Biochem
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- Created by: Alex
- Created on: 16-05-13 10:35
Do Purines have double or single rings
Double - containing carbon and nitrogen
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whats the difference between ribose and deoxyribose
on deoxyribose's C2 the OH group replace by H
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What's a nucleoside
Nitrogenous base linked to a sugar
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Pyrimidine bases
#cytosine, Uracil and Thymine
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Nucleotide
Molecule containing one of more phosphate groups, a 5-carbon ribose/deoxyribose sugar and a nitrogenous base (purine/pyrimidine)
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Where are phosphates added?
5' carbon of the sugar
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Do pyrimidines have double or single rings
Single
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Purine Bases
Adenine and Guanine
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Polynucleotide
Molecular chain of nucleotides linked by a sugar-phosphate backbone and joined by phosphodiester bonds. Phosphate is at 5' end and OH from sugar at 3'
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Whats ssDNA
Single stranded DNA e.g in bacteriophage
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What bases pairs to what
Pyrimidine to purine A-T G-C
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What type of bond forms between base pairs?
Hydrogen bonds
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whats dsDNA
Double stranded DNA loop. e.g in bacteria and viruses
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How many bonds form between G and C?
3
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What's normal DNA
Linear double stranded DNA, in eukaryotes & perfectly patallel
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Are DNA strands parallel of antiparellel
Antiparallel - attracted to each other, trying to collapse ladder causes helix
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most common type of helix
Alpha-helix
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3 main types of RNA
transfer(t), Ribosomal(r) and messenger(m) RNA
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messenger RNA
the template for protein synthesis; the form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell
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Transfer RNA
RNA consisting of folded molecules that transport amino acids from the cytoplasm of a cell to a ribosome
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Ribosomal RNA
structural component in ribosomes.
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Which type of RNA is most common?
rRNA
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Which type of RNA is transcribed from DNA?
mRNA
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What is rRNA measured in?
Svedbergs - rate at which particles of given size and shape travel to the bottom of a tube under centrifugal force
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what shape it tRNA
Clover leaf
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Which RNA is double stranded
None of these, numpty
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Where is the amino acid binding site on tRNA
3' end
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is the anticodon or codon on tRNA?
Anticodon
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What does mRNA specify?
A.Acid sequence of protein
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What does endonuclease do?
Enzyme that hydrolyses(breaksdown) the nucleotide chain by cleaving(splitting) the phosphodiester bond of the polynucleotide chain - breaks at the phosphate between the sugars.
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Size and submit structure of prokaryotic ribosome?
70s total. made of 30s and 50s
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How many different amino acids
20
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Whta is caused by a tyrosine deficiency?
Phenylketonuric subjects - can't synthesise tyrosine from phenylalanine due to lack of conversion enzyme
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what is tyrosine synthesised from?
non-essential a.acid synthesised from phenylalanine.
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Size and submit structure of eukaryotic ribosome?
80s made of 40s and 60s
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how many essential amino acids
10
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Use of tyrosine
In proteins and a precursor for molecules & neurotransmitters dopamine & norpinephrine
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What should phenylketonuric subjects have diets low in?
Phenylalanine and aspartame.
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What is caused by a deficiency in protein?
Kwashiorkor
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Symptoms of Kwashiorkor
Diarrhea, pot belly, risk of infection, enlarged liver. can cause physical and intellectual disabilities
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What is glyphosate?
A herbicide
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How does glyphosate act?
Inhibits enzyme involved in synthesis of tyrosine, tryptophan and phenylalanine (specifically needed for growth)
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Structure of an amino acid,
Central alpha-Carbon, hydrogen atom, carboxylic acid COOH group, Amino group NH3, R-group that chabges properties of A.acid
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Are amino acids chiral?
Yes, can exist in D or L form
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What form of amino acid (D or L) are constituents of proteins
L
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Different classifications of a.acids
Non-polar, polar uncharged, polar charged +, polar charged -
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Buffer
solutions that resist changes in ph upon an addition of an acid or base
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Non-polar amino acid
Hydrophobic, no charge on r-group, alkyl side chian, equal number of amino and carboxyl groups
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What can ph inbalance cause in the body?
Alkalosis or acidosis
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Polar-uncharged amino acid
No charge on R-group, participate in H bonding of protein strucute, no extra acid or base on side chian
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What bonds are A.acids linked by?
Peptide
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Polar-charged positive A.acid
Basic amino acid, positive charge on R group
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How amino acids bond/ how peptide bonds join
alpha-carboxyl group of one links to alpha-amino group of another. Water molecule is lost
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Polar-charged negative a.acid
Acidic amino acid, negative charge on r-group. has a COOH side chain, acid functional group.
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Whats a protein
Linear polymers built of monomers of amino acid units
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What structures can be present in the secondary structure of proteins?
Alpha-helices and Beta-pleated sheets
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whats al alpha-helix
coiled structure - determinded and maintained by H bonds between A.acids and backbone
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Whats a Beta-pleated sheet
two or more B-strands lying directly next to each other joined by H bonds. can be parallel or antiparellel
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Different forces in protein structure
Hydrophobic interactions, Hydrogen bnds, electrostatic interactions, metal ion coordination, covalent bonds and disulfide bonds
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Hydrophobic interactions
Hydrophobic amino acids clum together on the inside of the protein
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Electrostatic interactions
Attractions between negative and positive molecules
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Covalent bridges
When atoms share electrons
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Disulfide brideges
Strong covalent bond forming with two Sulfide molecules in middle
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What genetically causes Cystic Fibrosis?
Mutation in the CFTR gene- causes incorrect protein of protein that regulates cellular salt levels, leading to abnormal transport of chlorine and sodium across epithelium - exocrine glands produce sticky mucus
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Symptoms of CF
Chronic cough, wheezing, respiratory infections, salty skin & problems with water transport
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Gene therapy of CF
Viral vectors delivery correct versions of genes into cells - breathed in. would induce corrected phenotype
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Genetic cause of sickle cell anaemia
Valine is substituted for glutamic acid causing a mutant beta globin
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Steps in genetic engineering (basic)
1. obtain foreign gene 2.place gene into bacterial cell 3.ensure function of gene 4.identification of 'transformed' cells
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How to prepare foreign DNA
1. chemical synthesis 2.have mRNA strand 3.reverse transcriptase correspond into DNA 4.alkali destroys mRNA 5.DNA polymerase make perfect copy of original RNA (cRNA)
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How cDNA is taken up by host
Naturally by Bacteria as food, Incoroporated into a vector, Virus(one specifically stable in host) of plasmid
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problem of bacteria taking up cDNA naturally
Will digest it using nucleases
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what is a restriction enzyme linkers
Linkers are the chemically synthesized double stranded DNA oligonucleotides containing on it one or more restriction sites for cleavage by restriction enzymes
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What gene is put in artificially into a plasmid typically and why
Beta-galactosidase gene, right through the restriction endonuclease site. so if new foreign DNA added it interrupts the gene so the enzyme cannot be made
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What natural gene to help with identification may be found in plasmids?
Ampicillin resistance gene - so sells with a whole plasmid or hybrid plasmid + DNA will survive
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How to put DNA into a plasmid Vector
1. attach linkers to foreign DNA 2.Cut with restriction endonuclease enzyme 3.cut vector with same endonuclease 4.mix cut plasmid & DNA together 5. DNA hybridises into vector by sticky ends. 6.Dna ligases fixes DNA 6.1 in 10,000 join
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What to do after mixind plasmids and DNA
1. Take mixture and add to host bacterial cells 2.Ones with plasmid/hybrid plasmid survive 3.Identify Beta-galactosidase activity 4. Harvest correct bacteria
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How to monitor for Beta-galactosidase enzyme activity?
X-gal as enzyme substrate. X-gal is white but if Beta-galactosidase is present then it turns the substrate blue. Therefore you want to harvest the white colonies
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what is translation
step in protein biosynthesis wherein the genetic code carried by mRNA is decoded to produce the specific sequence of amino acids in a polypeptide chain. The process follows transcription in which the DNA sequence is copied (or transcribed) into an m
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types of RNA used in translation
rRNA(ribosomal), tRNA, and mRNA
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structure of tRNA
Transfer RNA. single stranded, ends with CCA at 3' end. Covalently linked to a A.acid that corresponds with the anticodon arm. anticodon arm has 7 bases and 5 base pairs in. Has 2 side arms with stem and loop - length & base number variable with type
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What is the Amino-acyle tRNA synthase reaction?
Reaction that joins Amino Acid + tRNA + ATP -> Amino-acyl tRNA (tRNA with a.acid attached) + AMP +PPi. an A.acid is added to ACC region.
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Protein synthesis
Synthesis of a protein, directed by the genetic code, which occurs by translation of mRNA into protein via tRNA. The ribosome attaches to the mRNA, using it as a template.
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Whats required to initiate Protein synthesis in prokaryotes
70s ribosome, mRNA, amino-acyl tRNA, Initiation factors IF-1,IF-2 and IF-3 and GTP
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What happens to ribosomes just before protein synthesis in prokaryotes?
They spontaneously dissociate as subunits split
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What binds to ribosomes to prevent re-association?
IF-1 and IF-3 bind to 30S sub-unit
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Whats an initiation complex?
tRNA fMET + IF-2 + GTP bing. If-2 and GTP help speed up reaction with start codon, it then binds to mRNA
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What happens when If-1 and IF-3 are released?
50s ribosomal sub unit rejoins - minds to mRNA aswell
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What is the purpose of GTP in initiation complex?
Hydrolysed to GDP, providing energy for IF-2 release
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What is elongation?
Addition of A.acids to the carboxyl end of the growing chain
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What is required for chain elongation?
70s initiation complex, EF-Tu (Elongation Factor), EF-Ts, GTP and Aminoacyl tRNAs
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Function of Elongation Factors
Deliver Amino-acyl tRNA to the Ribosome
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Function of GTP
to bind EF-TU to tRNA and then later is hydrolysed(when appropriate codon-anticodon formed) and energy is used to shift ribosome 3 nucleotides to the right.
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Function of EF-TU (another)
protects aminoacyl-tRNA from hydrolysis
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What bond is formed between amino acids?
Peptide
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What forms the bond between A.acids?
Peptidyl transferase
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How does Peptidyl transferase work?
catalyses bond between 2 a.acids. breaks bond between 1st tRNA and a.acid. Helps move ribosome 3 nucleotides to right. continues functioning until termination codon.
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Whats a nucleoside?
Nitrogenous base + sugar (generally tobose/deoxyribose
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What does De novo synthesis mean?
Synthesis from scratch
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Nitrogen cycle
Cyclic movement of nitrogen in different chemical forms from the environment, to organisms, and then back to the environment.
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Whats a nucleotide?
Nitrogenous base + sugar + phosphate ester
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Nitrogen fixation
The capture and conversion of atmospheric nitrogen gas into nitrogen compounds. e.g. N2 -> NH4+
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what % of global atmosphere is nitrogen?
78%
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What it NH3?
Ammonia gas
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What causes Nitrogen fixation?
The haber process, microorganisms and legumes with symbiotic bacteria in root nodules
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Name a symbiotic bacteria in legumes?
Rhizobium
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What benefits to Rhizobium get from plants?
Carbohydrate precursors, supply of leghaemoglobin
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What is NH4+
Ammonium ion
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What enzyme is used by microorganisms to fix nitrogen?
Nitrogenase
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Whats the minimum of molecules of ATP hydrolysed for each molecule of N2 reduced?
16
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What element inhibits nitrogenase in nitrogen fixation?
Oxygen
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What is NO3-?
NitrAte
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What's a heterotetramer?
A heterotetramer is protein containing four non-covalently bound subunits, wherein the subunits are not all identical. such as hemoglobin and nitrogenase
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How do plants reduce nitrate (NO3) to NH4+
Via nitrate reductase (NO3- to NO2-) and nitrite reductase (NO2- to NH4+)
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Nitrification
When ammonium compounds are turned to Nitrogen compounds
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Whats a homotetramer
a protein complex made up of four identical subunits which are associated but not covalently bound
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What bacteria turns ammonium compounds to nitrites?
Nitrosomonas
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What is ammonification?
When nitrogen compounds from dead organisms are turned into ammonium compounds by decomposers
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Denitrification
when nitrates in the soil are converted into N2 gas by denitrifying bacteria
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What beacteria changes Nitrites into nitrates?
Nitrobacter
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Whats a Nitrite
Contains anion NO2-
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NH4+ can be turned into what
Amino acids
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Schiff base
is a compound with a functional group that contains a carbon-nitrogen double bond with the nitrogen atom connected to an aryl or alkyl group, not hydrogen.
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Allosteric enzyme
are enzymes that change their conformation upon binding of an effector.
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Transaminaton
The transfer of an amino group from one molecule to another, esp. from an amino acid to a keto acid
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What amino acids do plants and microbes tend to be deficient in?
Lysine, methionine and tryptophan
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what percentage of cellular energy in animas in consumed by protein biosynthesis?
95%
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What is major site of amino acid breakdown in animals?
Liver
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whats a ketogenic amino acid?
One that cab give rise to ketone bodies or fatty acids
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whats a glucogenic amino acid?
an amino acid that has degraded into pyruvate, alpha-ketoglutarate, succinyl CoA, fumarate or ocalooacetate
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What is amino acid catabolism?
amino acid breakdown
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first step in amino acid catabolism?
The removal of unwanted NH4 (ammonium)
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What happens to removed ammonium?
Converted to urea and excreted
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2nd step in amino acid catabolism
The urea cycle
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What is another name for the urea cycle?
the ornithing cycle
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Enzyme lock and key model
Rigid stable enzyme with an active site that matches the substrate
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Enzyme induced fit model
Active site similar to substrate, substrate firces the enzyme's shape to fit it
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How do enzymes act as catalysts?
Reduce the activation energy of a reaction
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Activation energy
amount of energy needed to start the reaction.
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Transition state of a reaction
tate corresponding to the highest potential energy along this reaction coordinate - the most unstable state for the substrate
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How do enzymes act as catalysst
they interact chemically with the substrate
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covalent catalyst
an accelerated chemical reaction in which the substrate becomes temporarily bound through a covalent linkage (sharing of pairs of electrons between atoms) to an active site on the catalyst
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acid-base catalysis
The increase in speed of certain chemical reactions due to the presence of acids and bases. Read more: http://www.answers.com/topic/acid-base-catalysis#ixzz2TqFTeTYW
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metal ion catalysis
use of metal ions to activate bound water through the formation of a nucleophilic hydroxide ion.
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Enzymes are grouped into classes depending on what
types of reaction that catalyse
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Enzyme cofactor
Naturally occurring molecules that serve to activate specific enzymes
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Factors influencing enzyme activity
Environment - pH and temp, Inhibitors- competitive and non-competitive and covalent modification
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Effect of pH on enzyme activity
alters charge on amino acid. changes active site + whole enzyme
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Competitive inhibition
Inhibitor mimics substrate structure and competes for binding site
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Covalent modification of an enzyme
the reversible attachment of a chemical group such as phosphorylation
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Enzyme kinetics
The study of the rate of chemical reactions that are catalysed by enzymes
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Protease
Enzyme that breaks down proteins and peptides - needed for recycling of amino acids and activiation of enzymes
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non-competitive inhibitor
Changes binding site to prevent enzyme action
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What are 2 major differences in sugar & base composition between DNA & RNA
DNA uses Deoxyribose for sugar, RNA uses Ribose. DNA bases are GTAC, RNA bases are ATUC
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Reaction catalysed by endonuclease
hydrolysis/breakdown of the nucleotide chain by cleaving the phopsphodiester bond of the polynucleotide chain (breaks phosphate between sugars)
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Role of f-met-tRNA in procaryotes
(formyl-methionine) methionine is always the first amino acid in a peptide chain. it starts protein synthesis. goes into P (2nd site in ribosome)
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Job of phosphofructokinase
Controls production of ATP in glycolysis
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2 allosteric effectors of key glycolytic enzyme phosphofructokinase
When ATP becomes too high it becomes an allosteric inhibitor and inhibtis the breakdown of fructose-6-phosphate into fructose-1,6-biphosphate. decrease in pH also inhibits phosphofructokinase-augments inhibitory effect of ATP
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How electron transport chain can be used during respiration to make STP
Oxidative phosphorylation
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Oxidative phosphorylation
electrons from NADH pass down electron carriers & donated to O2 to form H2O. Carrier complexes 1,3 & 4 associated with Proton pumps. energy conserved by pumping protons out membrane setting up a conc gradient. Conc gradient used in energy for ATPsyn
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Amino acids considered essentialin the human diet
Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan & Valine
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Chargaffs law is
Purine = Pyrimidines in DNA. Shows purin always base pairs with PPyrimidines
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Photosystem that is involved in splitting water during photosynthesis
PS2
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What is energy?
The capacity to do work
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Bioenergetics
How living systems capture, transform and use energy to perform work and stay alive
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First law of thermodynamics
Energy within a system is conserved, it can be changed from one form to another, but cannot be created or destroyed. e.g. Glucose + O2 <--> CO2 H2O + energy
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What chemical modification differentiates sugar ribose from deoxyribose?
Deoxy = no Oxy = just a H on C1 Ribose has OH on C1
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What is meant be terms 5' and 3' end when describing a polynucleotide?
5' bond in on C5. 3' bond is on C3. Direction of Chain
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What is Chargaffs law?
Pyrimidine = Purine. T=A C=G
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General structure of an amino-acyl tRNA
3' end always ends in ACC - where the a.acid binds to. Cloved leaf shape. 3 stem and loop side arms, one is a anticodon arm with 5 base pairs & 7 bases in loop - same in all tRNA. Side arms variable in tRNA
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Competitive inhibition of an enzyme
Blocks an active site. doesn't bind to enzyme. Prevents substrate from binding
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Main role of fermentation during respiration under anaerobic conditions
Reproduce NAD. Kepps glycoloysis & muscles going for a short period of time before metabolism shuts down.
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Function of proton pumps associated with the mitochondrial eectron transport chain?
Energy for ATP synthesis. Oxidative phosphorylation. electrons from NADH passed down and combine with O2 to form water. Proton gradient used to power ATP synthase
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Describe reaction catalysed by ribulose bisphosphate carboxylase
= Ribose. Reacts with ribulose bisphosphate, joins a CO2. makes 2 molecules of glycerate 3-p. irreversibly fixes CO2
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Name 3 amino acids that can be synthesised from the precursors oxaloacetate, alpha ketoglutarate and pyruvate
Alanine, Arginine, Aspartate and Proline
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Name an amino acids considered essential in the human diet
Tryptophan, Phenylaline
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Defininf terms used, what thermodynamic quantity can be measured in a bomb calorimeter
Delta E. Delta=Change E=Energy. Change in energy produced by combusting or oxidising a substrate
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Defining terms used, write an equation that relates changes in standard free energy, enthalpy and entropy
DeltaG =DeltaH-TDeltaS (Gibbs-Helmhotz). DeltaG=change in standard free energy. DeltaH=change in enthalpy DeltaS=Change in Entrapy
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Enthalpy =
measure of heat change during a reaction whilst under constant volume etc
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Entrapy
Caos
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2nd law of thermodynamics
1. Free energy must increase DeltaG\<0 2.Energy must increase DeltaS>0
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Give an example of a redox couple in conventional format
NAD+/NADH Ferric/Ferrous
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What type of reaction is involved in glycosidic bond formation
Condensation. water given off
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What is meant by the term 'steroisomer'?
Same molecular formula, different arrangement in space
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What gives cellulose it's strength?
Hydrogen bonds between the glucose polymers
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Allopurinol is sometimes given to patients with acute leukemia who are being treated with anti-cancer drugs. why?
Cancer raises uric acid levels. Allopurinol reduces uric acid by non-competitively inhibiting Xanthine oxydase.
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The shape of hair is determined in part by the pattern of disulphide bonds in keratin, it's major protein. How can curl be induced?
Disulphide bonds in hair have been broken by addition of Thiol (SH) and heat. hair can be curcled and an oxidising agent added to refrm disulfide bonds and stabalise shape.
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Historically fluorouracil was an important drug used in cancer treatment. Discuss the rationale behind its application in the context of nucleotide biosynthesis
prevents tmp synthase production. cells need tmp synthase for the synthesis of DNA
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what is the product of the reaction catalysed by the enzyme acetyl coenzyme A carboxylase? ACC
malonyl CoA
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How many molecules of Malonyl Coenzyme A are required to make one molecule of Palmitoyl Conenzyme A (C16:0) in the reaction catalysed by fatty acid synthatse?
7
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In what part of a lipoprotein would you expect to fins a cholesterol ester?
Middle
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Which class of lipoprotein is primarily used in reverse cholesterol transport?
HDL
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How do fatty acids enter the mitochondira prior to being oxidised?
Carnitine binds to fatty acids to bring them into the mitochondria membrane. Carnitine + fatty acid = Acyl Carnitine
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Outline the reaction catalysed by a restriction endonuclease
Cuts DNA backbone. always cuts a palindromic sequence. recognises specific base sequence. can cut straight or stick ends.
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What is the role of f-met-tRNA in protein synthesis in procaryotes
Formyl-methionine-tRNA. specialised tRNA, needed to start synthesis. Binds in P peptidyl site in ribosome
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Name two environmental factors that can influence enzyme activity
pH and temp
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Name two allosteric effectors of the key glycolytic enzyme phosphofructokinase
ATP and Citrate
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Photosystem used for splitting water in photosynthesis
2
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What is an asymmetric Carbon?
One with a bond to 4 different groups
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Name 2 hexose sugars
Glucose & fructose
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What type of glycosidic link exists between the 2 monosaccharides that make up sucrose?
(glucose + fructose) alpha-1,2) glycosidic linkage
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What type of glycosidic link exists between the 2 monosaccharides that make up lactose?
Glucose + galactose (Beta-1,4)
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What type of glycosidic link exists between the 2 monosaccharides that make up maltose?
2x glucose (alpha-1,4)
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Which is the major storage polysaccharide found in animal cells
Glycogen
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What is the major storage polysaccharide found in plant cells?
Starch
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What is the major product of the reaction catalysed by the enzyme fatty acid synthase?
Palmitic acid
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What reaction is catalysed by the enzyme Delta9 Desaturase?
Stearic Acid -> oleic acid
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Name the major regulatory enzyme in the synthesis of cholesterol
HMG- CoA reductase
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In what part of a lipoprotein would you expect to find a phospholipid?
bound to a cholesterol to make up the membrane of a lipoprotein particle
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In what part of the cell are fatty acids oxidised?
Mitochondria.
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Michaelis Menton equation
Vo= Vmax x [s] / km + [s]
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Vo
velocity (rate) of a reaction
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km
Affinity of a substrate for enzyme. low km = high affinity
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S
substrate
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Lineweaver-burke equation
Vo = vmax + (vmax x [s] / km)
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vmax
maximum velocity - fastest speed of a reaction
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aldehyde group
H-C=O on end of a molecule
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Ketose group
=O coming of a C in the middle of a molecule
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carboxylic acid
COOH
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Throught biosynthesis there are several conserved mechanisms in which one carbon unit is donated to the process. name 2
Rubisco. acetyl CoA -> Malonyl CoA by Acetyl Coenzyme A Carboxylase (ACC)
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Defining all terms involved, write the equation where standard free energy can be determined from equilibrium studies
Delta G^o = -R.T. in Keq. (Keq = equilibrium constant, R=gas constant, T=temp, ln =natural log)
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Name one common reducing sugar
Glucose, fructose, lactose
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What two enzymes are required to produce oleic acid(C18:1) from palmitoc acid (c16:0)
elongase - adds malonyl coA for extra 2 C. Delta 9 dehydrogenase adds double bonds.
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What breaks down starch?
alpha amylase
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What breakse down cellulose?
cellulase
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Other cards in this set
Card 2
Front
whats the difference between ribose and deoxyribose
Back
on deoxyribose's C2 the OH group replace by H
Card 3
Front
What's a nucleoside
Back
Card 4
Front
Pyrimidine bases
Back
Card 5
Front
Nucleotide
Back
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