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cellular and molecular biology Flashcards

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1
Q

Explain the bonds found in each protein structure (primary, secondary, tertiary and quaternary)

A

primary - sequence of amino acids - peptide bond
secondary - alpha helix and beta pleated sheet - hydrogen bonds between repetitive back bone
tertiary - stabilised by side chain interactions - VDW, disulphide bridges, hydrophobic interactions and ionic bonds
quatenary -stabilized by weak interactions between exposed side chains, disulphide bridges, hydrophobic interactions and ionic bonds

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2
Q

What is an example of a membrane protein involved in transport

A

ATP synthase in mitochondrial membrane

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3
Q

Explain how a transmission electron microscope works

A

Thinly sliced specimen is coated with heavy metals.
Electrons are passed through specimen.
Varying amounts of electrons are absorbed by the different parts of the cell which uptake varying amounts of heavy metals.
Electrons detected on the other side of specimen produce the image – the electrons that transmitted through the specimen

Specimen must be dead (cannot see dynamic image, only a static one)

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4
Q

Explain how the scanning electron microscope works

A

Specimen must be dead (cannot see dynamic image, only a static one)

Specimen is coated in gold.
Electrons that hit the gold excite some of the secondary gold electrons. These excited electrons produce a 3d image of the specimen.

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5
Q

What is the main role of the nucleolus?

A

Site of ribosomal RNA synthesis

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6
Q

What is the function of the smooth ER?

A

synthesise and transport lipids and carbs in cell and stores calcium

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7
Q

What are microtubules used for?

A

road network for motor proteins (e.g. on vesicles from ER to golgi apparatus)
found in cilia and flagella

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8
Q

What are microfilaments used for?

A

Made of actin filaments and used for cell pseudopodia

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9
Q

What are intermediate filaments used for?

A

anchoring organelles within the cell

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10
Q

What are the two types of starch found in plants?

A

amylose and amylopectin (kind of branched)

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11
Q

What is the carbohydrate source of energy found in animals?

A

glycogen (extensively branched)

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12
Q

Is cellulose branched?

A

No - it is linear

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13
Q

What is chitin and what does it look like?

A

Found in animal exoskeleton and used in surgical procedures in stitches, it is a glucose molecule with a nitrogen appendage

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14
Q

Whats the difference between a pyrimidine and purine? Give examples of each

A

Pyrimidine has one ring, while purine has two rings:
Pyrimidines are thYmine and cYtosine and uracil
Purines are adenine and guanine

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15
Q

What role do glycoproteins play in the plasma membrane?

A

cell-cell recognition and cell-cell communication

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16
Q

What type of molecules can diffuse through plasma membrane?

A

Hydrophobic molecules and SMALL non-polar molecules (e.g. O2 and CO2) can diffuse through plasma membrane, but ions and large polar molecules cannot (e.g. K+ and glucose)

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17
Q

What is the dried composition of living matter, since 70% is water?

A 
50% C
15% H
20% O
10% N
Other ( S and P ) 5%
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18
Q

What are the four components of the cell theory?

A

They arise from pre-existing cells
Genetic info is stored as DNA/RNA
Proteins are synthesised on ribosomes
A selectively permeable membrane encloses every cell

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19
Q

What are the three aspects to microscopy?

A

Magnification
Resolution
Contrast

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20
Q

Where else apart from the nucleus can you find dan in a eukaryotic cell?

A

mitochondria and chloroplasts

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21
Q

Where do the proteins that the free ribosomes make go?

A

Stay in the cytoplasm

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22
Q

Where do the proteins that the rER bound ribosomes make go?

A

proteins to be secreted by the cell
proteins to be used by membrane enclosed organelles in the cell
membrane proteins

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23
Q

What is the endomembrane system?

A

the membrane enclosed organelles in the cell which are involved in moving materials around the cell

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24
Q

Explain cell fractionation

A

cells are homogenised
then placed in a centrifuge

Cell components separated according to density and size of components

1000G for 10 mins allows nuclear and cellular debris to separate
20,000G for 20 mins allows mitochondria and chloroplast to separate
80,000G for 60 mins allows microsomes to separate
150,000G for 3hrs allows ribosomes to separate

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25
Q

What is a junction found in plant cells similar to gap junction in animal cells called?

A

PLASMODESMATA

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26
Q

What are functions of proteins?

A 
SHITME RS
Structural
Hormone 
Immunity 
Transport 
Movement 
Enzymes 
Receptor 
Storage
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27
Q

What are chaperonins?

A

Molecules that assist in the folding of proteins
They protect polypeptide from degradation
And give optimal enviro for proteins to fold

they can also check and correct for correct folding, refold and mark for destruction

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28
Q

What defines each amino acid?

A

The side chain of the amino acid

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29
Q

What is the difference between hydrolysis and denaturation?

A

Hydrolysis breaks peptide bonds (primary structure of proteins)
Denaturations breaks secondary, tertiary and quartenary structures

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30
Q

Where are alpha helixes commonly found?

A

trans membrane proteins

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31
Q

Where are beta pleated sheets commonly found?

A

the core of globular proteins

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32
Q

What protein three alpha helixes intertwined around each other?

A

collagen

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33
Q

Explain anabolic reactions

A

energy enters system
bond making
endergenic
endothermic

34
Q

Explain catabolic reactions

A

energy exits system
bond breaking
exothermic
exergenic

35
Q

What is a prosthetic enzyme cofactor?

A

organic or inorganic molecules that are tightly bound to the protein
e.g. heme, vitamins, metal ions Cu 2+

36
Q

What is a coenzyme?

A

A cofactor that is a small organic molecule, NON COVALENTLY bonded to protein
eg vitamins

37
Q

How is enzyme activity regulated?

A 
switching on and off genes that encode particular enzymes
conversion of an inactive enzyme to an active form e.g. chemotrypsinogen to chemotrypsin 
cellular localization ( trapping enzymes inside organelles e.g. lysosomes)
allosteric regulation (non covalent)
38
Q

EXPLAIN DNA REPLICATION

A

DNA replication is semi-conservative and occurs during the S phase of interphase
Helicase unwinds and separates the double stranded DNA by breaking the hydrogen bonds between base pairs
This occurs at specific regions (replication origins), creating a replication fork of two polynucleotide strands in antiparallel directions
RNA primase synthesises a short RNA primer on each template strand to provide an attachment and initiation point for DNA polymerase III
DNA polymerase III adds deoxynucleoside triphosphates (dNTPs) to the 3’ end of the polynucleotide chain, synthesising in a 5’ - 3’ direction
The dNTPs pair up opposite their complementary base partner (adenine pairs with thymine ; guanine pairs with cytosine)
As the dNTPs join with the DNA chain, two phosphates are broken off, releasing the energy needed to form a phosphodiester bond
Synthesis is continuous on the strand moving towards the replication fork (leading strand)
Synthesis is discontinuous on the strand moving away from the replication fork (lagging strand) leading to the formation of Okazaki fragments
DNA polymerase I removes the RNA primers and replaces them with DNA
DNA ligase joins the Okazaki fragments together to create a continuous strand

39
Q

What is the role of single strand binding proteins?

A

they prevent single strand dna from repairing

40
Q

What is the role of topoisomerase?

A

breaks phosphodiester bonds between nucleotides and forms temporary bonds between nucleotides.
It breaks, swivels and rejoins parental dna ahead of replication fork.
reliefs strain caused by dna unwinding.

41
Q

What are telomeres?

A

Regions of repetitive nucleotide sequence at the end of each chromatid, which prevents the loss of genes near the ends in continuously dividing cells (e.g. gametes).

42
Q

Why does the dna molecule get shorter and shorter?

A

as the end primer is removed, it cannot be replaced with DNA as no 3’ end is available for DNA polymerase
After 1st round of replication lagging strand is shorter than template.
after 2nd round of replication new leading and lagging strands are shorter than original template.
Ends of chromosomes get progressively shorter as cell divides.

43
Q

What does a spliceosome consist of?

A

snRNA (Which has nucleotides which are complimentary to the introns split regions) + proteins

44
Q

What is an example of an enzyme that is not made up of protein?

A

snRNAs

45
Q

What is added to the 5’ end in RNA processing?

A

guanine triphosphate for stability and to promote exit out of nucleus. and the 5’UTR is added.

46
Q

What is added to the 3’ end in RNA processing?

A

polyA tail, which is a sequence of adenine nucleotides, which may promote exit out of nucleus and prevents degradation of mRNA (the more adenine nucleotides, the slower the digression of the molecule)
and the 3’ UTR

47
Q

Explain the initiation process in transcription

A

RNA polymerase binds to a nucleotide sequence called the promoter
• DNA strands unwind
• RNA polymerase initiates RNA synthesis at start point within promoter

48
Q

Explain the elongation process in transcription

A

RNA polymerase joins complementary RNA nucleotides to 3’ end of growing RNA transcript
• New RNA peels away from template strand
• Transcribed DNA rewinds into double helix

49
Q

What are the Functions of 5’ cap and 3’ poly-A tail?

A

Functions of 5’ cap and 3’ poly-A tail
• May promote export of mRNA from nucleus
• Protects mRNA from degredation
• 5’ cap facilitates ribosome attachment

50
Q

How are Specific amino acids joined to specific tRNA molecules?

A

Enzymes called aminoacyl tRNA synthetases attach the correct amino acid to each tRNA molecule
• tRNA is covalently bound to amino acid

51
Q

Explain initiation in translation

A

In eukaryotes the small ribosomal subunit binds to the initiator tRNA
• The 5’ cap of mRNA then binds to the small ribosomal subunit
• The initiator tRNA scans the mRNA molecule for the start codon (AUG)
• The anticodon of the initiator tRNA H-bonds to the start codon
• The large ribosomal subunit then binds and the initiator tRNA is
positioned in the P-site of the ribosome.
• Translation begins

52
Q

What is the start codon?

A

AUG

53
Q

What is the stop codons?

A

UAA, UAG or UGA

54
Q

Explain termination in translation

A

When the ribosome reaches a stop codon (UAA, UAG or UGA) the A site accepts a release factor
• The release factor promotes release of polypeptide from tRNA in P site, by hydrolysis.
• Polypeptide released through exit tunnel
• The mRNA and ribosomal subunits dissociate

55
Q

What is a polyribosome?

A

Polyribosome: a single mRNA strand along which many ribosomes are travelling
Each of these ribosomes is synthesising growing polypeptide chains

56
Q

Describe a key difference between prokaryotes and eukaryotes with regard to:translation

A

In prokaryotes:
Requires three release factors
It is a continuous process as translation and transcription occur at the same time in the cytoplasm while in
eukaryotes: It occurs in separately from transcription
requires only one release factor

57
Q

An enzyme, aminoacyl-tRNA synthetase, and a supply of ATP are required in order to attach a particular amino acid to the tRNA molecule that will transport it to the ribosome. Initially, the enzyme has an active site for ATP and another for the amino acid, but it is not able to bind the tRNA. What happens in order for the final attachment to occur?

A

The synthetase first binds ATP and the corresponding amino acid (or its precursor) to form an aminoacyl-adenylate, releasing inorganic pyrophosphate (PPi). The adenylate-aaRS complex then binds the appropriate tRNA molecule, and the amino acid is transferred from the aa-AMP to either the 2’- or the 3’-OH of the last tRNA nucleotide (A76) at the 3’-end.

The mechanism can be summarized in the following reaction series:

amino acid + ATP → aminoacyl-AMP + PPi
aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP

58
Q

How did they decipher the genetic code in vitro?

A

They synthesised artificial mRNA (poly uracil) UUU, ribosomes, amino acids and tRNA molecules
Which made the amino acid PHENYLALINE

59
Q

Define TOTIPOTENCY

A

Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism.

60
Q

What is a point mutation?

A

Change in single base pair

61
Q

How do point mutations arise?

A

mistakes made by DNA polymerase
mutagenic events such as UV light exposure
spontaneous reactions in cells

62
Q

What are three point mutations that can occur

A

silent - no effect on amino acid sequence
missense - one amino acid is wrongly made instead of another one e.g. sickle cell valine instead of glutamic acid
nonsense - a point mutation in a sequence of DNA that results in a premature stop codon

63
Q

What is a frameshift?

A

Nucleotide pair insertions or deletions

64
Q

How can damaged DNA be repaired?

A

Teams of enzymes detect and repair the damage
Nuclease cuts the damaged DNA
DNA polymerase adds correct DNA fragment in
DNA ligase seals new DNA to old DNA

65
Q

why do unsaturated fatty acids help keep any membrane more fluid at low temperatures

A

The double bonds form kinks in the fatty acid tails, preventing adjacent
lipids from packing tightly.

66
Q

How is cholesterol a fluidity buffer?

A

it can slow fluidity of membranes at hot temps

at cold temps it can prevent fats from solidifying and retains fluidity

67
Q

What are the functions of the protein in the plasma membrane?

A 
TESCAI 
Transport
Enzyme
Signal
Cell-cell communication 
Attachment 
Intercellular
68
Q

What confirmed the phospholipid bilayer model?

A

freeze fracturing membranes

69
Q

What direction do beta pelted sheets run from

A

c to n terminal

70
Q

Collagen has

A

3 alpha helices intertwined

71
Q

haemoglobin has

A

4 poly[e[tides with 2 alpha subunits and 2 beta pelted sheet subunits and heme and iron

72
Q

what is the role of helicase?

A

an enzyme which breaks down h bonds and untwists double helix at the replication fork

73
Q

what is the role of single strand binding proteins?

A

it prevents single strand dna from repairing

74
Q

Describe a key difference between prokaryotes and eukaryotes with regard to transcription

A

prokaryotes : rna polymerase proceeds to terminator sequence
eukaryotes : polyadenalation signal is present and the signal binds to proteins in the nucleus and this cuts the mrna from rna polymerase

75
Q

Explain sickle cell anaemia

A

glutamic acid is replaced with valine which affects the beta subunit of the secondary structure of the protein, thus has hydrophobic regions which means that mutant haemoglobin’s all cluster together and can’t carry an oxygen.

76
Q

What is the function of cillia?

A

allow bacteria to stick to surfaces and to other prokaryotes which in turn creates colonies

77
Q

difference between prokaryotes and eukaryotes in terms of dna replication?

A

Eukatyotes have multiple replication forks thus multiple origin points and prokaryotes only has one replication fork thus one origin of replication

78
Q

difference in production of mRNA molecules in eukaryotes vs prokaryotes?

A

eukaryotes have to have mRNA go through editing to remove introns, whilst prokaryotes do not have to go through this process as they do not have introns

eukaryotes synthesise their mRNA in the nucleus of the cell, whilst prokaryotes synthesis mRNA in the cytosol, as prokaryotes have no clearly defined nucleus, instead they have a nucleoid.

79
Q

difference in translation in eukaryotes vs prokaryotes?

A

eukaryotes - occurs on 80S ribosomes,
prokaryotes - occurs on 70S ribosomes.

eukaryotes - is a discontinuous process, as it occurs in the nucleus then gets moved to the cytoplasm to be translated, while in
prokaryotes - it is a continuous process and occurs simultaneously with transcription sometimes and occurs in the cytoplasm in both processes.

eukaryotes also require a single release factor, while prokaryotes require three.

80
Q

What did the experiments carried out by Nirenberg and Matthaei show about nucelotide sequences?

A

they produced UUU, artificially and showed that three base pair sequences coded for one amino acid. And that the amino acids were produced sequentially from 5’ end to 3’ end

81
Q

why does dna polymerase need an rna primer

A

It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA.

82
Q

Enzymes use a variety of mechanisms to lower activation energy, describe four.

A

Act as a template for substrate orientation. Stabilize transition states, stressing substrates. Provide favorable microenvironment. Participate directly in catylic reactions

biosci 101 (6 decks)

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