Gene Expression

explain why: organism's genotype (DNA) is not the only factor influencing gene expression and the resulting phenotype

-gene expression and phenotype of an organism results from interaction between the genotype + environment -environmental factors that exist internally/externally can change an individual's phenotype without changing the genotype (thus the changes to phenotype are not inheritable) -environmental factors can influence gene expression by limiting/changing the potential genotype expression w/o altering phenotype

describe: RNA structure + location

-found in nucleus/cytoplasm of cell -RNA is a single stranded polymer of repeating sub-units called nucleotides -nucleotides have a ribose sugar and phosphate that make up backbone of single strand, with a nitrogenous base joined to each sugar

describe: the effect of a mutation at the start of a gene/protein

-frameshift mutations near the start of the gene/protein will have a bigger impact on the final protein ->more amino acids coded for below mutation are likely to be different -->more of protein structure will be altered (especially if an early stop codon occurs, so amino acid chain is shorter)

describe: relationship between codons/triplets/anti-codons

codon=complementary triplet on DNA template strand anticodon= complementary to codon on mRNA --> 3 bases sequence on the anticodon is same as the 3 base sequence of the triplet on the DNA template strand, except if the triplet contained the base T then the anticodon would have the base U instead)

describe: purpose of transcription

copy code for making a polypeptide from DNA in nucleus onto mRNA that then carries it out to ribosomes in cytoplasm so that the original DNA does not get damaged leaving the nucleus

describe: gene relations to metabolic pathways (phenotype)

gene/genotype--> protein (eg. enzyme: a catalytic protein) --> metabolic pathway --> presence/absence/amount of specific products = phenotype

describe: cystic fibrosis (general)

inherited mutation in the CFTR, which is a often a deletion causing the altered function of a protein in the cell membrane of cells lining the respiratory and digestive systems -causes thick mucus in respiratory/digestive system, which leads to a high rate of lung infection and a lower nutrient absorption -->leading to a shortened life expectancy

define: polymer

large molecule of smaller repeating sub-units called monomers

define: polypeptide

long chain of amino acids joined together by peptide bonds

describe: three types of RNA

mRNA (messenger RNA)= carries genetic code to build a protein from the DNA in the nucleus, out to ribosomes in cytoplasm rNA (ribosomal RNA)- makes up ribosomes (along with protein) tRNA (transfer RNA) carries a specific amino acid from the cytoplasm to the ribosomes

describe: why not all environmental factors are mutagens + examples

mutagens= environmental factor that can CHANGE the genotype of an individual, by causing mutations eg. wind, temp, light intensity, nutrients can change phenotype but are not mutagens bc they don't change the base sequence in DNA --> changes are not inheritable

describe: mutated gene relations to metabolic pathways (phenotype)

mutated gene/genotype --> non-functional protein (eg. enzyme: a catalytic protein) -->steps in metabolic pathway do not work --> absence of product/build up of substrate =different phenotype

describe: how mutations can change an individual's phenotype

mutations alter genetic code which changes the protein produced, which can change the phenotype

define: phenotype

observable physical characteristics of an organism

describe: what is phenotype determined by?

phenotype is determined by the presence, absence, or amount of specific products/substrates in metabolic pathways

define: genetic code

sequence of nucleotides/bases in DNA, made up of 3 base combinations called triplets

define: genotype

set of alleles in our DNA which are responsible for a particular trait and individual possesses

define: amino acids

small molecules that are building blocks of polypeptide chains

define: nucleotide

the building block (monomer) of DNA and RNA

state: nitrogenous bases

A= adenine T= thymine U= uracil G= guanine C= cytosine

define: DNA & RNA

DNA= deoxyribose nucleic acid RNA= ribose nucleic acid both are used to carry the genetic code

describe: differences between DNA/RNA

-DNA sugar is deoxyribose, while RNA sugar is ribose -DNA has base T, RNA has base U -DNA is a larger, double stranded molecule used to store genetic code, RNA is a single stranded, shorter molecule as it is only a transcribed copy of a small section of DNA used for protein synthesis -DNA stores genetic code and acts as template, so remains in nucleus to stay protected from damage, and is stable, long lasting molecule -mRNA is a single stranded copy of a small section of DNA so is small enough to travel out of nucleus through nuclear pores to be used for protein synthesis in cytoplasm -->more prone to mutation, damage, and is broken down when finished being used in protein synthesis, so doesn't last long

describe: metabolic pathway

-a series of enzyme controlled biochemical reactions that are connected by their intermediates (where the product of one reaction becomes the substrate of another)

describe: cystic fibrosis (gametic mutation)

-an inheritable recessive mutation, and so can be passed on from generation to generation -if individuals receive at least one 'normal' dominant gene from one parent, they will not actually get cystic fibrosis -->heterozygous individuals may not have the disease, but will be carriers -only individuals who get two recessive alleles will have the condition

define: somatic mutation + examples

-are acquired mutations that occur in the body cells during the organism's lifetime -->will only affect the individual -->can not be inherited, and so cannot enter the gene pool ->somatic cells are not used in sexual reproduction/fertilisation -->cannot be passed on eg. colon cancers, melanomas

define: gametic mutation + examples

-are inherited, as they occur in gametes and so are able to be passed on to the next generation ->gametes are used in sexual reproduction/fertilisation -->offspring inherit the mutation in every one of their cells, and are able to pass it on again to the next generation -->are not limited to the individual in which the original mutation has occurred eg. cystic fibrosis, sickle cell anaemia

describe: effect of an insertion/deletion mutation

-both result in a frame shift effect, where reading frame of every triplet from mutation onwards is changed -->can change many of amino acids coded for ->redundancy in genetic code is unlikely to be able to buffer all changes in triplets due to frameshift -->would significantly alter structure of protein produced by gene -->insertion/deletion mutations= more likely to result in non-functioning protein

describe: causes of mutation

-can occur spontaneously due to errors in DNA replication -can be caused due to environmental mutagens

describe: colon cancer (somatic mutation)

-caused by somatic mutations that often occur due to exposure to environmental factors such as diet, toxins etc. during the individual's lifetime -->will have impacts on the individual, but will not be passed on through genetics to their offspring, as the mutation does not affect the gametes

define: ribosomes

-cell organelle that joins amino acids into polypeptide chain by reading copied code on mRNA 3 bases at a time (codon by codon)

describe: examples of environmental factors that limit/change the potential genotype expression w/o altering genotype

-child may have genotype to be tall, but due to lack of food/nutrients (environmental factors interacting w/ genotype) their phenotype is actually short (if they had grown up well fed w/ plenty of nutrients they would've been tall) -tree may genotype to be tall/straight, but due to growing on windy, exposed cliff (environmental factors interacting w/ genotype) it has short, bent phenotype (if grown in sheltered area w/ lots of nutrients it would've been tall + straight) -someone may have genotype for white skin, but due to fake tan chemicals/exposure to sun, actually have a darker skin phenotype (if environmental factors taken away, they would've had white skin)

explain: why cells continuously make mRNA molecules, but not DNA molecules

-continuously make mRNA because it only lasts for short period of time -unlike DNA, which is large, long lasting/stable molecule that stores genetic code/must act as template -->remains tightly wound in nucleus to protect from damage, instead of being out in cytoplasm making proteins repeatedly -cells also have increased demands for specific protein at certain times -->multiple copies of mRNA molecule= made -->more of that specific protein can be made simultaneously

describe: DNA structure

-double stranded polymer made up of repeating sub-units (monomers) called nucleotides -nucleotides have a deoxyribose sugar and phosphate that make up backbone of strand, and a nitrogenous base joined to each sugar via complementary base pairing which joins the 2 strands together -two strands (coding and template) are twisted together in a double helix

define: mutagens + examples

-environmental factors (chemical/physical agents) that cause changes in DNA -->increase frequency/rate of mutations eg. chemicals (cigarette smoke) radiation (UV light, x-rays) infectious agents (viruses/bacteria) diet

describe: enzymes relations to genes (metabolic pathways)

-enzymes are substrate-specific, meaning that a different enzyme is required for each biochemical reaction in a metabolic pathway, and every enzyme is coded for by a specific gene -since enzymes are PROTEINS that act as biological catalysts in chemical reactions one gene= one protein, so if several enzymes (catalytic proteins) control a pathway, this means there are several genes involved in the pathway

describe: overall effect of gene mutations

-gene mutation results in changes in amino acids coded for by triplets -->changes protein structure (eg. enzyme) produced by gene -->could change the protein's function (eg. enzyme could become non-functional/not work) -->since functioning of enzymes controls reactions of metabolic pathways, and phenotype of individual is determined by presence, absence, or amount of specific products from reactions in metabolic pathways... --- if a non-functional protein (eg. enzyme) is produced due to a gene mutation, could result in a substrate not being converted into a product which would alter the organism's phenotype

describe: how two parents with the same non-functioning metabolic pathway caused by recessive mutations can still have offspring with functioning metabolic pathway

-if each parent has a different gene mutated in the pathway, so the offspring is still able to inherit a functioning gene for each step of the pathway ->if mutation in gene that results in a non-functioning enzyme is a recessive allele, then the parent with the mutated gene and non-functioning enzyme must be homozygous recessive, and the other parents must be homozygous dominant or heterozygous for that same gene for their enzyme to function -->only then could the two parents produce offspring that are heterozygous for that gene and so have a functioning enzyme for that gene

describe: how two parents with the same non-functioning metabolic pathway caused by a dominant mutation can still have offspring with functioning metabolic pathway

-if if mutation in gene that results in a non-functioning enzyme is a dominant allele, then the parent with the mutated gene and non-functioning enzyme must be heterozygous, and the other parent could either also be heterozygous with a non-functioning enzyme for that same gene or be homozygous recessive with a functioning enzyme for that same gene -->only then, the two parents could produce homozygous recessive offspring that have a functioning enzyme for that gene however: if either parents were homozygous dominant for the gene, then they could produce offspring that were heterozygous/homozygous dominant with non-functioning enzymes for that same gene

describe: sickle cell anaemia

-inherited substitution mutation (GAG--> CTG) changes the shape of the protein -->causes red blood cells to sickle which can cause blockages that stop/slow the flow of blood -->oxygen is unable to reach nearby tissues -can lead to death, brain & liver damage

describe: protein synthesis overview

-involves two stages: transcription and translation, with each step involving enzymes

define: DNA function/location

-is a double stranded polymer molecule that carries the genetic information which codes for the formation of polypeptide chains (which form proteins) -it is only found in the nucleus of a cell

significance of relationship between triplets, codons, anticodons

-mRNA codon= complementary to DNA triplet -tRNA anticodon= complementary to that mRNA codon -->since specific tRNAs carry specific amino acids, it ensures tRNAs add the amino acids into the polypeptide chain in the correct order as coded for by DNA -->significant because sequence of amino acids determines structure of final polypeptide chain/protein -function of protein is determined by its structure -->is important that amino acids are added in correct order to end up with functional protein

describe: nucleotide structure

-made up of a phosphate, sugar (deoxyribose/ribose) and a nitrogenous base -phosphate and sugar make up the back bone of DNA/RNA -phosphate links neighbouring sugars -nitrogenous base is joined to each sugar (via complementary base pairing)

describe catalytic (globular) proteins + functions

-made up of one/more polypeptide chains folded into complex shapes -have chemical functions such a regulating/catalysing reactions eg. enzymes are catalytic proteins, controlling chemical pathways in organisms

describe structural (fibrous) proteins + functions

-made up of polypeptide chains that form rope like bundles -have mechanical functions of support, protection, contraction eg. form skin, hair, ligaments, tendons, contractile fibres (eg. muscle fibres)

describe: why genetic code having redundancy due to degeneracy is an advantage

-means if a mutation were to occur in the base sequence, there's a chance that the new base sequence will still code for the same amino acid -->structure of the protein produced, and its function remains the same

describe: significance of the shape of catalytic proteins in metabolic pathways

-metabolic pathways are a series of enzyme-controlled reactions within a cell -enzymes= catalytic proteins w/ specific tertiary/protein structure -specific area of enzyme= active site, where the substrate of the metabolic pathway joins to the enzymes and is then changed into the products/ intermediate substances in the pathway -if active site changes through mutation or denaturing, the substrate will be unable to bind to the active site -->the activity of the enzyme will be impaired, and so it may cause a metabolic pathway to slow down/stop completely -->could cause a build-up of intermediate substances/substrates, or a final product may not be made -->which could be harmful to the organism/lead it to not function correctly

describe: effect of a mutation at the end of a gene/protein

-most of the protein structure has been coded for correctly, and so still may be functional (especially if active site of enzyme is unaffected) -but even a single substitution mutation can affect functioning of an enzyme if it codes for an early stop codon/changes an amino acid in the active site of the enzyme

describe: protein tertiary structure

-occurs when sulphide bonds between folded secondary structures cause more irregular/complex folding which is specific for each protein bc it depends on the amino acid sequence -3ᵒ structure folds protein to form active site of enzymes (when enzyme denatures, it's sulphide + hydrogen bonds that break when temp is too high, resulting in loss of tertiary structure and so shape of active site)

describe: protein secondary structure

-occurs when the single chain/sequence of amino acids becomes folded/twisted due to hydrogen bonds which form between amino acids in chain (2 main types: alpha helix, and beta pleated sheet)

describe: investigations of environmental factors on gene expression

-often use identical organisms/individuals and place one of the identical individuals in one set of conditions (or control conditions) and the other identical individual in a different set of conditions (where one environmental factor has been changed) -->since they have identical genotypes, any changes in their phenotype must be due to the effect of the different (non-mutagenic) environmental factor on the gene expression and not a difference in their genotype

describe: effect of a substitution mutation

-only affects one triplet code -->only changes the one amino acid that a triplet codes for, so the effect on structure of protein produced by gene will usually be less significant -furthermore, due to redundancy in genetic code, there is a chance that the new base sequence in triplet will still code for same amino acid -->the protein, and its function will the remain the same NOTE: position of substitution effect= significant

describe: similarities between DNA/RNA

-phosphates are the same -both have bases A, C, G

describe: transcription

-process that copies the code on DNA into mRNA so that the code to build a polypeptide /protein can be carried out of the nucleus to the ribosomes purpose= copy code for making a polypeptide from DNA in nucleus onto mRNA that then carries it out to ribosomes in cytoplasm so that the original DNA does not get damaged leaving the nucleus

describe: translation

-process that makes a polypeptide chain/protein by using ribosomes to read the copied code on mRNA

describe: protein quaternary structure (4ᵒ)

-protein consisting of more than one amino acid chain

describe: significance of proteins

-proteins are the products of genes -have important structural + catalytic functions in living things (DNA --> mRNA --> polypeptide one gene --> one polypeptide gene/code determines protein structure, and correct protein function= determined by structure -->if gene/code changes, structure of final protein produced may change (primary, tertiary etc.) -->function may also change

define: gene mutation

-random, permanent change in individual bases of a gene

describe: how genetic code has redundancy due to degeneracy

-several of 3 base combinations code for the same amino acid -->thus why there are 64 three base combinations for only 20 amino acids

describe: protein primary structure

-single polypeptide chain has specific order of amino acids -specific order is unique to each protein, and determines properties of the protein

describe: the deletion of an entire codon

-sometimes the 3 nucleotides that code for an amino acid (complete codon) can be deleted -->means that an amino acid is not coded for -->final polypeptide chain/protein will be shorter -reading frame of other codons is unaffected, so they still code for same amino acids -but the protein will not be complete -->the folding of the protein will different from the normal protein, (changed shape) -->function of final protein is affected

describe: start + stop codons

-start codon (AUG) signals beginning of translation -stop codon ends translation, causing ribosome to stop translating and release polypeptide chain and mRNA -->they help ensure correct protein structure/length

describe types of gene mutation

-substitution= replacement of one base with another, in a triplet in DNA (eg. CAT --> CGT) -insertion= when a base is added into base sequence (eg. CATTAC --> CAATTA C) -deletion= a base is removed from the base sequence (CATTAC --> CTTAC)

describe: translation function

-use the copied code in mRNA to make polypeptide chain/protein, so that the protein can be used for structural or catalytic functions

describe: complementary base pairing

-when specific bases only pair/bond with each other in DNA: A-T, G-C in RNA: A-U, G-C

describe: how environmental factors can affect an individual's phenotype

-when they act as mutagens to change an individual's genetic code (but these changes are only inheritable if they occur in gametic cells)

describe: steps in transcription

1. enzyme unwinds DNA double helix by breaking hydrogen bonds between complementary bases, exposing bases on DNA template strand 2. DNA template strand carries code for making polypep/protein that is copied to make mRNA (role of DNA) 3. transcription starts at promoter sequence on template strand, where enzymes begins joining free RNA nucleotides to exposed DNA template strand bases via base pairing rule (U replaces T in mRNA) to build single stranded mRNA 4. transcription= complete when enzyme reaches terminator sequence on DNA, and the mRNA strand detaches 5. mRNA single strand leaves nucleus through nuclear pores, carrying copied cope to build polypep/protein out to ribosomes in cytoplasm (so DNA= not damaged)

describe: steps in translation

1. mRNA attaches to ribosome and protein synthesis begins at start codon AUG on mRNA 2. specific tRNA for each different amino acid, and tRNAs carry specific amino acid from cytoplasm to ribosomes (role of tRNA) 3. anticodon of tRNA is then complementary base paired to mRNA codon by ribosome, as it reads code on mRNA 3 bases at a time 4. peptide bonds form between neighbouring amino acids, building polypeptide chain 5. unloaded tRNAs leave mRNA-ribosome translation complex and return to cytoplasm to be reloaded with specific amino acid by an enzyme 6. a stop codon terminates protein synthesis, and polypeptide chain is released from ribosome 7. when protein synthesis is complete, mRNA is broken down

define: protein

a complex molecule composed of one of more polypeptide chains -can be fibrous proteins/globular proteins

define: mutation

a random and permanent change in the base sequence of a gene/DNA -which alter the protein produced, and so alter the phenotype

define: gene expression

the information in a gene on DNA which is used to synthesise a functional protein through the processes of transcription and translation, by using genetic code on DNA as a template (protein is then folded and modified into the final protein after translation)

describe: where both transcription + translation occur

transcription= occurs in nucleus, and each step is controlled by enzymes translation= occurs on ribosomes out in cytoplasm, and each step is controlled by enzymes

describe: triplets, codons, anti-codons

triplets= sequence of 3 bases in DNA that code for an amino acid (64 three base combinations code for 20 amino acids) codons= sequence of 3 bases in mRNA that is complementary to DNA triplet on template strand, and codes for a specific amino acid anti-codons= sequence of 3 bases on a tRNA molecule that is complementary to mRNA codon, each tRNA molecule carries specific amino acid