TOPIC 2 biology

Cohesion

Attraction between molecules of the same substance

Adhesion

An attraction between molecules of different substances

Solvent

A liquid substance capable of dissolving other substances

Metabolic reactions

Metabolic reactions are chemical processes that occur in the body that help sustain life

hydrophilic

substances that are chemically attracted to water

hydrophobic

Substances that are insoluble in water

Glucose

polar molecule hence freely soluble (carried by blood plasma)

Amino acids

Positive and negative charges therefore soluble in water (carried by the blood plasma)

Oxygen

Non-polar molecule (hemoglobin in red blood cells carry the majority of oxygen)

Fats

Large, non-polar molecules (insoluble in water) - carried in blood inside lipoprotein complexes (in the plasma)

Lipoprotein complex

Outer layer consists of single layer of phospholipid molecules - Proteins are also embedded

Cholesterol

molecules are hydrophobic - They are carried in blood in lipoprotein complexes (in the plasma)

Sodium Chloride

ionic compound (freely soluble in water) - carried in the blood plasma

Thermal

Water has - high specific heat capacity, high heat of vaporisation, high heat of fusion - due to many hydrogen bonds that need to be formed or broken to change the temperature or state of water

water vs methane

Methane is as waste product of anaerobic respiration in certain prokaryotes living in anaerobic conditions (can be used for fuel) - Methane: nonpolar, Water: Polar

Covalent bonds

strongest type of bond between atoms (Stable molecules can be formed)

Carbohydrates

Organic compounds consisting of one or more simple sugars

Lipids

group of organic molecules that are insoluble in water but soluble in non-polar organic solvents - triglycerides, phospholipids, steroids (more suitable for long-term energy storage in humans than carbohydrates)

Proteins

large organic compounds made of amino acids arranged into one or more linear chains

Nucleic acids

Chains of nucleotides which consist of base, sugar and phosphate groups covalently bonded together

Enzyme

globular protein that increases the rate of a biochemical reaction by lowering the activation energy threshold

Catalyst

substance that increases the rate of a chemical reaction without itself undergoing any permanent change

Condensation

Makes bonds - water releasing

Hydrolysis

breaks bonds - water splitting

Anabolic Reactions

build molecules (eg. protein synthesis)

Catabolic Reactions

Break down molecules (eg. digest)

"dehydration reaction"

when the water molecule has come from one of the reactants

Synthesis of urea

Wöhler accidentally synthesised urea in 1828 - undermine Vitalism as organic chemicals were previously thought to be synthesised only by organisms

Monosaccharide

Glucose, Galactose, Fructose, Ribose

Disaccharides

Maltose, Lactose, Sucrose

Polysaccharides

Cellulose, Amylase/ Amylopectin - Starch, Glycogen

Cis-isomers

the hydrogen atoms are on the same side of the two carbon atoms (usually liquid at room temperature)

Trans-isomers

the hydrogen atoms are on different sides of the two carbon atoms (usually solid at room temperature)

Mass used for storage (FORMULA)

(energy contained in) 1g lipids/ (energy contained in) 2g carbohydrate + 4g associated water

Glycogen

the medium-term energy storage molecule in animals (stored in the liver and muscles)

Glucose

for immediate use and will either be used in respiration to yield ATP or converted to glycogen or fat (in the bloodstream)

Body Mass Index (CALCULATIONS)

mass in kilograms/ (height in metres)^2

Ribosomes

molecules within cells that facilitate the formation of peptide bonds and hence where polypeptides are synthesized

Hydroxyproline

an amino acid created not by the genetic code, but modification, after polypeptide formation, of proline (by the enzyme prolyl hydroxylase)

modification of proline

increases the stability of the collagen triple helix

Collagen

a structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls

Genes

Codes for making polypeptides

mRNA (messenger RNA)

a single-stranded RNA molecule that encodes the information to make a protein (message from the nucleus to the ribosome)

Primary Structure

Formed by covalent peptide bonds between adjacent amino acids (Controls all subsequent levels of structure) (Polypeptide)

Secondary Structure

The chains of amino acids fold or turn upon themselves - Held together by hydrogen bonds between (non-adjacent) amine (N-H) and carboxylic (C-O) groups - (Fibrous proteins)

Tertiary Structure

The polypeptide folds and coils to form a complex 3D shape (Globular proteins)

Quatenary Structure

The interaction between multiple polypeptides or prosthetic groups (Fibrous and Globular proteins)

Fibrous vs Globular proteins

Fibrous: long and thin shaped; less soluble in water.

Globular: compact and relatively spiral; more soluble in water.

Catalysis

A process by which a chemical agent called a catalyst selectively increases the rate of a reaction

Muscle contraction

Actin and myosin together cause the muscle contractions used in locomotion and transport around the body

Cytoskeletons

Tubulin is the subunit of microtubules that give animals cells their shape and pull on chromosomes during mitosis

Tensile strengthening

Fibrous proteins give tensile strength needed in skin, tendons, ligaments and blood vessel walls

Blood clotting

Plasma proteins act as clotting factors that cause blood to turn from a liquid to a gel in wounds

Transport of nutrients and gases

Proteins in blood help transport oxygen, carbon dioxide, iron and lipids

Cell adhesion

Membrane proteins cause adjacent animal cells to stick to each other within tissues

Membrane transport

Membrane proteins are used for facilitated diffusion and active transport, and also for electron transport during cell respiration and photosynthesis

Hormones

insulin, FSH and LH are proteins, but hormones are chemically very diverse

Receptors

Binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes and smells, and also receptors for light in the eye and in plants

Packing of DNA

Histones are associated with DNA in eukaryotes and help chromosomes to condense during mitosis

Immunity

most diverse group of proteins, as cells can make huge numbers of different antibodies

Rubisco

Enzyme - catalyses the reaction that fixes carbon dioxide from the atmosphere

Insulin

A hormone - signals many cells (e.g. liver cells) to absorb glucose and help reduce the glucose concentration of the blood

immunoglobulins

Binding sites vary greatly between immunoglobulins (hypervariable) to enable them to respond a huge range of pathogens

rhodopsin

A pigment that absorbs light - Membrane protein of rod cells of the retina

collagen

Forms a mesh of fibres in skin and in blood vessel walls that resists tearing

spider silk

Dragline silk is stronger than steel and tougher than Kevlar - stretched the polypeptide gradually extends, making the silk extensible and very resistant to breaking

Genome

all of the genes of a cell, a tissue or an organism

Proteome

all of the proteins produced by a cell, a tissue or an organism

Denaturation of proteins

The three-dimensional conformation of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule (heat, extreme levels of pH, substrate concentration)

Substrate

Reactant in biochemical reaction

Active Site

Region on the surface of an enzyme to which substrates bind and which catalysis the reaction.

The Lock-and-Key hypothesis

The idea that enzymes are specifically shaped to fit only one type of substrate - NOT TRUE because that would mean that one enzyme would only catalyse one reaction (the enzyme changes the shape to fit the substrate)

collision

The coming together of a substrate molecule and an active site - result of the random movements of both substrate and enzyme

Detergents

contain proteases and lipases to help breakdown protein and fat stains

textiles

industry enzymes help in the processing of fibres

brewing

enzymes help a number of processes including the clarification of the beer

Advantages of enzyme immobilization

Concentration of substrate can be increased, Recycled enzymes can be used many times, Separation of the products is straight forward, Stability of the enzyme to changes in temperature and pH is increased reducing the rate of degradation

DNA characteristics

double helix, sugar-phosphate backbone, bases join two strands by two hydrogen bonds, millions of base pairs in length, and is coiled up to make chromosomes

Complementary base pairing

C-G (via three hydrogen bonds)/ T-A (via two hydrogen bonds)- ensure that mistakes are not made when copying or transcribing DNA

nucelotide

a single unit of a nucleic acid

Nucleic acids

very large molecules that are constructed by linking together nucleotides to form a polymer (DNA and RNA)

four nitrogenous bases in DNA

Purine: Adenine (A), Guanine (G)/ Puramidines: Thymine (T), Cytosine (C)

four nitrogenous bases in RNA

Adenine (A), Uracil (U), Guanine (G), Cytosine (C)

Genetic Code

set of rules by which information encoded in mRNA sequences is converted into proteins (amino acid sequences) by living cells (Nucleotides are linked into a single strand via a condensation reaction - bonds are formed between the phosphate of one nucleotide and the pentose sugar of the next \= phosphodiester bond)

Watson and Crick

Used stick-and-ball models to test their ideas on the possible structure of DNA - DISCOVERED: DNA must be a double helix, The strands must be anti-parallel to allow base pairing to happen, The relationship between the bases and base pairing

Helicase

enzyme - often formed from multiple polypeptides and doughnut in shape - unwinds and unzips DNA (Separates the two polynucleotide strands by breaking the hydrogen bonds between complementary base pairs) - ATP required

DNA Polymerase

enzyme - creates complementary strands - consists of multiple polypeptides sub-units (condensation reaction) (5' to 3' direction)

Polymerase Chain Reaction (PCR)

amplify small samples of DNA to produce large quantites \= Denaturation: DNA sample is heated to separate it into two strands, Annealing: DNA primers attach to opposite ends of the target sequence, Elongation: A heat-tolerant DNA polymerase (Taq) copies the strands

Meselson and Stahl's

work with DNA to discover the mechanism of semi-conservative replication

transcription (in nucleus)

cell's machinery copies the gene sequence into messenger RNA

Translation

Ribosome reads the mRNA sequence and translates it into the amino acid sequence of the protein (each 3 nucleotide codons specifies a particular amino acid)

Messenger RNA (mRNA)

A transcript copy of a gene used to encode a polypeptide

Transfer RNA (tRNA

A clover leaf shaped sequence that carries an amino acid

Ribosomal RNA (rRNA)

A primary component of ribosomes

Process of Transcription

enzyme RNA polymerase binds to a site on the DNA at the start of a gene separating the DNA strands and synthesising a complementary RNA copy from the antisense DNA strand by covalently bonding ribonucleoside triphosphates that align opposite their exposed complementary partner

Process of Translation

ribosomal subunits assemble together like a sandwich on the strand of mRNA - Each subunit is composed of RNA molecules and proteins, The small subunit binds to the mRNA, The large subunit has binding sites for tRNAs and also catalyzes peptide bonds between amino acids

Diabetes

destruction of cells in the pancreas that secrete the hormone insulin - treated by injecting insulin into the blood - they all bind to the human insulin receptor and cause lowering of blood glucose concentration

Restriction enzymes

'cut' the desired gene from the genome

recombinant plasmid

inserted into the host cell. It now expresses the new gene. An example of this is human insulin production.