biochemistry 1st year

biochemistry

study of chemistry of living organisms

atoms and atomic structure (4)

number of protons— atomic number— number of electrons

number of electrons lead to different number of orbitals

s orbitals: spherical

p orbitals: dumbbell shaped

valence electrons

electrons in outer shell that are available to combine with the electrons of other atoms to form bonds

chemical bonds and molecules

incomplete valence shells can share or transfer valence electrons with certain other atoms, resulting in atoms staying close together called chemical bonds

molecule

2 or more atoms bonded together

compound

molecule composed of 2 or more elements

molecular formula

contains chemical symbols of elements found in a molecule, subscript indicates how many of each atom are present

octet rule

atoms are stable when outer shell is full

covalent bonds

atoms share pair of electrons

strong chemical bonds, behave as if they belong to each atom

occurs between atoms whose outer electron shells are not full

polar covalent bonds (3)

electronegativity: atoms attraction for the electrons in a covalent bond, more electronegativity the stronger it pulls shared electrons toward itself

polar covalent bonds occur because the distribution of electrons around the atoms creates a polarity across the molecule

water soluble

non polar covalent bonds (3)

atoms share electron equally

bonds between atoms with similar electronegativities

water soluble poor

ionic bonds (4)

an ion is an atom or molecule that has gained or lost one or more electrons, now has net electric charge

cations: net positive charge

anions: net negative charge

ionic bond occurs when cation bonds to anion

hydrogen bonds

hydrogen atom from one polar molecule attracted to an electronegative atom

organic molecules

carbon containing molecules

functional groups (5)

carbohydrates, lipids, protein and nucleic acids contain small reactive groups of atoms called functional groups

confer specific properties to biological molecules

groups of atoms with special chemical features that are functionally important

each have special chemical properties

most common are hydroxyl, carbonyl, carboxyl, amino, phosphate and sulfhydryl

condensation/ dehydration reaction

links monomers to form polymers

hydrolysis

polymers broken down into monomers

carbohydrates (3)

composed of carbon, hydrogen and oxygen

most of the carbons linked to a hydrogen atom and hydroxyl group

most have 5 or 6 carbons

monosaccharides (8)

linear form, each carbon has -H and -OH attached except one

the remaining is part of carbonyl group

if has more than 5 carbons can fold back on themselves to ring form

has 4 different structures

1. location of carbonyl group

2. number of carbon atoms present

3. spatial arrangement of groups

4. linear and alternative ring forms

disaccharides (4)

composed of two monosaccharide monomers

joined by dehydration/ condensation reaction

broken apart by hydrolysis

glycosidic bond

polysaccharides (3)

any monosaccharides linked together to form long polymers

may be linear, unbranched molecules or may contain one or more branches in this side chains of sugar units attach to a main chain

2 functions: energy storage and structural role

lipids (2)

do not form polymers

hydrophobic

phospholipids (4)

two fatty acids attached to glycerol

amphipathic molecules

hydrophilic head hydrophobic tail

major component of all cell membranes- bilayer

steroids (4)

four interconnected rings of carbon atoms

usually insoluble in water

tiny differences in structure can lead to different specific biological properties

eg. oestrogen vs testosterone

fats

made of glycerols and fatty acids

glycerol: 3 carbon alcohol with hydroxyl group to each carbon

fatty acid: carboxyl group to long carbon skeleton

saturated fats: all carbons linked by single covalent bonds, solid at room temp

unsaturated fats: contain one or more double bonds, liquid at room temp

diet rich in saturated fats may contribute to cardiovascular disease

fat used as insulation

glycerol enters glycolysis

2 carbon molecules help makes AcetylCoA

nucleic acids (2)

polymer of nucleotide monomers

responsible for storage, expression and transmission of genetic information

nucleotide

phosphate group, five carbon sugar and either single or double ring of carbon and nitrogen atoms called nitrogenous base

DNA structure (5)

purine: adenine and guanine

pyrimidine: cytosine and thymine

pairs held together by hydrogen bonds

2 H bonds between A and T

3 H bonds between C and G

DNA vs RNA

Deoxyribonucleic acid ribonucleic acid

deoxyribose ribose

thymine uracil

2 strand double helix single strand

1 form several forms

diversity of protein function (6)

motor proteins- initiate movement

defence proteins- protect against infection/ disease

cell signalling- cell to cell communication

structural proteins- provide support

transport proteins- movement of solutes across plasma membrane

enzymatic proteins- many proteins are specialised to catalyse or speed up reactions

metabolism

biochemical modification and use of organic molecules and energy to support the activities of life

metabolic pathways

series of chemical reactions that occur in a cell

protein (2)

biologically functional molecule that consists of one or more polypeptides

composed of carbon, hydrogen, oxygen, nitrogen and other trace elements

protein structure (4)

1. primary structure: unique sequence of amino acids

2. secondary structure: found in most proteins, consists of coils and folds in the polypeptide chain

3. tertiary structure: determined by interactions among various side chains (R groups)

4. quaternary structure: protein consists of multiple polypeptide chains

Catabolism

breakdown of products to components, releases usable energy in the process

eg carbohydrates into water

anabolism

synthesis of complex products from simpler components

eg amino acids to proteins

metabolism (C&A)

sum total of all the anabolic and catabolic reactions in a cell

cellular respiration definition

breakdown of energy rich molecules to produce cellular energy, O₂ and water necessary

cellular respiration(4)

production of organic fuels

glycolysis

citric acid (krebs) cycle

oxidative phosphorylation

oxidation and reduction(3)

transfer of electrons during chemical reaction are referred to as reduction-oxidation reactions (redox)

oxidation: loss of electrons

reduction: gain electrons

cellular respiration, stage 1 glycolysis (9)

energy investment

• steps 1 to 3

• 2 ATP hydrolysed to create fructose-1, 6 bisphosphate

Cleavage

• steps 4 to 5

• 6 carbon molecules broken down into two 3 carbon molecules of glyceraldehyde-3-phosphate

energy liberation

• steps 6 to 10

• two glyceraldehyde-3-phosphate molecules broken down into two pyruvate molecules- produces 2 NADH and 4 ATP

cellular respiration- stage 2 pyruvate breakdown (5)

in eukaryotes, pyruvate transported into the mitochondrial matrix

broken down by pyruvate dehydrogenase

molecule of CO₂ removed from each pyruvate

remaining acetyl group attached to CoA to make acetyl CoA

yield= 1 NADH for each pyruvate

cellular respiration- stage 3 citric acid cycle (4)

metabolic cycle, some enters and some leave, series of organic molecules regenerated in each cycle

acetyl removed from acetyl CoA attached to oxaloacetate to form citrate(citric acid)

series of steps releases 2 CO₂, 1 ATP, 3 NADH and 1 FADH₂

oxaloacetate regenerated to start cycle again

cellular respiration- stage 4 oxidative phosphorylation (10)

high energy electrons removed from NADH and FADH₂ to make ATP

requires oxygen

oxidative process involves electron transport chain

phosphorylation occurs by ATP synthase

electron transport chain

• NADH donates electrons to complex 1 | H⁺ pumped across

• FADH₂ donates electrons to complex 2

• when electrons are passed along | H⁺ pumped across membrane

• H⁺ passed back through ATP synthase where 1 ATP molecule is produced

30-32 ATP produced

fermentation (4)

make ATP my glycolysis only

muscle cells produce lactate

yeast make ethanol

produces less ATP