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Biology 1B - DNA/RNA and proteins Flashcards

1
Q

what is the structure of DNA (Watson and crick model)

A

A polymer of nucleotides ( base, deoxyribose sugar, phosphate)
DNA strands run antiparallel with 10 base pairs per turn of double helix

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2
Q

Describe the charges in DNA

A

Made up of the sugar phosphate backbone which is highly charged and hydrophilic (polar)
and nitrogenous bases in the centre as they are hydrophobic (non polar)

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3
Q

why does DNA dissolve in water

A

due to the highly charged sugar phosphate backbone

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4
Q

describe purines

A

purines are a type of nitrogenous bases
Adenine and guanine are purines
purines contain two infused rings composed of carbon and nitrogen atoms

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5
Q

describe pyrimidines

A

pyrimidines are a type of nitrogenous bases
Cytosine and Thymine are pyrimidines
pyrimidines are a 1 ringed structures composed of carbon and nitrogen atoms

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6
Q

describe the 5’ and 3’ end of DNA

A

5’ - has phosphate attached meaning you cannot add a new nucleotide at this end
3’ - there is a H rather than a Hydroxyl on the deoxyribose sugar 2nd carbon meaning you can add new nucleotides

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7
Q

what did Rosalyn franklin do

A

played huge role in discovering the structure of DNA by helping Watson and crick

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8
Q

describe the role of hydrogen bonds in base pairing

A

specific base pairing is due to the number of hydrogen bonds
A&T - have two hydrogen bonds between them
G&C -have 3 hydrogen bonds between them
bases pair this way as purines and pyrimidines pair together

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9
Q

who discovered specific base pairing

A

Watson and crick with help from Rosalyn franklin

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10
Q

what provided evidence that DNA carries genetic information

A

studies of bacteriophages showing only the DNA and not the protein enters the bacterial cell
showing DNA and not protein carries genetic material

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11
Q

what is the semiconservative model of DNA replication proposed by Meselson-Stahl

A

Two strands of parental molecule separate and each functions as a template for synthesis of a new, complementary strand

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12
Q

describe the Meselson-Sthal experiment that demonstrated the semi conservative replication of DNA

A

1) DNA from E.coli cultured in medium containing 15N (isotope) and then transferred to medium containing 14N

2) Extracted DNA at time intervals (after first and second replication)

3) after 1 replication - DNA formed a single intermediate band, indicating each DNA molecule contained one old (heavy) and one new strand (light)

4) after two replications - two bands appeared, one intermediate and one completely light

5) proved semiconservative model where each inherits one strand from parent and synthesises a new complementary strand

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13
Q

what is helicase function in DNA replication for leading and lagging strand

A

unwinds parental double helix at replication forks

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14
Q

what is single-strand binding protein function in DNA replication for leading and lagging strand

A

binds to and stabilises single stranded DNA until it can be used as a template

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15
Q

what is topoisomerase function in DNA replication for leading and lagging strand

A

corrects overwinding ahead of replication forks breaking, swivelling and re-joining DNA strands

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16
Q

what is primase function in DNA replication for leading and lagging strand

A

leading - synthesises a single RNA primer at 5’ end of leading strand

lagging - synthesises an RNA primer at 5’ end of each Okazaki fragment

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17
Q

what is DNA polymerase III function in DNA replication for leading and lagging strand

A

leading - continuously synthesises leading strand from primer

lagging - elongates each Okazaki fragment leading onto the primer

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18
Q

what is DNA polymerase I function in DNA replication for leading and lagging strand

A

leading - removes primer from 5’ end of DNA, adding onto the adjacent 3’ end

lagging - the same for each fragment

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19
Q

what is DNA ligase function in DNA replication for leading and lagging strand

A

leading - joins the 3’ end of the DNA that replicates the primer to the rest of the leading strand

lagging - joins the Okazaki fragments

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20
Q

why is error rate in DNA replication very low

A

a combination of specific base pairing , supplemented by proof reading
all DNA polymerases have proof reading abilities that can detect and remove incorrectly added bases

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21
Q

what can cause harm to DNA

A

high energy radiation (UV) - can be repairs by nucleotide excision repair to remove a thymidine dimer formed by UV radiation
chemicals (mutagens)

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22
Q

describe mitochondrial DNA

A

mtDNA
found near mitochondrial membrane and is double stranded and circular
codes for proteins in respiratory chain (ETC)
passed from generations via maternal lineage
mutations in mtDNA cause diseases centred around inability to generate enough energy

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23
Q

what evidence shows the link between genes and proteins

A

first proposed by Garrod (1909) who studied inherited disease. He linked symptoms of inherited disease with a persons inability to make a certain protein/enzyme, establishing genes dictate phenotypes

later beadle and Tatum studied mutations in bread mould. “experiments lead to one gene one enzyme” hypothesis

concluded that genes don’t directly build proteins instead mRNA acts as in intermediate

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24
Q

describe the differences between DNA and RNA

A

DNA never leaves nucleus but RNA does
they are both polynucleotides but RNA has ribose instead of deoxyribose sugar and uracil instead of thymine
RNA has no regular 3d structure but can form double helix (usually single stranded)

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25
describe transcription process
- catalysed by RNA polymerase, unwinds the double helix and makes a complementary copy of one strand of DNA
26
what are the three stages of transcription
initiation elongation termination
27
what happens during the initiation phase of transcription
RNA polymerase binds to promotor site on DNA at start of every gene transcription factor binds which orientates RNA polymerase signals start of transcription
28
what happens during the elongation phase of transcription
RNA polymerase unwinds 1 to 2 turns of DNA and adds nucleotide units to complementary copy uses triphosphates to supply nucleotide units RNA chain grows in 5'to3' direction DNA rewinds as the RNA polymerase proceeds along the template strand many RNA polymerase molecules can be transcribing a particular gene simultaneously
29
what happens during termination step of transcription
when RNA polymerase transcribes termination sequence (AAUAAA) RNA polymerase is signalled to come off DNA and find another RNA transcript is cut free from polymerase and released
30
what are the 3 main RNAs in eukaryotes and prokaryotes
mRNA (messenger) tRNA (transfer) rRNA (ribosomal)
31
describe mRNA processing
primary RNA transcript is modified before leaving the nucleus A cap is added to 5' end and a polyA tail to the 3' end this protects mRNA from degradation, aids export from nucleus and helps mRNA to anchor to ribosomes
32
what is the purpose of mRNA splicing
to remove non coding regions (introns) and only leave coding regions (exons)
33
what carries out mRNA splicing
particles known as small nuclear ribonucleoproteins (snRNPs)
34
what are snRNPs
carry out mRNA splicing consist of small nuclear RNA and various proteins several snRNPs and other proteins form a spliceosome complex they play both a catalytic and structural role
35
how are different proteins made from the same gene
alternative mRNA splicing different depending on what's cut out splicing increases range of possible protein products
36
what are splice sites
short nucleotide sequences at the end of introns that are recognised by snRNPs
37
what are codons
3 bases on mRNA = codon each codon codes for an amino acid
38
briefly describe what happens during translation
mRNA is moved through a ribosome, codons are translated into amino acids one by one bt tRNA when anticodons recognise the codons
39
what is a key part of accuracy of information transfer in translation
accurate base pairing of bases by hydrogen bonding
40
how often can each tRNA molecule be used
each tRNA molecule is used repeatedly
41
what does tRNA do
its a small nucleic acid that transfers amino acids to the ribosome
42
how many different tRNAs are there
20 different ones for each of the 20 amino acids and each has a distinct anticodon
43
what does aminoacyl-tRNA synthase do
loads tRNA with its correct amino acid
44
how many different aminoacyl-tRNA synthases are there
20, one for each amino acid each has an active site that houses a specific combination of tRNA and amino acid
45
what is the "wobble" in translation
when some anticodons can pair with more than one codon
46
what is a key factor in accurate information transfer during translation
specificity of enzyme action (aminoacyl-tRNA synthase)
47
what is required for loading tRNA with amino acids
ATP
48
what is a key component of ribosomes
rRNA
49
what do ribosomes consist of
2 subunits one large (50S) one small (30S)
50
when do the subunits in ribosomes join togetehr
when mRNA is present
51
what catalyses the formation of peptide bonds
rRNA
52
what subunit does the mRNA transcript bind to
small subunit
53
what are the key binding sites for translation in the ribosomes
1) a site for binding mRNA (30S subunit) 2) P site (50S subunit), binds the growing peptide chain 3) A site (50S subunit), binds the incoming aminoacyl-tRNA 4) E site (50 subunit), exit site to allow the discharged tRNA to leave the ribosome
54
what are the 3 stages of translation
initiation elongation termination
55
what happens in the initiation stage of translation
30S subunit binds to the correct site on mRNA at the start codon binding site is specified by the 5' cap on the mRNA (eukaryotes) special initiator tRNA carrying amino acid methionine binds to start codon (AUG) on mRNA 50S subunit binds to form initiation complex
56
what are the three steps in the elongation stage of translation
codon recognition peptide bond formation translocation
57
what happens during elongation stage of translation
amino acids are added one at a time peptide chain grows from the amino acid towards the carboxyl end
58
what happens during codon recognition in translation
brings the correct aminoacyl-tRNA into the A site requires an energy input of 2xGTP increases accuracy and efficiency
59
what happens during peptide bond formation in translation
newly arrived amino acid is joined to the growing peptide chain anchored in the A site catalysed by rRNA (large subunit)
60
what happens during translocation in translation
ribosome moves the tRNA in the A site to the P site the discharged tRNA in the P site is moved to the E site to leave the ribosome required energy input (GTP)
61
what direction does the ribosome move along the mRNA
5' -> 3'
62
what is required for elongation in translation
various elongation factors/proteins
63
when does elongation in translation stop
when a STOP codon appears in the A site of the ribosome (UAA, UAG or UGA)
64
what happens in the termination stage of translation
a release factor protein binds and the completed peptide chain is freed by the action of release factor from P site (adds a water instead of amino acid to end of chain) the components of the system come apart from each other and can be used for later cycles of translation
65
how much polypeptides can ribosomes make
an average sized polypeptide in a minute many copies can be made simultaneously by polyribosomes
66
what type of code is the code for converting nucleotide language into amino acid language
nucleotide language - 4 letters amino acid language - 20 letters 3 nucleotides for 1 amino acid triplet code (non-overlapping) - 64 different possibilities
67
what are some features of mRNA genetic code
- shows redundancy but not ambiguity - there are well defined start and stop signals - code is universal with some minor exceptions
68
give examples of post translational modification that can occur
- protein chain can fold up to its correct 3 dimensional structure required for function - other components such as sugars or lipids can be added or some amino acids may be removed - the protein may have to be moved to its required location
69
where does protein synthesis always start
ribosomes can be free or attached to ER but protein synthesis always starts in cytosol
70
how do proteins destined for export from the cell get to their correct location after synthesis
they have a signal sequence of about 20 amino acids at the N-terminus which directs the polypeptide to specific locations
71
describe insertion, deletion and substitution mutations
insertion - addition of one or more nucleotides in DNA sequence, causes frameshift disrupting the whole protein deletion -removal of one or more nucleotides from DNA sequence, causes frameshift disrupting whole protein (both could result in early stop codon) substitution - a single nucleotide is replaced with another (point mutation) can have silent, missense or nonsense affect
72
describe missense and nonsense mutations
missense - a single nucleotide change in DNA leads for one amino acid to be changed to another nonsense - a nucleotide change creates a premature stop codon resulting in an incomplete codon
73
what can frameshift cause
- immediate nonsense - extensive missense (shifts reading frame but doesn't immediately create stop codon)
74
what happens when insertion or deletion of 3 nucleotide occurs
no frameshift but extra or missing amino acid
75
what mutation causes sickle cell haemoglobin
a single substitution mutation causing missense
76
what holds together proteins defined 3 dimensional structure (fold)
stabilised mainly by non covalent bonds Hydrogen bonds, ionic bonds and hydrophobic bonds
77
how do proteins recognise other molecules
various parts of protein (backbone or sidechains) contact the target molecule precisely via non-covalent interactions Hydrogen bonds, Ionic bonds, hydrophobic interactions
78
are proteins 3 dimensional structure rigid or flexible
flexible
79
what are hydrogen bonds
weak electrostatic bonds formed because N and O are more electronegative than H individually weak but collectively strong
80
what are ionic bonds
electrostatic interactions between full positive and negative charges
81
what are hydrophobic interactions
non-polar side chains cluster together excluding water and allowing water molecules to form H bonds between themselves
82
what are van der Waals interactions
weak forces between adjacent neutral atoms
83
why are proteins important
they play key structural and functional roles provide structure (collagen) catalyse reactions (enzymes) storage transport (around body e.g. haemoglobin and across membranes e.g. porin) communication (hormones) movement defence (antibodies)
84
what kind of structure do proteins have
large and complex
85
describe the basic structure that makes a protein
polymers of amino acids linked by peptide bonds they contain 20 different amino acids with different side chains each with a unique amino acid sequence determined by the DNA sequence of its gene each polypeptide chain folds up into a specific 3 dimensional structure defined by its amino acid sequence, this allows proteins to bind specifically to other molecules
86
what is a peptide bond
chemical bond that links amino acids together in a polypeptide chain result of condensation reaction between the amino group of one amino acid and the carboxyl group of the next one they are planar and very stable
87
describe the structure on an amino acid
contains an amino group (protonated) a carboxyl group (unprotonated) and R group (sidechain) a H
88
what is a polypeptide chain
they are linear and unbranched the two ends are distinct chains are always drawn and numbered from the N terminal and to C terminal end on average have around 500 amino acids
89
what type of bonds can charged side chains form
ionic bonds
90
what type of bonds can polar side chains form
hydrogen bonds
91
what amino acids would be on the surface of a protein
ones with charged or polar (hydrophilic) side chains as they can interact with water
92
what do the properties of amino acids determine
protein shape
93
what are the four terms for describing different aspects of protein folding
primary structure secondary structure tertiary structure quaternary structure
94
what is primary structure
the amino acid sequence
95
what is secondary structure
ways in which the backbone folds regularly; stabilised by H bonds between the backbone C=O and N-H groups
96
what is tertiary structure
the way in which the polypeptide chain folds into a compact 3 dimensional shape, stabilised with H bonds, ionic bonds, hydrophobic interactions and disulfide bonds involving backbone or sidechain groups
97
what is quaternary structure
not all proteins have it arrangement of subunits (chains) in protein containing two or more polypeptide chains; stabilised as for tertiary structure
98
what are the 2 specific patterns of folding that make up proteins secondary structure
helix sheet
99
describe helix structure in proteins
forms rigid rod with sidechains round the outside
100
describe sheet structure in proteins
forms flat surface that can be twisted into a cylinder side chains alternately above and below the sheet
101
how do proteins fold in terms of charge
fold with hydrophobic groups inside and charged and polar groups outside
102
what are three important implications that the conformation of a protein is held together by a large number of mainly weak interactions
1) protein conformation is flexible - not rigid, can change conformation which is sometimes essential for function 2) protein conformation can be easily be destroyed (denaturation) 3) the functioning of many proteins can be regulated by events that cause a change in conformation - binding to another molecule
103
what can cause proteins to become denatured
high temperatures detergents changes in pH
104
what can help proteins fold up
chaperonins environment inside helps proteins fold properly
105
what are protein domains
independently stable part of a polypeptide usually with a specific function e.g. ability to bind to a molecule
106
what can cause evolution of new proteins
domain swapping
107
what is de novo protein synthesis
when cells synthesize new proteins from scratch is possible to treat disease and overcome problems
108
how do enzymes lower activation energy
brings substrate into an environment where it has correct orientation to react stressing the substrates and stabilizing the transition state
109
where do substrates bind to enzymes
active site
110
describe how substrates bind to enzymes
1) substrates enter active site; enzyme changes shape to enfold substrate (induced fit) 2) substrate held in active site by weak interactions 3) active site lowers activation energy 4) substrates converted to products and released and is now available for more
111
what are proteases and lipases
proteases - break down proteins lipases - break down lipids
112
what is an example of enzyme use in industry
glucose isomerase to produce high fructose corn syrup
113
how are enzymes regulated
proteases in the blood end product inhibition binding of another molecule e.g. phosphate group
114
describe the structure of antibodies
contain 2 heavy and 2 light chains joined by disulfide bridges both types of chain have variable and constant regions antigen specificity is conferred by the variable regions
115
what part of an antigen does an antibody recognise
the epitope
116
what is the sigmoid O2 saturation curve of haemoglobin
represents the relationship between the partial pressure of oxygen and the percentage of haemoglobin saturated with oxygen allows it to bind to o2 in the lungs and release it in the capillaries in oxygen deprived tissues haemoglobin unloads large amount of o2 and in oxygen rich tissues is fully saturated changes in partial oxygen pressure lead to significant o2 binding and releasing
117
what two states can haemoglobin be in (regulatory)
T state - binds to O2 poorly R state - binds O2 well
118
what are some functions of membrane proteins
cell-cell recognition signal transduction via hormone receptors transport
119
what are filaments
fibrous proteins associate to make filaments e.g. actin filament - a polymer of mainly actin
120
what is myosin ATPase
powers the sliding of actin (thin) filaments over myosin (thick filaments) in muscle contraction

1st year (17 decks)

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