Topic 1- A Level Edexcel Biology B

coding DNA

2% of human DNA codes for proteins some code for a particular amino acid others code for the beginning or ending or a particular amino acid sequence genetic code is not only a triplet code but also non overlapping and degenerate

β glucose

isomer

𝛼 glucose

isomer

primary structure of proteins

linear sequence of amino acids in a polypeptide chain

water- hydraulics

liquid can't be compressed

measuring rate of rection

measure initial rate of reaction each time the independent variable is changing have a large excess of substrate measure amounts of product over time measuring the initial rate only means other factors don't have time to influence the rate

temperature coefficient (Q10)

measure of effect of temperature on the rate of reaction

cell regulation or reactions

membrane compartments keep reactions apart pH can change the rate of enzyme catalysed reactions amount of substrate available regulatory enzymes have a site specifically for non competitive inhibition

anabolic + catabolic

metabolism

polar molecule

molecule containing a dipole

nitrate ions (NO3)-

needed in plants for formation of amino acids and DNA

anion

negative ion formed when an atom gains an electron

temperature affects the rate

no. of successful collisions leading to a reaction increases with temperature at 40oC, most proteins denature as the shape of the active site changes thermophilic bacteria have temp. resistant proteins which have a high density of H and disulphide bonds with hold strong at high temperatures

deoxyribonucleic acid

nucleic acid that acts as the genetic material in many organisms

ribonucleic acid

nucleic acid which can act as the genetic material in some organisms and is involved in protein synthesis

molecular activity/ turnover number of an enzyme

number of molecules transformed per minute by a single enzyme molecule normally around 1000 per minute

point mutation- subsititution

one bases substitutes for another

lock and key hypothesis

over simplified version only a specific type of substrate will fit in the active site formation of the enzyme substrate complex lower the activation energy active site affects the bonds in the substrate making it easier for them to break the complex breaks up, releasing the products and freeing the enzyme for further catalytic action

non overlapping code

overlapping is very economical but also limiting as the amino acids that could be coded for side by side would be limiting if there is no overlapping, then a mutation would only affect 1 amino acid

lipids

part of cell membranes used as an energy store

ribose

pentose sugar that makes up part of the structure of RNA

mutation

permanent change in DNA of an organism

cation

positive ion formed when an atom loses an electron

magnesium ions (Mg)2+

produces chlorophyll in plants

conjugated protein

prosthetic group-what some protein molecules are joined with glycoproteins- have a carb prosthetic group so can hold a lot of water and harder for proteases to break them down lubricants- slippery glycoproteins lipoproteins- lipid prosthetic group LDLs and HDLs- 2 types of lipoproteins

base containing nitrogen in nucleotide

purines- 2 rings- adenine and guanine pyrimidines- 1 ring- cytosine and and thymine/ uracil A+T/U= 2 hydrogen bonds C+G= 3 hydrogen bonds

condensation reaction

reaction in which a molecule of water is removed from the reacting molecules as a bond is formed between them

anabolic reaction

reaction that builds up (synthesises) new molecules in a cell

catabolic reaction

reaction which breaks down substances within a cell

hydrogenation of sugars

reduces energy they provide but taste sweet so used for weight loss

non competitive inhibition

reversible inhibitor forms a complex either with enzyme or with enzyme/ substrate complex not competing for the active site only the concentration of the inhibitor affects the level of inhibition inhibitor deforms or changes shape of the active site so that it can no longer catalyse the reaction

competitive inhibition

reversible inhibitor molecule is similar shape to the substrate molecule competes with the substrate for binding with the active site, forming an enzyme/ inhibitor complex more substrate molecules, less likely inhibitor molecules will bind to the active site

allosteric enzyme

separate site to have an either activating or inhibitory effect

metabolic chain/ pathway

series of linked reactions in the metabolism of the cell

water- high SHC

slow to absorb and release heat and a large amount of energy is needed to change temp of large bodies

complementary strand

strand of mRNA formed from the DNA during replication a reverse image of the original base sequence

enzyme inhibators

substances that slow down enzymes or stop them from working

sucrose

sweet tasting disaccharide formed by the joining of a glucose and fructose by a glycosidic bond

amylose

long chains of 𝛼 glucose- unbranched and spirals so very compact only 1,4 glycosidic bonds so release glucose slowly over long time

semi- conservative replication

DNA unzips and new nucleotides aligned across each strand each new double helix contains one new strand of original DNA and one strand of new material this is the accepted model of DNA replication

tertiary structure of proteins

alpha helices and beta sheets folded further with bonds holding 3d shapes in place

secondary structure of proteins

alpha helix caused by peptide bonds with the R group sticking out beta sheets held together by hydrogen bonds fibrous

ATP

adenine triphosphate supplies energy to cells in all living organisms energy in phosphate bonds joined together by condensation reactions and 2 water molecules are eliminated

sickle cell disease

affects protein chains making up haemoglobin in red blood cells result of a point mutation causing the haemoglobin to stick together to form rigid rods that give the red blood cells a sickle shape don't carry oxygen very efficiently and block the smallest blood vessels

glycogen

aka animal starch- storage carb in fungi and very similar to amylopectin- even more 1,6 glycosidic bonds so many side branches s can be broken down even more rapidly source of glucose for active tissue (muscle)

point mutation- deletion

base is completely lost in the sequence

enzymes

biological catalysts which control the rates of reactions speed up the reactions without altering the conditions in the cytoplasm globular proteins- produced during protein synthesis have a very specific shape changes in temperature affect the efficiency of the enzyme because they affect the intra molecular bonds within the protein that are responsible for the shape of the molecule doesn't always speed up a reaction, can slow it down or stop all together

RNA

carry information from nuclear DNA to enzymes on ribosomes ribose sugar Uracil instead of Thymine single helix- small, simple molecule

extracellular enzymes

catalyse reactions outside of the cell in which they are made e.g. digestive enzymes, lysozyme (tears)

intracellular enzymes

catalyse reactions within the cell e.g. DNA polymerase, DNA ligase

chromosomal mutations

changes in the position of genes within the chromosomes

pH affects the rate

changes the structure because it changes the formation of the bonds

benedicts test- reducing sugars

colour change from blue copper ii ions to orange copper i ions, forming a precipitate- all monosaccharides and disaccharides

haemoglobin

conjugated and globular protein

end product inhibition

control system in many metabolic pathways enzyme at the beginning of the pathway is inhibited by one of the end products of the reaction

glycosidic bond

covalent bond formed in a condensation reaction

reversible inhibition

doesn't permanently affect the functioning of the enzyme often used to control rates of reaction e.g. metabolic pathway examples are competitive and non competitive inhibition

activation energy

energy needed to start a reaction lowered by enzymes

starch

energy store in plants made of amylose and amylopectin. Insoluble and compact and can be broken down rapidly to release glucose

whole chromosome mutations

entire chromosome lost during meiosis or duplicated in one cell e.g. down syndrome- 3 copies of chromosome 21

number of substrate molecules affects the rate

enzyme becomes saturated, no more active sites free only an increase in enzyme concentration will increase the rate of reaction

relationship between structure and function of enzymes

enzymes controlled reactions are affected by the concentration of the enzyme very specific to reaction that they catalyse inorganic catalysrs frequently cataluse different reactions, often at extremes of temp or pressure some enzymes are so specific they will only catalyse one particular reaction others are either specific to a group of molecules that are all the same shape or to a type of reaction that always includes the same groups therefore no physical site within the enzyme with a particular shape into which a specific enzyme will fit

point mutation- insertion

extra base is added- either repetition of a base or a completely new one

induced fit hypothesis

flexible active site once the produce has left the enzyme reverts to inactive relaxed form until another substrate molecule binds active site not fully complementary until substrate fits into it

ester bond

formed between glycerol and fatty acids

protein synthesis

genetic code is transcribed onto mRNA mRNA attaches to a ribosome in the cytoplasm tRNA carry amino acids to the surface of the ribosome tRNA anticodon lines up alongside a complementary codoon in the mRNA, held in place by hydrogen bonding while enzymes link the amino acids together tRNA breaks away to pick up another amino acid ribosome moves along mRNA, leaving a completed polypeptide chain nucleus= transcription cytoplasm=translation

polysomes

groups of ribosomes joined by mRNA thread ribosomes attach in a steady stream to mRNA and produce identical polypeptides

mutations affecting phenotypes

if the different arrangement of nucleotides code for the same amino acid a point mutation will have no effect rarely, a mutations occurs that results in the production of a superior protein, which may give the organism a reproductive advantage most mutations are neutral, so they neither worsen nor improve the chances of survival

mutagens

increase the rate at which mutations occur e.g. radiation, chemicals, x rays

irreversible inhibition

inhibitor combines with the enzymes by permanent covalent bonding to one of the groups vital for catalysis to occur changes the shape and structure of the molecule so it can't be reversed occurs more slowly than other forms of inhibition never used to control metabolism

triplet code

3 bases

non- coding DNA

98% of human DNA is non coding involved in regulating the protein coding sequences/ turning genes on and off

phospholipids

created when hydroxyl groups of glycerol react with a phosphate instead of fatty acid in the cytoplasm

proteins

made up of amino acids

nucleotide

building block of DNA

polymer

long chain molecule made up of many smaller repeating monomer units joined together by chemical bonds

phosphate in nucleotide

(PO4)3- present in cytoplasm acidic and negatively charged

nucleic acids

10 base pairs for each turn of double helix phosphodiester bonds between the nucleotides sugar phosphate backbone 5' and 3' ends opposite ends 5' end has free phosphate 3' end has free -OH sugar group

DNA replication

2 strands of DNA unzip along the line of hydrogen bonds by DNA helicase exposed bases attract free DNA nucleotides and new hydrogen bonds are formed between matching base pairs DNA polymerase lines up the nucleotides DNA ligase catalyses the formation of phosphodiester bonds between nucleotides the result is 2 new strands of DNA identical with the original piece the new molecules automatically coil up into the double helix as weak hydrogen bonds form within the structure

amino acids

20 different naturally occurring types that combine in different ways to produce different proteins

degenerate code

aka redundant contains more information than is needed if each amino acid was 1 codon, then a mutation would be a disaster however if a find base is changed, a mutation could still produce the same amino acid

lipids' energy

3 times more energy than carbohydrates released during condensation reaction, so 3 water molecules released

collagen

35% of protein in our bodies is collagen and it is very strong

quaternary structure of proteins

3d arrangement of tertiary polypeptide chains

protein bonds- ionic

form between very strong + and - chains aka salt bridges very strong but not common

water- polar solvent

ionic substances dissolve in it and can carry other substances

protein bonds- disulphide

oxidation reaction between 2 sulphur containing R groups very strong but not many

deoxyribose

pentose sugar that makes up part of the structure of DNA

pentose in nucleotide

ribose in RNA deoxyribose (1 less oxygen) in DNA

hydrogen bonds

weak electrostatic intermolecular bonds formed between polar molecules containing at least one hydrogen atom

water- high surface tension

attraction between molecules is greater than attraction to air, so helps life at surface of ponds

ionic bonds

attractive forces between oppositely charged ions

1,4 glycosidic bond

bond between carbon 1 and carbon 4

1,6 glycosidic bond

bond between carbon 1 and carbon 6

hydrolysis

breaking of a glycosidic bond with the addition of a water molecule

protein bonds- hydrogen

formed between + change of H and - charge of O of the carboxyl group very weak easily break of pH or temp changes

peptide bond

formed between the carboxyl group and amino group of amino acids

mRNA

formed in nucleus carries instructions for polypeptide from DNA to ribosomes forms on 3' or antisense strand mRNA formed is a sense strand form a triplet code

covalent bonds

formed when atoms share electrons

phosphate ions (PO4)3-

forms ATP, ADP, DNA and RNA

calcium ions (Ca)2+

forms calcium pectate for middle lamella between cell walls

tRNA

found in cytoplasm has a complex shape due to hydrogen bonds between different bases has the anticodon which consists of 3 bases has a binding site where an amino acid attaches anticodon lines up with codon of mRNA and drops off and amino acid, and a peptide bond is formed between them 61 types

sucrose (1,2)

glucose and fructose- found in sugar cane

lactose (1,4)

glucose and galactose- present in mammalian milk

maltose (1,4)

glucose and glucose- formed by amylase in starch

polysaccharides' properties

good storage and can form compact molecules, also inactive and not very soluble so doesn't interfere with osmosis

benedicts test- non reducing sugars

heat with HCl and neutralise with sodium hydrogen carbonate to hydrolyse the glycosidic bonds, producing monosaccharides

glucose

hexose sugar

micelle

hydrophilic head hydrophobic tail

water- density

ice is less dense than water, and maximum density at 4C

cellulose

insoluble and keeps cell wall strong made of β glucose and help together by 1,6 glycosidic bonds every other glucose is inverted for bonding and H bonds form between hydroxyl group and oxygen toms known as cross linking and holds neighbouring chains together doesn't coil or spiral and cannot be digested by animals so acts as roughage in human diet

properties of lipids

insulators low density so float dissolve in solvents but insoluble in water so don't interfere with reactions in the cytoplasm

amylopectin

long chains of 𝛼 glucose- branched so terminals break off easily when energy is needed mainly 1,4 glycosidic bonds but a few 1,6

fibrous proteins

long parallel polypeptide chains with cross linkages that form fibres insoluble in water

rRNA

makes up 50% of structure of ribosome made in nucleus and moves into cytoplasm where it binds with proteins to form ribosomes

water- incompressibility

molecules are close together so can't be compressed

isomers

molecules that have the same chemical formula, but different molecular structures

DNA replication- nitrogen

only source of nitrogen is N15 (radioactive), which is denser than the usual N14 bacteria takes up radioactive isotope to make DNA and proteins after several generations, all DNA labelled with N15 then moved to a medium containing only N14, and density of DNA is measured as they reproduce if conservative either all N15 or N14 if semi conservative,, which it is, all half N15 half N14

polysaccharides

polymer made up of long chains of monosaccharide units joined by glycosidic bonds

dipole

separation of charge in a molecule when the electrons in a covalent bond are not evenly shared

codon

sequence of 3 bases in DNA or mRNA

gene

sequence of bases on a DNA molecule contains coding for a sequence of amino acids

monosaccharides

single simple sugar molecule

monomer

small molecule that is a single unit of a larger molecule called a polymer

conservative replication

somehow a new, identical double helix is formed made up of entirely new material

water- adhesive

stick to other molecules and helps plant transport systems and surface tensions

water- cohesive

sticks together and helps movement of water from root to leaves

water- transport

substances dissolve in it and can be transported

disaccharides

sugar made up off two monosaccharide units joined by a glycosidic bond formed in a condensation reaction

triose sugar

sugar with 3 carbon atoms and important in mitochondria

pentose sugar

sugar with 5 carbon atoms and important in nucleic acid

hexose sugar

sugar with 6 carbon atoms and taste sweet

globular proteins

tertiary and quaternary structure folded into spherical shapes keep the structure in the cytoplasm instead of dissolving in water they form a colloid as so big

macromolecule

very large molecule formed by polymerisation