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week 3 Flashcards

1
Q

what is mitochondrial DNA, where is it found and what are the consequences of mutations

A

found near mitochondrial membrane and is called mtDNA
it is like bacterial DNA
mutations cause diseases centred around inability to generate enough energy

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1
Q

what is the error rate of DNA repair and why

A

very low as the cell goes to lengths to keep genetic material correct

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2
Q

what is the one gene one mutant theory and what is its importance

A

in experiment each mutant could only grow if supplied with a compound made after the defective step
showed that each gene codes for a single polypeptide, and that genes control metabolism

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3
Q

what are the main structural differences between dna and rna

A

Uracil instead of thymine, bonds with Adenine
made of ribose, doesn’t have a regular 3d structure but can form a 3D shape
single stranded

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4
Q

what is transcription and its catalyst

A

synthesis of RNA, catalysed by RNA polymerase

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5
Q

what are the steps of transcription

A

3 stages - initiation, elongation and termination

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6
Q

what occurs during initiation (transcription)

A

happens at a promoter site containing a particular sequence of bases
in prokaryotes the rna polymerase recognises and binds to promoter site
in eukaryotes a set of proteins called transcription factors are involved in the binding of rna polymerase to the promoter (TATA box)

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7
Q

what occurs during elongation (trascription)

A

local unwinding of 102 turns of DNA and addition of nucleotide units
DNA rewinds as the RNA polymerase proceeds along the template strand
many RNA polymerase molecules can be transcribing a particular gene simultaneously, allowing large amounts of protein to be made

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8
Q

what occurs during termination (transcription)

A

not well understood, appears to be signalled by the sequence of the RNA transcript itself
after this sequence has been transcribed proteins bind the growing transcript and cut it free from the polymerase, the transcript is released and the RNA polymerase detaches from the DNA

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9
Q

what are the three main types of RNA

A

mRNA - messenger
rRNA - ribosomal
tRNA - transfer

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10
Q

what makes RNA in prokaryotes

A

a single RNA polymerase

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11
Q

how is the primary RNA transcript modified before leaving the nucleus in eukaryotes and what is their affect

A

a cap is added to the 5’ end
polyA tail is added to the 3’ end
they protect the mRNA from degrading, aid export from the nucleus and help the mRNA to anchor to the ribosomes

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12
Q

what is mRNA splicing

A

the removal of non-coding regions, leaving exons
carried out by snRNP’s, which consist of small nuclear RNA and various proteins
several snRNP’s and other proteins form a spliceosome complex

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13
Q

how are splice sites marked

A

short nucleotide sequences at the end of introns mark the splice sites for recognition of snRNP’s
often there are more untranslated pre-mRNA sequences like introns, 5’ cap, polyA tail - than translated sequences like exons

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14
Q

why is splicing important

A

helps increase the range of possible protein products from a given gene (alternative)
alternative splicing of RNA leads to male and female Drosophila, and switches between classes of certain antibodies for examples
final transcript after splicing = mature mRNA

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15
Q

what was Garrod’s work to do with metabolism about

A

studied rare genetic diseases and discovered that some disorders were caused by faulty metabolism due to missing or defective enzymes.

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16
Q

what is the overall process of translation

A

mRNA is moved through a ribosome, codons are translated into amino acids one by one
tRNA codons add amino acid cargo to growing polypeptide chain when anticodon recognises codon

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17
Q

what happens during initiation (translation)

A

occurs in ribosome, ribosome binds to the mRNA at the start codon (AUG)
tRNA attaches to AUG using its anticodon (UAC)

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18
Q

describe elongation (translation)

A

inside ribosome
tRNA molecules bring amino acids based on the mRNA codons
ribosomes forms peptide bonds between amino acids, creating a growing polypeptide chain
ribosome moves along the mRNA 5’-3’

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19
Q

what occurs during termination (translation)

A

ribosome reaches the stop codon
release factor binds to the stop codon instead of tRNA
ribosome disassembles and the new protein is released
protein undergoes folding and modification

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20
Q

what enzyme is responsible for loading of a tRNA molecule with its correct amino acid

A

aminoacetyl-tRNA

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21
Q

how do enzymes interact with amino acids

A

there are 20 enzymes - one for each amino acid, each one has an active site that houses a specific combination of tRNA and amino acid

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22
Q

what are ribosomes made up of

A

2 subunits, large and small, and they only join together then mRNA is present
65% of the mass of a ribosome is rRNA, the rest is proteins
they have a p site, an a site and an e site

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23
Q

what does each site on a ribosome do

A

P site: peptidyl-tRNA site: binds to the growing peptide chain
A site: aminoacyl-tRNA site; binds the incoming aminoacyl-tRNA
E site - exit site to allow the discharged tRNA to leave the ribosome

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24
how is protein structure stabilised
non-covalent interactions eg H bonds, ionic bonds and hydrophobic bonds
25
how do hydrophobic interactions on proteins work
non-polar side chains cluster themselves together excluding water and allow water molecules to form H bonds between themselves
26
give a few examples of proteins and their functions
enzymes = biological catalysts structural proteins for supporteg collagen hormones for signalling eg haemoglobin recpetors for signalling eg insulin receptor
27
do all proteins look the same?
no, their structures vary in relation to their function
28
what are proteins made up
polymers of amino acids liked by peptide bonds
29
how are peptide bonds formed
condensation between the alpha amino group of one amino acid and the carboxyl of the next one they are planar and very stable
30
how many amino acids make up a protein
20, each protein also has different side chains
31
how are the unique amino acid sequences of each protein determined
by the DNA sequence of its gene
32
how is the 3D structure of a protein determined
by its amino acid sequence, allowing the protein to bind specifically to other molecules
33
how are the 2 ends of a polypeptide chain defined
N or amino terminus (NH3) , and C or carboxy terminus (COOH)
34
what are main functions of proteins in the body
communication, movement and defence
35
what is the general formula for an amino acid
NH2 - RCH - COOH
36
what is the general formula for a peptide bond
C-N bond resulting from a reaction between an amine and carboxylic acid group
37
what is the average number of amino acids in a protein, an what is unusual
average = 500 less than 20 amino acids are called aligopeptides
38
why do sidechains arise
non-polar side chain cluster together due to hydrophobic interactions, due to H bonds formed between water molecules and other polar molecules
39
what is the primary structure of a protein
the amino acid sequence
40
what is the secondary structure of a protein
the way the backbone folds regularly, stabilised by H bonds between backbone C=O and N-H groups
41
what is the tertiary structure of a protein
the way the polypeptide chain folds into a compact 3D shape, stabilised by H bonds, ionic bonds, hydrophobic interactions and disulphide bonds involving backbone or sidechain groups
42
what is the quaternary structure of a protein
arrangement of subunits in proteins containing 2 or more polypeptide chains, stabilised as tertiary structure not in all proteins
43
what is the alpha helix and beta sheet
both types of secondary protein different proportions exist in different proteins alpha helix = rigid rod with sidechains on the outside beta sheet forms a flat surface that can be twisted into a cylinder, with sidechains alternatively above and below the sheet, and chains running parallel or antiparallel
44
what strength of interactions stabilise a protein and what are the implications
held by a number of weak interactions means protein conformation is flexible also conformation can be easily destroyed/denatured eg heating also means the function of a protein can be regulated by events that cause a change in conformation eg binding to another molecule
45
what causes denaturation
high temps, detergents, changes in pH
46
in some proteins, what aids folding
chaperone proteins
47
what is a protein domain
they are an independently stable part of the polypeptide, usually with a specific function most proteins contain 2 or more domains, each often corresponding to an exon
48
how can evolution of new proteins happen
via domain swapping
49
how do proteins bind to other molecules
by making many precise weak interactions with their target - ionic bonds to the negatively charged phosphate groups - H bonds to the OH groups pf ribose - hydrophobic interactions with the adenine ring - H bonds to the N atoms of the adenine
50
what is de novo protein synthesis
synthesis of complex molecules from simple molecules such as sugars or amino acids, as opposed to recycling after partial degradation
51
how is de novo synthesis used in vaccine progression
to generate a better immune response to RSV a resp virus use proteins to breakdown gluten in the stomach for a treatment for celiac disease
52
what are challenges and aims in using de novo synthesis
finding a universal flu vaccine to find a lifetime using new version of amino acids new proteins to help ecological problem
53
what are possible new drug developments using constrained peptides
peptide library creation novel amino acids tight structure - resistant to breakdown protein inhibitors or molecular glue
54
what are the characteristics of enzymes as catalysts
very successful and specific speed up reactions and reduce activation energy each enzyme can catalyse several hundred reactions per second they bind to their substrate and catalyse the reaction at the active site
55
explain induced fit model
1. substrates enter active site, enzyme changes its active site shape to enfold substrate 2. substrate held in the active site by weak hydrogen and ionic bonds 3. active site can lower activation energy and speed up reaction via a few methods 4. substrates are converted to products 5. products are released 6. active site is now available for 2 new substrate molecules
56
how can active sites lower activation energy and speed up a reaction
acting as a template for substrate orientation stressing the substrates and stabilising transition state providing a favourable microenvironment participating directly in a catalytic reaction
57
how are enzymes used in industry
proteases and lipases in biological detergent and glucose isomerase to product fructose corn syrup
58
name some places enzymes are regulated
proteases in the blood end product inhibition binding of another molecule eh phosphate group
59
what is the structure of antibodies
2 heavy and 2 light chains joined together by disulphide bridges both types of chain have variable and constant regions antigen specificity is conferred by the variable regions an antibody recognises just a small part of the antigen called the epitope
60
how is protein funtion regulated
regulatory proteins can occur in two or more conformations with different properties regulation is crucial in homeostasis a single mutation can have severe consequences
61
which proteins are usually spanning membranes
alpha helices or beta Barrells the parts exposed to the membrane is hydrophobic, the parts exposed to the inside and outside of the cells are hydrophilic
62
name functions of membrane proteins
they have many, some include cell-cell recognition, signal transduction via hormone receptors and transport many hormone receptors are targets for drugs eg beta blocker
63
how do fibrous proteins contribute
strength or flexibility some proteins associate to form filaments eg myosin and actin in muscles

bio 1B (11 decks)

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