into secretory vesicle for export or directly releases it into the cytosol

secretory vesicles

transports proteins and releases the proteins within into the extracellular enviro via exocytosis

structural genes

• code for proteins involved in structure or function of an organism

  • eg. enzymes, protein channels, hormones

regulatory genes

• code for proteins that influence the expression of structural genes

what are regulatory genes responsible for?

• Turning genes on or off

• Increase or decrease the expression of a gene

• Control alternative splicing

tryptophan

• regulator of homeostatic mechanisms in E. coli, helping to maintain balance and stability within the cell.

• the production of tryptophan is switched on or off based on its levels

structural genes in tryptophan production

• Bacterial cells regulate tryptophan production by activating specific genes. The order of structural genes is E, D, C, B, and A.

• The operator region is located prior to trpA.

• The promoter region is also upstream of trpA

high tryptophan

1. A repressor (regulatory gene) protein is transformed.

2. The repressor binds to tryptophan, becoming an active repressor

3. This complex then binds to the operator region (where the active repressor binds to inhibit transcription)

4. This action blocks the promoter region, preventing RNA polymerase from binding and initiating transcription.

5. As a result, the transcription of genes needed to produce tryptophan is stopped.

low tryptophan

1. No tryptophan present in the cell, therefore unable to activate repressor – inactive repressor

2. RNA polymerase is able to transcribe trp E, D, C, B, A to produce tryptophan

attenuation

• in response to the amount of tRNA-bound tryptophan

  1. RNA polymerase runs along the leader and transcribes into mRNA. At the same time, a ribosome translates the mRNA to create a polypeptide chain

  2. When the ribosome reaches the UGG code for tryptophan, tRNA with tryptophan joins to the polypeptide chain

  3. Once the ribosome reaches the STOP codon, RNA polymerase continues to read the DNA, however the ribosome stops translating the mRNA. This causes region 3 and 4 to pull and form a “hairpin”. RNA polymerase therefore stops reading after the attenuated region.