BIOL1007 Module 1- Information Transfer

Properties of living organisms

Properties of living organisms

CHEREC
Cells, homeostasis, energy, reproduction, evolution, complex and organised.

Prokaryote

unicellular organism lacking a nucleus

Eukaryote

A cell that contains a nucleus and membrane bound organelles

Three domains of living things

Archea, Bacteria, Eukarya

Archaea

Domain of unicellular prokaryotes that have cell walls that do not contain peptidoglycan

Bacteria

Domain of unicellular prokaryotes that have cell walls containing peptidoglycan

Eukarya

Domain of all organisms whose cells have nuclei, including protists, plants, fungi, and animals

Main elements present in living organisms

CHNOPS
Carbon, hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur

Mass of water in body

49kg

Molecules of life

nucleic acids, carbohydrates, lipids, proteins

Importance of carbon

- simultaneously form multiple bonds
- compounds inert or kinetically regulated
- good targets for enzymatic control

General features of Biopolymers

- defined beginning and end
- synthesised in one direction only
- some of monomer is lost in polymerisation, leaving residue incorporated into chain
- synthesis through anabolic dehydration reactions

Number of pairs and proteins in genes

23 pairs
20000 proteins

Genome

DNA

Transcriptome

the set of all RNA molecules in one cell or a population of a cell

Proteome

the complete set of proteins expressed by an organism, cell or tissue type

Chromosome

DNA molecule with all or part of the genome

Biopolymer

a polymeric substance occurring in living organisms

Central Dogma of Molecular Biology

DNA -> RNA -> Protein

Bacterial genome

single circular chromosome

Nucleotide

sugar, phosphate, base

Nucleoside

sugar, base

nucleobase

nitrogenous base

purine

a nitrogenous base that has a double-ring structure, either adenine or guanine

pyrimidine

a nitrogenous base that has a single-ring structure; thymine, cytosine, or uracil

B-DNA

the standard conformation of double-helix DNA

Hydrogen bond

attraction between partially electronegative and electropositive atoms

Phosphodiester bond

covalent bond between nucleotides

Deanimation

loss of amine

Electrophoresis

separation of particles in a liquid based on size by application of an electrical field

Tm (melting temperature)

the temperature at which 50% of the double helix structure is lost

Electrostatic repulsion

repulsing between charged atoms of the same charge

N-glycosidic bond

covalent bond between sugar and base in RNA/DNA

Base pairing

hydrogen bonding between bases

major groove

wide groove in B-DNA

minor groove

narrow groove in B-DNA

5' phosphate

negatively charged molecule at the beginning of the polymer

3' hydroxyl

-OH group at end of polymer

Sugar phosphate backbone properties

- negative charge
- hydrophilic

ethanol precipitation

nucleic acids made unsolubel by mixing with salt and ethanol

Mononucleotide

one phosphate group

Nucleobase absorption

260nm

Number of bonds in GC and AT/AU bonding

3 hydrogen bonds in GC, 2 hydrogen bonds in T/AU

Direction of double helix

right handed double helix

Helical structure

due to angle of bond between the base and sugar

DNA as a genetic store

Double stranded: Provides two copies and a template for repair
Stable: not prone to degredation- cells can repair cytosine de-animation

Major features of proteins

peptide bond, amino and carboxyl terminals, side chains, alpha carbon

Alpha amino acid

COOH, H2N, R side chain

Peptide bond

covalent bond formed between amino acids through energetically unfavourable condensation polymerization

Primary structure

protein sequence of amino acids

secondary structure

local interactions in the polypeptide chain with defined hydrogen bonding patterns and backbone bond angles

tertiary structure

overall fold of a protein

side chain

functional groups which distinguish amino acids from each other

alpha helix

form of protein secondary structure that forms a right handed helix

beta strand

extended form of protein secondary structure

beta sheet

assembly of beta strands

quaternary structure

arrangement of folded protein subunits

protein folding

process of forming tertiary structure

N-terminus

amino-terminal end of a protein or peptide

C- terminus

carboxy-terminal end of a protein or peptide

Beta turn

form of protein secondary structure, often formed between beta strands in a beta sheet

Proteins make up what percentage of a cell by dry weight?

50%

Ribosomal RNA

type of RNA that associates with proteins to form peptide bonds

resonance

Variations of the same molecule caused by rotation about a single bond

hydrophobic aliphatic

Amino acid side chain containing CH2

Aromatic

Amino acid side chain containing rings with conjugated bonds and an absorbance of 280nm

Polar and non ionic side chains

side chains with OH, SH or ONH2

Acidic side chains

Side chains with RCOO-

Basic side chains

Side chains with N+

Parallel beta strand

Strands pointing in the same direction on a beta plated sheet

Antiparallel beta strand

Strands pointing in opposite directions on a beta plated sheet

Nitrogen to carbon

Direction of arrows on beta strand

Hydrophobic effect

Driving force for protein folding

pH, solvents and temperature

important influencers on maintaining protein structure

Cysteine

A covalent bond formed between cystine residues under oxidizing conditions outside the cell

5-50 degrees

the range wherein most of life exists on earth

protein hydrolysis

the breakdown of proteins into their constituent amino acids in very acidic or basic conditions with added heat or pressure

1.2 nm

the diameter of alpha helix and the width of B-DNA major groove

Exergonic

Favourable reaction involving the release of energy

Endogonic

Unfavourable reaction requiring energy input

Substrate

Under standard conditions, does the substrate or product contain more energy in a reaction?

Product formation

At equilibrium, is product formation or substrate formation favoured?

Induced fit model

An enzyme will change shape/conformation as it binds to the substrate to help stabilize the transition state.

Characteristics of enzymes

Mostly proteins (can be RNA)
Highly varied in terms of size, function, need for co factors and ability to be regulated

Compartmentalization

A method of regulating proteins to ensure they are performing the appropriate function

Same amount of product

When the amount of enzymes are doubled, the reaction will happen faster but will end with ________

Linear rate of dP/dt

The measured reaction rate

5' to 3'

The direction in which DNA is copied

phosphodiester bond

formed by DNA and RNA polymerases

Pyrophosphate

molecule released by RNA and DNA polymerases that breaks into 2 and creates energy to drive reactions.

Are polymerases biologically favourable or unfavourable?

unfavourable

nucleotide monophosphate

the monomer which is added to the 3' end of a growing RNA/DNA chain by polymerase

Unique properties of DNA polymerase

- Need a primer
- Proofreads last nucleotide
- Use deoxynucleotide triphosphates as substrate
- makes single new template for next generation of cells

Unique properties of RNA polymerase

- Don't need a primer
- don't proof read last nucleotide
- Use ribonucleotide triphosphates as substrates
- Many copies transcribed

Reverse transcriptase

DNA polymerases made by retroviuses that make DNA from an RNA template

Activation energy

The energy required to initiate a reaction

Catalyst

speeds up reaction rates, not used up in a reaction and doesnt affect equilibrium

Equilibrium

rates of forward and reverse reactions are the same

Kinetics

how quickly an event happens

Thermodynamics

measures and transitions of intrinsic energy