Molecules of life Flashcards

Question

what is the 3 and 1 letter codes for cysteine

Answer 1

3 letter cys 1 letter C

Answer 2

Disulfide bond are formed between the thiol (-SH) groups of cysteine residues – they occur most commonly in extracellular proteins. Disulphide bonds can connect Cys residues in the same peptide chain (intra-chain) or link different peptide chains (inter-chain).

Answer 3

3 letter lys 1 letter K

Answer 4

3 letter Arg 1 letter R

Answer 5

3 letter his 1 letter H

Answer 6

3 letter asp 1 letter D

Answer 7

3 letter Glu 1 letter E

Answer 8

bacterial polypeptides; enzymatically synthesized rather than ribosomally synthesized (stable to peptidases)

Answer 9

the reaction of two amino acids is a condensation reaction with the elimination of water to produce a dipeptide, this results in an amide/peptide bond formation. The reaction is very slow without an enzyme catalyst or chemical activation

Answer 10

peptides have between 2-50 amino acids whereas proteins have more than 50 amino acids

Answer 11

N - terminus C - terminus

Answer 12

peptide/ amide bonds are sp2 hybridised (trigonal planar) with partial double bond character. the peptide unit is nearly always trans the bonds between the alpha carbon and the carbonyl and the alpha carbon and the nitrogen are pure single bonds which are free to rotate small peptides form flexible chains

Answer 13

rotation only possible about 2 bonds on the main chain alpha carbon - carbon alpha carbon - nitrogen

Answer 14

The a helix is a rod like structure The peptide main chain forms the inner part of the rod, the side chains extend out from the rod Stabilised by hydrogen bonds between every main chain C=O and the N-H group four residues ahead in the sequence Can have left or right handed turn – right handed in proteins

Answer 15

The b sheet is made from almost fully extended peptide chains called b strands. The structure is stabilised by hydrogen bonds between strands. Strands can run in the same direction (parallel sheet) or opposite (antiparallel sheet) Structures with 2-5 strands per sheet are common

Answer 16

secondaryprotein structure characterized by a tight turn of the polypeptide chain. it ususally involves 4 amino acid residues and often helps to reverse the diraction of the protein chain. they are crutial for protein folding and stability

Answer 17

Disulfide bonds are formed between two cysteine residues Disulfide bonds from crosslinks within the peptide backbone or peptide chains

Answer 18

chemical degradation

Answer 19

Acid hydrolysis (6M HCl, heat up to 100-110C for >24 hr)followed by amino acid analysis gives the amino acid composition The amino acids are reacted with a chromogenic or fluorescence label then identified by HPLC or ion exchange chromatography / comparison with standard

Answer 20

The N terminal amino acid residue reacts with phenyl isothiocyanate, treatment with two different acids produces a phenyl thiohydantoin (PTH) Analysis of PTH derivative by highperformance liquid chromatography reveals the amino acid at this position The process can be repeated until all the amino acid residues are analysed

Answer 21

1. Structural – form bigger structures, involved in movement and organisation 2. Storage – biological reserves of metal ions and amino acids 3. Transport – moving essential molecules (e.g. O2) 4. Enzymes – catalyse chemical reactions e.g. bond forming, bond breaking, oxidation, and reduction 5. Signalling – required for information processing within cells 6. Antibodies – bind to foreign matter in vivo 7. Transcription factors – bind to specific sites on DNA and are involved in gene activation

Answer 22

green fluorescent protein it is used to tag other proteins and make them visible

Answer 23

G-protein coupled receptors they are transmembrane receptors that sense a molecule outside a cell and produce a signal on the inside of the cell a very large superfamily of proteins important drug targets

Answer 24

1. ultracentrifugation 2. gel filtration chromatography 3. ion-exchange chromatography 4. affinity chromatography 5. gel electrophoresis

Answer 25

Centrifugation separates biological macromolecules on the basis of their relative buoyancy Samples are spun at high speed on a short rotor producing a centrifugal force

Answer 26

gelfiltration chromatography is used to separate molecules based on size. The sample passes thrrough a column packed with porous beads and therefor takes longer to travel through the column while larger molecules move quickly

Answer 27

Proteins can be separated on the basis of a specific interaction with another molecule bound to a column of beads Proteins that interact stick to the beads, others do not and are washed off Purified protein is then released from the column

Answer 28

Proteins can be separated on the basis of their net charge by ion exchange chromatography Proteins with a net positive charge bind to a column of beads containing carboxylate groups Proteins are eluted with increasing concentrations of sodium chloride solution Proteins with the least charge elute first, highly charged proteins last

Answer 29

Charged molecules move in an electric field – electrophoresis The velocity of migration (v) depends on the field strength (E), the net charge on the protein (z) and on the radius of the sphere (r) and the viscosity of the medium (h) The medium used is PolyAcrylamide Gel This can be used to separate DNA, RNA, and proteins.

Answer 30

denaturing SDS-PAGE is a method to separate proteins based on their molecular weight. it involves denaturing using SDS which unfolds them and gives them a uniform negative chare. the proteins are then separated on a polyacrylic gel matrix by applying an electric current. small proteins migrate faster toward the positive while larger ones move slowly

Answer 31

The proteins samples are mixed with an organic acid and then dried on a metal target.Light from a laser ionizes the proteins, which “fly” down a tube to a detector. Their time of flight is inversely proportional to their mass and directly proportional to the charge on the protein.

Answer 32

A beam of X-rays is shone through the crystal Part of the beam is scattered or diffracted by the electrons of each atom in the crystal The diffraction pattern can be used to determine the precise location of each atom in the crystal

Answer 33

adenine guanine

Answer 34

uracil, thymine and cytosine

Answer 35

base and sugar if adenine is the base the nucleoside is adenosine

Answer 36

nucleoside and phosphate

Answer 37

Nucleotide residues of nucleic acids are linked by a phosphodiester backbone *The phosphate group links the 3’-OH of one sugar to the 5’-OH of the next polyanionic at physiological pH

Answer 38

the strand is written from 5 prime to 3 prime

Answer 39

1. Hydrogen Bonds: Hydrogen bonding between base pairs. 2. Stacking Interactions: van der Waals forces between base pairs. 3. Hydrophobic effects: burying hydrophobic purine and pyrimidines within the helix increases stability. 4. Charge-charge interactions: Electrostatic repulsion of the negatively charged phosphates is minimised by the presence of ions e.g. Mg2+, and proteins

Answer 40

RNA is made of 4 ribonucleotides: G, C, A, U Can form base pairs G-C and A-U RNA can hybridise with DNA forming G-C, A-T and U-A base pairs Usually single stranded but can form double helices including a hairpin loop

Answer 41

DNA is stable to hydrolysis in aqueous solution Anionic phosphate ester groups repel any negatively charged nucleophile

Answer 42

RNA contains a hydroxyl group at the 2 prime position of its ribose sugar making it more susceptibal to hydrolysis compared to DNA

Answer 43

coenzyme A - fatty acid synthesis, enzyme production ATP - chemical energy in cells S-adenosyl methionine - cofactor used in enzymes nicintinamide adenine dinucleotide - cofactor used in many enzymes for redox

Answer 44

DNA is compactly packaged inside the cell, wrapped around histone proteins, and organised into structures called chromosomes DNA contains the coded instructions that govern life. The code is split into smaller chunks called genes

Answer 45

International team of scientists working together to decode the human genome World’s largest collaborative biological project. First draft sequence published in 2001, completed 2003 3 billion nucleotides, appx 30,000 genes 98% of our genome is non-coding DNA

Answer 46

Packaging enables the long DNA strands to be physically accommodated within a small space in the nucleus. Packaging serves to protect the genetic material from damage e.g. by UV radiation and oxidative agents. Packaging regulates access by the transcription machinery to portions of the chromosome. DNA needs to unwinds off the nucleosome for replication and transcription to occur

Answer 47

a sequence that codes for a functional molecule

Answer 48

Every cell in the body contains the same DNA sequence Specific genes can be switched on and off, allowing for different genes to be expressed (epigenetics)

Answer 49

One of the stands of each daughter DNA molecule is newly synthesised the other comes from the parent

Answer 50

The experiment that proved this used the 15N isotope of nitrogen to label DNA in growing bacteria The bacteria were transferred to medium containing the 14N isotope, After one generation the DNA contained half 15N and half 14N. After a second generation half of the DNA was the 15N and 14N hybrid, the other half was 100% 14N containing

Answer 51

unwinds the DNA strand

Answer 52

makes new DNA strand It catalyses the step-by-step addition of deoxyribonucleotide units to a growing DNA chain

Answer 53

makes RNA primers on the lagging strand

Answer 54

removes RNA primers

Answer 55

joins the okazaki fragments to create one continuous strand

Answer 56

dATP, dGTP, dTTP and dCTP and Mg2+ to work

Answer 57

DNA polymerase adds deoxyribonucleotide units to the 3’-hydroxyl group of a DNA chain – this is called the primer A DNA template is essential – this can be single or double stranded if it contains breaks in the phosphate backbone The reaction is a nucleophilic attack of the 3’-OH terminus of the primer DNA on the innermost phosphorus atom of a deoxynucleoside triphosphate The reaction releases a diphosphate unit which is hydrolysed by inorganic pyrophosphatase – this provides the energy for the reaction

Answer 58

Strand separation – the two strands of DNA are separated by heating Hybridisation of primers – short strands of DNA flanking the 3’ ends of both strands of DNA are hybridised to the sequences DNA synthesis – DNA polymerase is added and elongation of both primers occurs

Answer 59

The PCR process can be repeated over many cycles to amplify a sequence 20 cycles This can be used to diagnose diseases, e.g. HIV or tuberculosis, by amplifying and detecting viral or bacterial DNA sequences PCR is used in genetic fingerprinting for forensics. DNA isolated from human samples at a crime scene can be amplified. Dinosaur DNA can be amplified from insects trapped in amber – but the sequences are too short to be useful

Answer 60

Ribose (2’-OH) RNA is made of 4 ribonucleotides: G, C, A, and U Can form base pairs G-C and A-U Usually single stranded but can form double helices including a hairpin loop

Answer 61

mRNA is a short lived molecule Its base sequence reflects the DNA sequence mRNA is complementary to its DNA template mRNA varies in length depending on the gene The synthesis of mRNA is called transcription

Answer 62

DNA templates contain promoter sites that bind to RNA polymerase and position it in the correct place to start synthesis These are on the 5’ side of the DNA (upstream) Specific DNA sequences stop the synthesis

Answer 63

The genetic code (right) is a non overlapping, comma free, degenerate, triplet code. Only Met and Trp, two of the least common amino acids in proteins, are specified by a single codon.

Answer 64

The ribosome uses the instructions from the mRNA and builds a new protein. The ribosome uses activated amino acids which are attached to transfer RNA (tRNA). The ribosome has space for two tRNA units and catalyzes the formation of a new peptide bond between the two amino acids

Answer 65

Amino acid is activated by reaction with ATP to form aminoacyl-adenylate Mixed anhydride then reacts with tRNA to form aminoacyl-tRNA and AM

Answer 66

1. Single chains of 73-93 nucleotides 2. They contain unusual bases 3. The 5’ end is phosphorylated 4. The base sequence at the 3’ end is CCA. The activated amino acid is attached using an ester group to the 3’OH of the ribose unit. 5. Base pairing within tRNA produces a distinctive structure with an anti-codon loop that recognises the mRNA template.

Answer 67

tRNA is recycled by a group of enzymes that recognise the specific tRNA and add a new amino acid unit Each amino acid has it’s own synthetase These are highly specific reactions The enzyme must be able to recognise the matching tRNA and the incoming amino acid which may only differ by a CH2 group

Answer 68

conformational entropy H-bonding to water +190kCal/mole

Answer 69

hydrophobic collapse intramolecular H-bonding van der waals interactions -200kCal/mole

Answer 70

proteins do not fold randomly protein folding goes through two stages - hydrophobic collapse to molten globule - progressive stabilization form in the molten globule at multiple points

Answer 71

Inheritance – mutated genes can be inherited from parental genes Ageing – the normal process of DNA replication during cell division can introduce errors Environmental Damage - Radiation – UV and ionising radiation damages DNA - Chemicals – some chemicals can react covalently with DNA causing damage

Answer 72

Germline mutations (Inheritable) – mutations occur in gametes and passed onto offspring

Answer 73

Somatic mutations (cannot be inherited) – mutations occur in a single body cell

Answer 74

- Change of DNA sequence – changes protein sequence e.g. BRAF - Modifications to control regions of genes – altered gene expression - Gene deletions – result in severe mental and physical disabilities e.g. Prader Willi syndrome - Extra genes – result in mental and physical differences e.g. Down’s syndrome (Trisomy 21) - Chromosome breakage and translocation – results in mutant genes

Answer 75

Silent – code is degenerate Missense – codes for another amino acid Nonsense – codes for STOP Frameshift – deletion or insertion of one base changes the meaning of the DNA downstream

Molecules of life Flashcards

(102 cards)