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biosci 101 > cellular and molecular biology > Flashcards

cellular and molecular biology Flashcards

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
What is a junction found in plant cells similar to gap junction in animal cells called?
PLASMODESMATA
26
What are functions of proteins?
``` SHITME RS Structural Hormone Immunity Transport Movement Enzymes Receptor Storage ```
27
What are chaperonins?
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
28
What defines each amino acid?
The side chain of the amino acid
29
What is the difference between hydrolysis and denaturation?
Hydrolysis breaks peptide bonds (primary structure of proteins) Denaturations breaks secondary, tertiary and quartenary structures
30
Where are alpha helixes commonly found?
trans membrane proteins
31
Where are beta pleated sheets commonly found?
the core of globular proteins
32
What protein three alpha helixes intertwined around each other?
collagen
33
Explain anabolic reactions
energy enters system bond making endergenic endothermic
34
Explain catabolic reactions
energy exits system bond breaking exothermic exergenic
35
What is a prosthetic enzyme cofactor?
organic or inorganic molecules that are tightly bound to the protein e.g. heme, vitamins, metal ions Cu 2+
36
What is a coenzyme?
A cofactor that is a small organic molecule, NON COVALENTLY bonded to protein eg vitamins
37
How is enzyme activity regulated?
``` 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
EXPLAIN DNA REPLICATION
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
What is the role of single strand binding proteins?
they prevent single strand dna from repairing
40
What is the role of topoisomerase?
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
What are telomeres?
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
Why does the dna molecule get shorter and shorter?
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
What does a spliceosome consist of?
snRNA (Which has nucleotides which are complimentary to the introns split regions) + proteins
44
What is an example of an enzyme that is not made up of protein?
snRNAs
45
What is added to the 5' end in RNA processing?
guanine triphosphate for stability and to promote exit out of nucleus. and the 5'UTR is added.
46
What is added to the 3' end in RNA processing?
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
Explain the initiation process in transcription
RNA polymerase binds to a nucleotide sequence called the promoter • DNA strands unwind • RNA polymerase initiates RNA synthesis at start point within promoter
48
Explain the elongation process in transcription
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
What are the Functions of 5’ cap and 3’ poly-A tail?
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
How are Specific amino acids joined to specific tRNA molecules?
Enzymes called aminoacyl tRNA synthetases attach the correct amino acid to each tRNA molecule • tRNA is covalently bound to amino acid
51
Explain initiation in translation
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
What is the start codon?
AUG
53
What is the stop codons?
UAA, UAG or UGA
54
Explain termination in translation
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
What is a polyribosome?
Polyribosome: a single mRNA strand along which many ribosomes are travelling Each of these ribosomes is synthesising growing polypeptide chains
56
Describe a key difference between prokaryotes and eukaryotes with regard to:translation
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
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?
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
How did they decipher the genetic code in vitro?
They synthesised artificial mRNA (poly uracil) UUU, ribosomes, amino acids and tRNA molecules Which made the amino acid PHENYLALINE
59
Define TOTIPOTENCY
Totipotency is the ability of a single cell to divide and produce all of the differentiated cells in an organism.
60
What is a point mutation?
Change in single base pair
61
How do point mutations arise?
mistakes made by DNA polymerase mutagenic events such as UV light exposure spontaneous reactions in cells
62
What are three point mutations that can occur
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
What is a frameshift?
Nucleotide pair insertions or deletions
64
How can damaged DNA be repaired?
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
why do unsaturated fatty acids help keep any membrane more fluid at low temperatures
The double bonds form kinks in the fatty acid tails, preventing adjacent lipids from packing tightly.
66
How is cholesterol a fluidity buffer?
it can slow fluidity of membranes at hot temps | at cold temps it can prevent fats from solidifying and retains fluidity
67
What are the functions of the protein in the plasma membrane?
``` TESCAI Transport Enzyme Signal Cell-cell communication Attachment Intercellular ```
68
What confirmed the phospholipid bilayer model?
freeze fracturing membranes
69
What direction do beta pelted sheets run from
c to n terminal
70
Collagen has
3 alpha helices intertwined
71
haemoglobin has
4 poly[e[tides with 2 alpha subunits and 2 beta pelted sheet subunits and heme and iron
72
what is the role of helicase?
an enzyme which breaks down h bonds and untwists double helix at the replication fork
73
what is the role of single strand binding proteins?
it prevents single strand dna from repairing
74
Describe a key difference between prokaryotes and eukaryotes with regard to transcription
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
Explain sickle cell anaemia
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
What is the function of cillia?
allow bacteria to stick to surfaces and to other prokaryotes which in turn creates colonies
77
difference between prokaryotes and eukaryotes in terms of dna replication?
Eukatyotes have multiple replication forks thus multiple origin points and prokaryotes only has one replication fork thus one origin of replication
78
difference in production of mRNA molecules in eukaryotes vs prokaryotes?
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
difference in translation in eukaryotes vs prokaryotes?
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
What did the experiments carried out by Nirenberg and Matthaei show about nucelotide sequences?
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
why does dna polymerase need an rna primer
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
Enzymes use a variety of mechanisms to lower activation energy, describe four.
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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