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166 Cards in this Set
- Front
- Back
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What does every organism need to stay alive? And why? Lecture 1 |
A carbon source (to build stuff) An energy source (to allow the building of stuff) |
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Which carbon sources can be found on earth? Lecture 1 |
Food CO2 |
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Which type of organism uses food as a source of energy? Lecture 1 |
Heteretrophs |
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Which type of organisms use CO2 as a source of energy? Lecture 1 |
Plants Autotrophs (bacteria) |
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Name an example of an autotroph? Lecture 1 |
Cyanobacteria |
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Which energy sources are there on the planet for organisms? Lecture 1 |
light chemical energy |
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Organisms that use light as a source of energy are? Lecture 1 |
Plants Bacteria (phototrophs) |
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Organisms that use chemical energy are? Lecture 1 |
chemotrophs |
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What does ATP stand for? Lecture 1 |
Adenosine triphosphate |
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How is energy made usefull in organisms? Lecture 1 |
by converting it into ATP |
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What two procedures constitute metabolism? Lecture 1 |
Catabolism Anabolism |
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Describe the process of catabolism shortly Lecture 1 |
release of energy through breakdown of molecules |
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Describe the process of anabolism shortly Lecture 1 |
Recharge of energy through build up of molecules |
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What is an atom? Lecture 1 |
Basic unit of matter |
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What are the two main parts in an atom? Lecture 1 |
nucleus electrons |
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What two parts does the nucleus of an atom consist of? Lecture 1 |
Protons Neutrons |
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What is the charge of a proton? Lecture 1 |
+1 |
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What is the charge of a neutron? Lecture 1 |
no charge |
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What is the charge of an electron? Lecture 1 |
-1 |
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How large is an atom? Lecture 1 |
10^-8 cm |
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How large is a nucleus? Lecture 1 |
10^-12 cm |
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What does the size of an atom compared to its nucleus tell you? Lecture 1 |
That the distance between nucleus and its electrons is hugeeee |
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What do you cal the pathway of an electron? 3 different names. Lecture 1 |
shell orbital energy level |
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What is the movement from an electron around the nucleus like? Lecture 1 |
An electron moves all over the place within its shell unlike planets. |
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How many electrons can an atom have in its first shell? Lecture 1 |
2 |
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How many electrons can an atom have in its second shell? |
8 |
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What does the atomic number tell you about an atom? Lecture 1 |
The number of protons it has. |
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What does the mass number tell you about an atom? Lecture 1 |
The number of protons and neutrons added up. |
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Who came up with the table of elements? Lecture 1 |
Dmitri Medeleev |
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How is the table of elements sorted? Lecture 1 |
An increasing atomic number from left to right and top to bottom. |
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What do the columns in the table of elements represent? Lecture 1 |
Groups or families |
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What is characteristic about noble gasses? Lecture 1 |
They have a completely filled shell. They are therefore stable/unreactive. |
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What is an isotope? Lecture 1 |
Atoms with the same number of protons, but a different amount of neutrons. |
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What can you say about the electrons closest to the nucleus? Lecture 1 |
They have the lowest energy? |
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What are the main electron shells divided in? Lecture 1 |
Subshells |
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What do electrons do within their orbital? Lecture 1 |
They pair up. |
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What is a valence electron? Lecture 1 |
A valence electron has the highest energy and can participate in bonding. |
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In the periodic table, how can you tell how many valence electrons an element has? Lecture 1 |
Column 1 has 1 valence electron in their outer shell - left to right- group 18 has a full outer shell (noble gasses) |
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What happens during a single covalent bond? Lecture 1 |
two atoms contribute 1 electron to form a shared pair. |
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What is special about the covalent bond? Lecture 1 |
It is the strongest bond. |
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What can you say about the reactivity of an atom with more valence electrons than a filled shell? Lecture 1 |
The extra valence electrons can be removed To form a positive ion which is called a cation |
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What can you say about the reactivity of an atom that has fewer electrons than a filled shell? Lecture 1 |
It gains missing electrons to form a negative ion which is called an anion it can also share electrons to form a covalent bond. |
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What is the octet rule? Lecture 1 |
There is a tendency to form a filled s^2 p^2 shell. |
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What does the octet rule apply to? Lecture 1 |
smaller atoms in the periodic table. |
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What is electronegativity? Lecture 1 |
A chemical property that descrbed the tendency of an atom or a functional group to attract electrons. |
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What types of chemical bonds between atoms are there? Lecture 1 |
Pure (nonpolar) covalent bond Polar covalent bond Ionic bond |
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What is a pure (nonpolar) covalent bond? Lecture 1 |
Electrons are shared equally between atoms. |
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What is a polar covalent bond? Lecture 1 |
ELectrons are shared unequally. |
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What is an ionic bond? Lecture 1 |
When an electron is transferred. |
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What can you say about the electronegativity of atoms in relation to the periodic table? Lecture 1 |
electronegativity increases more towards the rigght side of the periodic table. |
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How many electron bonds can the following elements make? C N H O S Lecture 1 |
C 4 N 3 H 1 O 2 S 2 |
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Which element is an exception to the octet rule and how many bonds can it make? Lecture 1 |
P 5 bonds |
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What is organic chemistry mostly about? Lecture 1 |
Carbon compounds |
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What are alkanes? Lecture 1 |
Carbon compounds with: only single bonds |
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What is an alkane called becuase it has only single bonds? Lecture 1 |
A saturated molecule |
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What is the formula for Alkanes? Lecture 1 |
Cn H 2n+2 |
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What are Alkenes Lecture 1 |
Carbon compounds with: Double bonds (unsaturates molecules) |
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What is the formula for Alkenes? Lecture 1 |
Cn H 2n |
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What are the three ways of writing down a structural formula? Lecture 1 |
1. Condensed 2. Expanded 3. Skeletal |
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What are isomers? Lecture 1 |
Compounds with the same molecular formula but a different structural/spatial formula. |
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What types of isomers are there? Lecture 1 |
1. Constitutional isomers 2. Stereo isomers |
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What is a constitutional isomer? Lecture 1 |
Same molecular formula, but different structural formula. |
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What is a stereo isomer? Lecture 1 |
Same molecular formula but different spatial arrangement |
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What types of stereo isomers are there? Lecture 1 |
cis-trans isomerism Enantiomers |
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What does lecture 2: amino acids: synthesis, structures and functions discuss? lecture 2 |
1. The role of amino acids 2. The importance of water and pH 3. amino acids: - chemical characteristics - structures - synthesis - role in metabolism |
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What are the 2 main functions of amino acids? Lecture 2 |
1. Building blocks of proteins (polypeptides) 2. pre-cursor of non-protein biomolecules.
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What is another word for an amino acid as a pre-cursor for non-protein biomolecules? Lecture 2 |
A metabolic intermediate. |
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What types of groups does an amino acid exist of? Lecture 2 |
1. amino group 2. acid group 3. H-group 4. Rest group |
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What is tryptophan a precursor of? Lecture 2 |
Serotonin - neurotransmitter |
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What is tyrosine a precursor of? Lecture 2 |
Neurotransmitters: 1. dopamine 2. epinephrine 3. norepinephrine |
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What is Glycine a precursor of? Lecture 2 |
porphyrins; e.g. heme |
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What is arginine a precursor of? Lecture 2 |
nitric oxide |
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What are aspartate, glycine and glutamine precursors of? Lecture 2 |
nucleotides |
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What is an amino acid? Lecture 2 |
Organic compounds with an amino and a carboxyl group. |
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Allmost all amino acids are alpha-amino acids. what does this mean structure wise? Lecture 2 |
Both the amino and carboxyl groups are attached to the alpha-carbon atom of a carboxylic acid. |
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What can you say about amino acids spatial wise? Lecture 2 |
Almost all of them are chiral. |
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What does it mean when an amino acid is chiral? Lecture 2 |
Two molecules can be mirrored. |
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Most natural amino acids use the L/D sytem instead of the R/S system regarding spatiality. What is the orientation of most amino acids? Lecture 2 |
L-amino acids |
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Which amino acid is the only one that is nonchiral and why? Lecture 2 |
Glycine: Is the R-side chain is not H the molecule is chiral, however the R-side chain of glycine is H. Thus it is nonchiral. |
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In neutral solutions, amino acids exist as zwitterions. What are zwitterions? Lecture 2 |
Ions that carry both a positive and negative charge on the same group of atoms. |
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How is an amino acid a zwitterion? Lecture 2 |
The H atom of the -COOH group is donated to the -NH2 group of the same molecule. |
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Because a zwitterion has a pos. and a neg. charge, it is amphoteric. What does this mean? Lecture 2 |
It acts as a base in an acidic solution ad as an acid in a basic solution. |
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Bases and acids: What is an acid-base conjugate pair? Lecture 2 |
It is the pair in a redox reaction where for eg H2O is transformed into H3O+ . |
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Why is water importand for acid/base reactions? Lecture 2 |
It can act as a proton donor and acceptor. H+ |
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What is the pH and log of pure awtaer at 25 C? Lecture 2 |
pH = -log 10^-7 = 7 |
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What is the internal pH of most living cells? Lecture 2 |
Close to 7. |
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What is the pH of human blood? Lecture 2 |
7.4 |
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In a reaction, what does pK1 and pK2 say about it? Lecture 2 |
They say sth about the neutral form of the amino acid. |
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What is another name for Ka? Lecture 2 |
Acid dissociation constant. |
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What does Ka measure? Lecture 2 |
It is a quantitative measure of the strength of an acid in a solution. |
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What is the Ka value? Lecture 2 |
it is the equilibrium constant for dissociation of acid HA into H+ and A. |
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The larger the Ka value, the .....? Lecture 2 |
the large the Ka value,, the more dissociation of the molecules in solution and thus the stronger the acid. |
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How is Ka determined? Lecture 2 |
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The higher the Ka value, the... the pKa value, and thus the .... te acid? Lecture 2 |
smaller stronger |
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The stronger the acid, the ... its conjugate base? Lecture 2 |
weaker |
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What is the relationship between pH and pKa? lecture 2 |
pH= pKa |
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WHta is the isoelectric point? lecture 2 |
The pH at which amino acids have a neutral charge. |
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What does the pI depend on? lecture 2 |
The structure of the side chain. |
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what is the pKa1 and what is the pKa2? lecture 2 |
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What is the name for the isoelectirc point? Lecture 2 |
pI |
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How can you calculate the isoelectric point? Lecture 2 |
pI=(pKa(n) + pKa(n))/2 n= values that surround the neutral form in the reaction formula. |
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What values does the pl have depending on acidity? Lecture 2 |
acidic amino acid: +/- 3 Basic aa: +/- 9 neutral aa: 5-6 |
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How many naturally occuring amino acids are there? Lecture 2 |
20 |
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How many essential amino acids are there and what are they? Lecture 2 |
9 amino acids that we cannot produce ourselves, we have to eat them to get them. |
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How many amino acids does the 'average' protein have? Lecture 2 |
300 |
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Which groups link together when amino acids bond? Lecture 2 |
Trhough their amino and carboxyl group. |
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What happend during the bond between amino acids? Lecture 2 |
One H2O group is lost. |
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What is the bond between amino acids called? Lecture 2 |
Pbond. |
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The ptide bond between amino acids has a special feature, what is it? Lecture 2 |
it is an amide bond. |
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What is an amide bond? Lecture 2 |
it has a partial double bond character. This makes the amides rigid, stable and neutral. |
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What does the amide bond cause spatiality wise? Lecture 2 |
Causes planar geometry. |
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What are polypeptides? Lecture 2 |
Chains of amino acids. |
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Where are polypeptides coupled in the cell? Lecture 2 |
In the ribosomes. |
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How are amino acids classified? Lecture 2 |
According to their (-R)side-chain properties. |
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What classifications of amino acids are there? Lecture 2 |
1. nonpolar (hydrophobic) 2. polar, uncharged (hydrophilic) 3. acidic (neg. charge) 4. basic (pos. charge) |
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Give an example of a nonpolar (hydrophobic) amino acid. Lecture 2 |
Glycine |
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Give an example of a polar, uncharged amino acid. Lecture 2 |
Serine |
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give an example of an acidic amino acid. Lecture 2 |
Aspartic acid |
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What is important about the acidic amino acids? Lecture 2 |
Their -COOH group allows them to coordinate metal ions. |
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Give an example of a basic amino acid? Lecture 2 |
Lysine |
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What does the R-group allow between amino acid residues? Lecture 2 |
Different chemical bonds. |
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Most amino acids are derived from two central pathways in cellular metabolism. Which are they? Lecture 2 |
Glycolisis Citric acid cycle |
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The citric acid cycle is amphibolic, what does this mean? Lecture 2 |
It has both an anabolic and catabolic function. |
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Various intermediates of glycolisis and te citric acid cycle give rise to ... families of chemically related amino acids? Lecture 2 |
6 |
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What are the two common reactions in amino acid biosynthesis? Lecture 2 |
Transamination One-carbon transfer (formyl or methyl groups) |
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How many amino acids do plants and bacteria synthesise? Lecture 2 |
all of them? |
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How many amino acids do humans synthesise? Lecture 2 |
about 11(non-essential amino acids) |
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Which amino acids produced by plants and bacteria do we need to eat? Lecture 2 |
phenylalanine threonin tryptophan valine |
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Some of the building blocks in the citric acid cycle and glycolisis are used to make other amino acids. like families. Which families are there? Lecture 2 |
Serine Pyruvate Aspartate Aromatic Glutamate Histidine |
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What does lecture 3: proetin synthesis, structure and function discuss? |
1. protein synthesis = translation 2. protein structures 3. post-translational modifications 4. protein functions |
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What are the learning goals of lecture three? |
1. describe connection between amino acids, peptides and proteins. 2. describe process of protein translation. 3. Name and understand teh function of different types of post-translational modifications 4. know different protein structures and functions |
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What is the relation between amino acids and proteins? Lecture 3 |
Amino acids are the building blocks of proteins. |
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How do amino acids form a peptide bond? Lecture 3 |
Through their -N and -C terminus. |
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A peptide bond is an amide bond. What is this? Lecture 3 |
Amide bond has a partial double bond character. |
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Wat does an amide bond have as a consequence structure wise? Lecture 3 |
The molecule will be rigid (lack of rotation). Very stable and neutral. |
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What type of mRNA is translated into protein? Lecture 3 |
Only properly processed mRNA. |
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What is the central dogma around RNA translation? why is it false? Lecture 3 |
DNA-> RNA-> protein Scientists identified that virusses can make DNA from RNA, so dogma is false. |
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What kind of code is the genetic code? Lecture 3 |
A triplet code. |
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How does one triplet encode for? Lecture 3 |
An amino acid. |
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Can the same amino acid be encoded for by different codons(triplets)? Lecture 3 |
yes. |
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How many codons are there? Lecture 3 |
64 |
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How many different amino acids do these 64 codons code for? Lecture 3 |
20 |
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In translation, what is wobble base pairing between codons and anticodons? Lecture 3 |
look up. |
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What are the two positives of wobble base pairing? Lecture 3 |
1. Allows for variation in allowed pattern of hydrogen bonding. 2. Minimises damage caused by misreading the code. |
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What does tRNA synthetase do? Lecture 3 |
It is an enzyme that ensures accuracy in translation. |
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How does tRNA synthetase ensure correct translation? Lecture 3 |
1. It has a high affinity binding of correct amino acids in active-site pocket. 2. Correct amino acids are excluded from editing pocket. 3. Hydrolityc editing: removes wrong amino acid at active site on synthetase molecule. and transfers it to editing site. 4. Recognition of correct tRNA by synthetase through nucleotide complementarity. |
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How does tRNA synthetase decide which amino acids are excluded from editing? Lecture 3 |
1. It has a high affinity binding of correct amino acids in active-site pocket. 2. Correct amino acids are excluded from editing pocket. |
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How does tRNA correct a mistake in the tRNA sequence? Lecture 3 |
3. Hydrolityc editing: removes wrong amino acid at active site on synthetase molecule. and transfers it to editing site. 4. Recognition of correct tRNA by synthetase through nucleotide complementarity. |
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In which direction is an amino acid incorporated into protein and why? Lecture 3 |
Stepwise growth of polypeptide chain from: amino(N) to carboxy(C) - terminus. It is an energetically favourable formation of the peptide bond. |
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Where in the cell does mRNA translation occur? Lecture 3 |
Ribosomes |
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Which subunits does a ribosome exist of? Lecture 3 |
1. a large ribosomal subunit. 2. A small ribosomal subunit. |
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What are the RNA binding sites in a ribosome? Lecture 3 |
E site P site A site |
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What type of molecule can a ribosome be compared with? Lecture 3 |
A complex catalytic machine. |
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What are the steps of translating mRNA into protein in ribosomes? 4 steps Lecture 3 |
1. tRNA binding 2. Peptide bond formation 3. large subunit translocation 4. small subunit translocation |
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Which cofactors do the proofreading in the ribosome of the codon-anti-codon match? Lecture 3 |
EEF1 EEF2 |
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How do EEF 1 and 2 bind to the ribosome? Lecture 3 |
Through the GTP molecule. |
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What do EEF1 and EEF2 do? Lecture 3 |
GTP hydrolisis = kinetic proofreading. |
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What happens if EEF1 and 2 find a mistake? Lecture 3 |
If the wrong codon is bound, the elongation factor will release. |
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How much do EEF1&2 increase accuracy? Lecture 3 |
99.99% due to affinity conformational change and tRNA dissociation rate |
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How do EEF1 & 2 know whether it is correct? Lecture 3 |
From kinetic proofreading: enzyme knows from duration whether it is correct or not. |
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How is protein synthesis initiated? Lecture 3 |
1. translation initiation site sets the reading frame. 2. Met-tRNAi is recognised by eukaryotic initiation factors (eIFs) 3. Rate determining step for protein synthesis |
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How is the reading frame seat exactly? Lecture 3 |
on the 5' untranslated region: initiator tRNA until startcodon UAG. Startcodon sets the reading frame. |
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Translation in happens in polysomes. what does this entail? Lecture 3 |
Many proteins can be made from 1 RNA molecule. Protein synthesis takes seconds to minutes. |
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Stopcodons are not recognised by tRNA, what makes translation stop? Lecture 3 |
A release factor. |
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What does a release factor do? |
It catalyses the addition of H2O instead of an amino acid. |
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How is translation ended? Lecture 3 |
1. binding of release factor the A site 2. termination 3. ribosome dissociates 4. protein goes into cytoplasm |
