Chapter 2 - nucleic acids and proteins

Amino acids

The building blocks of proteins

Polypeptide chain

A polymer of amino acids.

Proteome

The complete collection of proteins in a space

Proteins

Large complex structures which serve a variety of purposes

Enzymes

Molecules that speed up chemical reactions

Transport proteins

Control entry and exit of substances within a cell

Structural proteins

Support cell and tissue shape

Hormones

Chemical messengers to communicate and make changes in cells

Receptors

Receive signals from the environment

Defence proteins

Recognising and destroying pathogens

Motor/contractile proteins

Movement of muscles, internal cell contents, movement of cilia and flagella

Storage proteins

Reserves for metal ions and other molecules

Amino acid structure

Chemical structure: central carbon atom, carboxyl group, amino group, R-group, hydrogen atom

Primary structure

Sequence of amino acids in a polypeptide chain

Secondary structure

Amino acid chains form either alpha helix, beta pleated sheets, or random coils

Tertiary structure

The functional 3D shape of a polypeptide chain.

Quaternary structure

Where multiple polypeptide chains bond together, or other non-protein groups are added to form a fully functional protein.

RNA polymerase

Enzyme that synthesizes RNA from DNA template

Haemoglobin

Protein responsible for carrying oxygen in red blood cells

Protein

A polymer made of amino acid chains

Polypeptide

A long chain of amino acids

Enzyme

A molecule that speeds up specific reactions

Antibody

A protein produced by plasma cells during the adaptive immune response that is specific to an antigen and combats pathogens, also known as immunoglobulin

Amino group

The functional group of amino acid molecules that is made up of one nitrogen and two hydrogens (NH2)

Hydrophobic

Repels water

Hydrophilic

Attracts and dissolves in water

Monomer

A molecule that is the smallest building block of a polymer

Polymer

A large molecule made up of small, repeated monomer sub units

Peptide bond

The chemical bond between two amino acids

Alpha helix

An organised coiled secondary structure of proteins

Beta pleated sheets

An organised folded secondary structure of proteins

Random coil

Irregular secondary structure of proteins, neither an alpha helix or a beta pleated sheet

Disulphide bond

Strong covalent bond between two sulphur atoms

Prosthetic group

A non protein group bound to a protein, eg a vitamin or ion

Nucleic acids

Two types of nucleic acids - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

Nucleotide

Every nucleotide contains: phosphate group, 5 carbon sugar, nitrogenous base

Sugar phosphate backbone

The structural framework of nucleic acids, formed by alternating sugar and phosphate groups

Messenger RNA (mRNA)

Carries genetic information from nucleus to ribosomes for protein synthesis

Transfer RNA (tRNA)

Delivers specific amino acids to the ribosome after recognising specific nucleotide sequences on mRNA

Ribosomal RNA (rRNA)

Serves as the main structural component of ribosomes within cells

DNA

Double stranded nucleic acid that contains deoxyribose sugar, nucleotides ATGC, and is inherited for long term storage

RNA

Single stranded nucleic acid that contains ribose sugar, nucleotides AUGC, and is temporary, short-lived molecules

Universal genetic code

The same codons specify the same amino acids in almost all living organisms

Degenerate genetic code

Multiple different codons may code for the same amino acid

Transcription

The process where DNA triplets are used as a template to produce mRNA codons

Translation

The process where mRNA codons are used to code for specific amino acids within a polypeptide chain

Promoter

Upstream binding site for RNA polymerase, indicates the starting position and direction of transcription

Introns

Regions of non coding DNA that don't contribute to the final proteins

Exons

Regions of coding DNA which are transcribed and translated into the final protein

Operator

Serves as the binding site for repressor proteins which can then stop gene expression

Codon

3 bases in mRNA are known as a codon

Anticodon

3 bases in tRNA are known as an anticodon.

Genes

Sections of DNA that code for protein

Template Strand

The strand of DNA that RNA polymerase uses to transcribe RNA.

Pre-mRNA

The immediate product of transcription.

RNA Processing

Modifies pre-mRNA into mRNA.

Splicing

Removal of introns and joining of exons in pre-mRNA.

Alternative Splicing

A process where exons can be removed, allowing one pre-mRNA strand to produce many different mRNA molecules.

Ribosome

Assembles the protein using mRNA as instructions.

tRNA

Delivers the correct amino acid to the ribosome.

Peptide Bonds

Bonds that join amino acids together via a condensation reaction.

Gene Expression

The process of reading information stored within a gene to create a functional product (e.g., a protein).

mRNA

RNA molecules that are produced during transcription and carry genetic information from the nucleus to the ribosomes

rRNA

RNA that makes up ribosomes which assemble proteins

Structural gene

responsible for producing proteins that play a role in the structure/function of a cell

Regulatory gene

responsible for coding for proteins and other small molecules that control the expression of structural genes.

Repressor proteins

Can prevent/control the expression of structural genes

Activator proteins

Can increase the expression of structural genes

Operon

a group of related structural genes under the control of a single promoter - mainly in prokaryotes

trp operon

a group of genes that work together to produce tryptophan in bacteria

Repression

responds to the intracellular concentration of tryptophan

Attenuation

responds to the amount of tRNA bound tryptophan

Exocytosis

A secretion vesicle containing secretory products is transported to the plasma membrane.

Protein secretory pathway

The process involving ribosomes, rough ER, transport vesicles, Golgi apparatus, and secretory vesicles in the export of proteins from a cell.

Rough ER

Folds and transports proteins; ribosomes are usually attached to ER, making it rough.

Transport vesicle

Transports proteins; buds off of the rough ER and travels to the Golgi apparatus.

Golgi apparatus

Modifies and packages proteins; can add or remove chemical groups.

Secretory vesicle

Contains proteins for export; buds off the Golgi apparatus and travels through the cytoplasm.