Topic 2 Wood Flashcards
Amino acids molecules
- carbon
- oxygen
- hydrogen
- nitrogen
- sulphur (only 2 of them)
Structural protein
tendons, cartilage, hair, nails
Contractile protein
muscles
transport protein
haemoglobin
storage protein
milk
hormonal protein
insulin, growth hormones
enzyme protein
catalyses reactions in cells
protection protein
immune response
What are proteins used for?
- catalysis: catalyzing the breakdown of products
- transport: some proteins transport various substances
- information transfer: for example hormones
Where does the bond form between amino acids?
between the carboxyl and amino group
How are two amino acids joined together?
in a condensation reaction, removing water and forming peptide bonds (add water in hydrolysis to reverse)
Primary structure of a protein
the sequence of amino acids joined together to form a polypeptide chain
What does the shape of a protein determine?
its function
Amino acids are soluble in water
- they form ions in solution as a hydrogen ion leaves the carboxyl group and a hydrogen ion joins the amine group
- this means the molecule becomes dipolar (with the amine group positive)
Secondary structure of a protein
localized 3D shape formed by a polypeptide chain e.g. alpha helix or beta pleated sheet (only hydrogen bonds)
Tertiary structure of a protein
Overall compact 3D shape formed by a fully folded polypeptide. Multiple bonds: hydrophilic/phobic interactions, disulphide bridges, ionic, hydrogen
Quarternary structure of a protein
combination of different polypeptide chains and sometimes non-protein groups
Alpha helix
coiled, corkscrew shape held by hydrogen bonds
beta pleated sheet
folded, held side by side
Hydrophilic/phobic interactions
trap water in 3D shape
disulphide bridge
bond between two sulphurs (only in two amino acids)
Ionic bond
bond between charged molecules
van der Waales forces of attraction
block between CH3
Two groups proteins can be split into:
globular - blob shape and fibrous - thin shape line
Globular proteins
- folded into a compact spherical shape
- are soluble due to hydrophilic side chains that project from the outside of the molecule
- 3D shape is crucial in ability to form enzyme-substrate complex and catalyse reactions within cells
- 3D shape critical in roles in binding to other substances (e.g. antibodies, enzymes, insulin)
Fibrous proteins
- remain as long chains
- several polypeptide chains can be cross-linked for extra strength
- are important structural molecules (e.g. hair skin collagen, tendons, bones, cartilage)
What type of protein are enzymes?
globular proteins
What reactions does an enzyme speed up?
both anabolic (building up) and catabolic (breaking down) reactions but not reactions that otherwise wouldn’t occur
How do enzymes work?
they lower the activation energy required for the reaction to occur
Key features of an enzyme:
- don’t get used up
- the active site is where the substrate binds to
- many enzymes are specific to just one reaction
Lock and key theory
- various substrate molecules approach the enzyme’s active site
- only one with a specific shape will fit
- this binds to the active site forming an enzyme-substrate complex
- the enzyme catalyses the reaction either breaking bonds or making them
- then the products are released
Features of the lock and key theory
- lowers the activation energy
- still there at the end (doesn’t get used up)
- only one reaction can occur at a time as only one enzyme-substrate complex can be formed at a time
Induced fit theory
- substrate molecule moves into the active site (only needs to be a similar shape)
- forces between the two molecules distorting the enzyme and its active site so it tightly envelopes the substrate
- enzyme-substrate complex is formed
- breaks down/builds up
- leaves
- enzyme springs back into shape
Enzyme
biological catalyst
Biological catalyst
globular protein that speeds up a reaction by lowering the activation energy
activation energy
energy required to start a reaction
active site
where the enzyme-substrate complex forms and the reaction occurs
enzyme-substrate comlpex
where the substrate binds to the active site
lock and key theory definition
the substrate fits exactly into the active site
induced fit theory definition
substrate forces its way into the active site
Factors affecting the rate of reaction:
- temperature –> bonds break, change active site shape, can’t bind, no reaction
- pH
- enzyme concentration –> increase rate of reaction
- substrate concentration
Competitive enzyme inhibitors
- active site directed
- all heading for active site,different substrate goes to active site, slows down doesn’t stop
Non-competitive inhibitors
- non-active site directed
- binds to elsewhere on enzyme, active site changes shape, no reaction can occur
- when removed goes back to normal
Enzyme inhibitors
- can be either reversible or irreversible
- can be competitive or non-competitive
DNA
deoxyribose nucleic acid (without oxygen/lacking)
RNA
ribose nucleic acid
Nucleoside
- (pentose) sugar + nitrogenous base
- formed in a condensation reaction
Nucleotide
- nucleoside (sugar + nitrogenous base) +phosphoric acid
- formed in a condensation reaction
What is the bond between a phosphate group and sugar called?
phosphoester bond
Name the four nitrogen bases
- adenine
- thymine (in RNA uracil is used instead)
- cytosine
- guanine
Purine base
2 carbon rings e.g. adenine and guanine
Pyrimidine base
1 carbon rings e.g thymine, cytosine and uracil
Which bases are matched together
- adenine and thymine (2 hydrogen bonds)
- cytosine and guanine (3 hydrogen bonds)
5 prime end: carbon 5 at the top
will have a 3 prime end: carbon 3 at the other end
Opposite strand 3’ end at top
will have a 5’ end at bottom –> strands run antiparallel
How is DNA packaged
- DNA is wrapped around histone proteins
- These histone proteins are packaged together into octaves (groups of eight)
- This forms chromatin which in turn forms chromosomes
Gene
sequence of bases on a DNA molecule coding for a sequence of amino acids in a polypeptide chain
Locus
position on a chromosome
Triplet code
is degenerate which means that each amino acid is coded for by more than one triplet/amino acid
Sequence of bases in DNA tells…
the cell which amino acids link together to make a protein
RNA is…
single stranded
DNA is…
double stranded
Why is DNA being double stranded an issue?
because it can’t leave the nucleus but it needs to get the information to the cytoplasm
Where can you find most DNA?
in the nucleus
What does DNA contain?
information/code that determines the cell structure and function by telling the cell which proteins to make
How does RNA leave the nucleus?
through a nuclear pore
What are the 3 types of RNA involved in protein synthesis?
- mRNA (messenger)
- tRNA (transfer)
- rRNA (ribosomal)
Transcription summary
- DNA unwinds
- DNA is copied into mRNA which can then leave the nucleus through a nuclear pore
Translation summary
- mRNA passes through the ribosome
- tRNA brings the amino acids to the ribosome and temporarily bonds to the mRNA
- the codon and anticodon match up
- This codes for a protein before the tRNA leaves and the next protein is translated
- this creates a polypeptide chain
Conservative DNA replication
- new strands of DNA form alongside existing double helix
- one double helix has parents, one is new
Semi-conservative DNA replication
- DNA unzips (proteins and enzymes involved) and new nucleotides form alongside each strand
- one parent strand, one new strand for each double helix
Dispersive DNA replication
- DNA completely breaks down then reforms using pre-existing and new nucleotides
- both double helixes are mixed and matched
How does DNA replicate?
by a semi-conservative method
Replication fork
the point at which the two strands are separated
Leading strand
runs in a 5’ to 3’ direction, replicated continuosly
Lagging strand
runs in a 3’ to 5’ direction, replicated discontinuosly
Two strands of DNA run in…
an antiparallel direction. Each strand is replicated in the same way
