*Cellular Control

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Gene Mutations

MUTATION = a random change to the sequence of bases of DNA. Involve changes to the STRUCTURE/NUMBER of chromosomes

GENE MUTATION = an alteration in the sequence of bases for one gene. Arise SPONTANEOUSLY in DNA replication, or by MUTAGENIC AGENTS (chemical/biological/physical) - x-rays, smoking etc.

DNA molecules are fairly STABLE + fairly resistant to corruption of genetic info in it.

Mutations associated with mitosis = SOMATIC MUTATIONS (not inherited by offspring) eg. cancers

Mutations associated with MEIOSIS + gamete formation can be inherited

2 main classes of DNA mutation = POINT MUTATIONS (a change to a single nucleotide base - substitutions), INSERTION/DELETION (INDEL) mutations = one or more nucleotides inserted/deleted - causes a FRAMESHIFT

POINT MUTATIONS

SILENT MUTATION (no change to primary structure of polypeptide as genetic code is DEGENERATE)

MISSENSE MUTATION (change to a single amino acid - change to the primary structure leads to change in tertiary structure - shape altered so may not carry out usual function) - SICKLE CELL ANAEMIA

NONSENSE MUTATION (new amino acid is now a stop codon, so translation stops at site of mutation -> TRUNCATED PROTEIN that won't function) eg. DUCHENNE MUSCULAR DYSTROPHY

INDEL MUTATIONS = frameshift mutations - base is lost/inserted. Genetic code = NON-OVERLAPPING and read in 3's so all the SUBSEQUENT base triplets are altered (primary + tertiary structure much altered - protein can't carry out normal functions)

DELETION = the removal of a single nucleotide base. If a triplet removed, loss of an AMINO ACID (not frameshift)

INSERTION = the addition of a single nucleotide base. If triplet inserted, extra amino acid (not frameshift)

Reading frame = way of dividing sequence of nucleotides on DNA/RNA into triplets

Downstream = in a frameshift mutation, every amino acid DOWNSTREAM is changed

Mutations can be HARMFUL (sickle cell anaemia), BENEFICIAL (melanin in skin, blue eyes) or NEUTRAL (different shaped earlobes)

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Regulating Gene Expression

Needed as some proteins are needed all the time (insulin, enzymes for metabolism), and some are only needed at certain times, by certain cells (eg. some ezymes)

PRE-TRANSCRIPTIONAL REGULATION (mostly eukaryotes): gene expression should only happen during a proportion of interphase + genes shouldn't be able to be accessed at other times eg. mitosis. DNA in chromatin complex, wound around histone proteins = EUCHROMATIN. DNA SUPERCOILS in prophase -> CHROMATIN REMODELLING - produces HETEROCHROMATIN (tight structure) that RNA polymerase can't access, so no transcription.

DNA = -ve charge, Histones = +ve charge. HISTONE MODIFICATION = addition of molecules to the histone, resulting in a CHARGE SHIFT -> leads to tighter/looser coiling (affects gene ACCESSIBILITY)

TRANSCRIPTIONAL REGULATION (LAC OPERON) = genes are turned on/off. PROMOTER = RNA polymerase binds here for transcription. TRANSCRIPTION FACTORS = proteins that help RNA polymerase to bind (ACTIVATORS) or hinder it (REPRESSORS).

OPERON = a group of genes functioning as a single transcription unit

E coli usually metabolises GLUCOSE for respiration. In absence, LACTOSE is used (glucose + galactose). Enzymes are needed for the absorption/hydrolysis of both. Lactose induces the production of LACTOSE PERMEASE and LACTASE (B-galactosidase)

IN THE PRESENCE OF GLUCOSE = Regulatory gene is transcribed and translated, coding for a REPRESSOR PROTEIN, that binds to the OPERATOR , preventing RNA polymerase from binding to promotor so NO transcription of genes coding for lactase and lactose permease (not needed)

IN THE PRESENCE OF LACTOSE, AND ABSENCE OF GLUCOSE = lactose binds to repressor protein, changing its SHAPE so cant bind to operator. RNA polymerase binds to promoter. Transcription of structural genes lactase and lactose permease occurs -> lactose INDUCES enzymes needed

Transcription factors = short, non-coding pieces of RNA

POST TRANSCRIPTIONAL REGULATION (mRNA modified). Exons = protein-coding regions of a gene, Introns = non-protein coding regions of a gene (important in gene expression). mRNA after transcription = pre/primary mRNA (includes introns).

For mRNA to be functional, RNA introns must be removed by SPLICING (catalysed by nucleus spliceosome).

PRIMARY STAGE = introns spliced out (snRNP's bind to introns, causing it to FOLD, bringing the 5' and 3' exons closer together)

SECONDARY STAGE = mRNA is CAPPED and TAILED to stabilise it for cytoplasm. Exons covalently bond, ENDONUCLEASE ENZYME may be involved.

TRANSLATIONAL REGULATION (translation stopped/started)= an INHIBITORY protein may bind to the mRNA, preventing it from binding to ribosome, preventing translation. Production of INITIATION FACTORS may aid binding of mRNA to ribosome

POST-TRANSLATIONAL REGULATION: (activating the proteins): Methods of protein modification (all lead to shape changes, altering the function):

Addition of non-protein groups eg. carbohydrates

Modification of amino acids so protein bonds eg. disulfide bridges

Folding/shortening of protein

Activation of the protein eg. by cyclic AMP, which alters the tertiary structure. Some proteins aren't functional after synthesis, and need activation

cAMP process (second messenger involved in activation):

Non-steroid hormone eg. adrenaline (1st messenger) binds to receptor protein

1st messenger activates an EFFECTOR (eg. a G protein)

G - protein activates 2nd messenger - conversion of ATP to cAMP by activating ADENYL CYCLASE ENZYMES

cAMP can act directly on another protein OR activates a cascade of intracellular enzyme-controlled reactions. Can activate tertiary structures or PROTEIN KINASES for PHOSPHORYLATION (most enzymes are phosphorylated to activate them.) Protein kinases are enzymes that catalyse the addition of phosphate to the protein -> changes the BONDING, so the protein SHAPE (phosphorylation may cause it to enter nucleus + act as a transcription factor)

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Body Plans and the Homeobox

In multicellular organisms, growth and development is controlled and coordinated so cells/tissues/organs grow in the right places.

Development of a zygote to a multicellular organism: MITOSIS, CELL DIFFERENTIATION, MORPHOGENESIS (process causing organisms to develop their shape)

MORPHOGENESIS = regulation of the pattern of development, following a strict body plan, also controlled by regulating gene expression

Genes involved in body development can be activated by other genes. Eukaryotes = expression of certain genes have consequences in expression of others.

HOMEOBOX (HOX GENES IN HUMANS/animals) GENES can SWITCH other genes on/off!

HOMEOBOX GENES = control the body plan. They're 180 base pairs long (excluding introns) that code for small protein transcription factors (60 amino acids long), called a HOMEODOMAIN SEQUENCE, that cam fold + bind to DNA, switching on/off many genes (regulatory genes)

Homeobox genes are HIGHLY CONSERVED between species (animals, plants, fungi)

HOMEOBOX SEQUENCE = the part of the homeobox genes that codes for the homeodomain.

HOMOEDOMAIN = highly conserved sequence of amino acids in all homeobox proteins, binding to DNA + regulating transcription of DEVELOPMENTAL GENES

The transcription factor (homeodomain) binds to the operator, to control transcription of developmental genes (can activate/repress)

Homeobox genes control: polarity of body, polarity of segments + development of individual segments. Homeobox genes can mutate in a species

Body Plans and Apoptosis

Mitotic cell divisions, whilst developing + growing, are regulated with Homeobox/Hox genes (ensures each new daughter cell contains full genome + is a clone of the parent cell)

Normal body cells divide a certain number of times (50) before undergoing programmed cell death.

NECROSIS = traumatic cell death due to invasion/damage of pathogens, releasing hydrolytic enzymes

APOPTOSIS = programmed cell death, occuring after multiple mitotic divisions (shows 'blebbing')

Apoptosis can be stimulated by EXTERNAL STIMULI (eg. stress, lack of nutrients) or INTERNAL STIMULI (DNA damage, cell cycle checkpoints). Too much apoptosis = cell loss + tissue degredation, too little apoptosis = tissue accumulation (cancer)

PROCESS OF APOPTOSIS:

Enzymes break down cell cytoskeleton

Cytoplasm becomes dense, with tightly packed organelles

Chromatin condenses + nuclear envelope breaks

DNA and organelles break down

'Blebs' form in cell membrane

Cell breaks into vesicles (apoptotic bodies), which are PHAGOCYTOSED

Reasons for apoptosis = allows 'digits' to form (removes webbing), removes ineffective/harmful T-lymphocytes as immune system develops, tadpoles lose tails when turning into frogs, when cells get too old

Mitosis + apoptosis = controlled by Hox genes. Mitosis, differentiation, morphogenesis and apoptosis shape organisms.