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BIOSCI 101 > Section 2: Cellular and Molecular Biology > Flashcards

Section 2: Cellular and Molecular Biology Flashcards

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1
Q

Characteristics common to all cells

A

Arise from pre-existing cells
Genetic info stored as DNA in chromosomes
Proteins synthesised on ribosomes
Selectively permeable plasma membrane encloses every cell
Sub-cellular components suspended in cytosol

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2
Q

What is cytosol

A

A semi-fluid substance

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3
Q

Cell size range

A

Vary a lot because they exist in diff environments and have diff functions
10-100µm

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4
Q

What is angstrom used to measure

A

Size of molecule

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5
Q

What can you see with a light microscope

A

Most plant and animal cells

Some larger organelles and bacteria

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6
Q

What can you see using super-resolution microscopy or electron microscopy

A

Smaller components, e.g. smallest bacteria, viruses, ribosomes

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7
Q

Important parameters in microscopy

A

Magnification (enlargement) of image
Resolution - measure of clarity of image
Contrast - difference in brightness between light and dark areas of an image

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8
Q

What is resolution

A

The shortest distance between 2 separate objects that can still be distinguished from one another

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9
Q

Types of microscopes

A 
Light microscope (LM):
- fluorescence microscope

Electron microscope (EM):

  • transmission EM (TEM)
  • scanning EM (SEM)
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10
Q

What is light microscopy used for

A

Used to visualise whole cells and large subcellular organelles (nucleus, chromosomes)

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11
Q

How do light microscopes work

A

At bottom, there is a light source which is focused onto a specimen on the stage
Image of specimen is magnified by lenses which can then be projected into the eye or a digital camera

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12
Q

Types of light microscopy

A

Brightfield
Brightfield (stained specimen)
Phase-contrast
Fluorescence

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13
Q

Light microscopy: Brightfield

A

Stained cells to make them more obvious

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14
Q

Light microscopy: Phase-contrast

A

Increases contrast to see cells relative to background

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15
Q

Light microscopy: Fluorescence microscope - steps

A

Take specimen and add antibodies, each of which is bound to a diff fluorophore and are capable to binding to and recognising distinct molecules in a cell
Incubate for a period and wash away antibodies that haven’t bound
Put specimen under microscope to study

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16
Q

Light microscopy: Fluorescence microscope - what do you see

A

An image where diff fluorophores have bound to diff cells / regions within cells –> indicates cells with diff regions have specific molecules –> differentiate types of cells

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17
Q

Light microscopy - advantage

A

Can visualise dynamic processes (not just static)

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18
Q

Electron microscopy - disadvantage

A

Can’t watch dynamic processes because have to fix and coat samples (i.e. must be dead)

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19
Q

Electron microscopy - how does it work

A

Instead of light, EMs use electromagnets to focus a beam of e- through the specimen (TEM) or onto its surface (SEM)

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20
Q

Electron microscopy: TEM - how does it work

A

Take sample and stain with a heavy metal, which binds to certain regions of cell
Specimen is put into TEM and e- are focused down onto specimen

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21
Q

Electron microscopy: TEM - what do you see

A

Places where there are heavy metals, the e- can’t get through, but regions where there aren’t many heavy metals, e- will go through
This info about the e- that pass though is collected and translated into an image
Can see lots of internal structures within cell

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22
Q

Electron microscopy: SEM - how does it work

A

Coat specimen with a layer of gold
Focus beam of e- which excite secondary e- on surface of tissue of cell
Info from secondary e- being excited is translated into SEM

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23
Q

Electron microscopy: TEM vs SEM

A

TEM:

  • Resolution 2nm (very good)
  • Used to study internal cell structure
  • Focus beam of e- through specimen

SEM:

  • Resolution 10nm (still pretty good)
  • Used to study cell surface and generate 3D images
  • Focus beam of e- onto surface of specimen
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24
Q

What does cell fractionation isolate cell components based on

A

Size and density

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25
Q

Cell fractionation - order of isolation?

A

Isolates largest organelles first and smallest organelles last via homogenisation

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26
Q

Cell fractionation - steps

A

Centrifuged at 1000g for 10 min - pellet rich in nuclei and cellular debris
Supernatant poured into next tube, centrifuged at 20,000g for 20 min - pellet rich in mitochondria (and chloroplast)
Supernatant poured into next tube, centrifuged at 80,000g for 60 min - pellet rich in microsomes
Supernatant poured into next tube, centrifuged at 150,000g for 3 hours - pellet rich in ribosomes

Isolated organelles taken to study

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27
Q

Cell fractionation involves…

A

Differential centrifugation

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28
Q

Prokaryotic cells - structure

A

No nucleus
Little or no internal structure/organelles
Flagella anchored to cell wall/membrane

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29
Q

Prokaryotic cells - flagella

A

Anchored to a motor through hook
Motor spans over cell wall and plasma membrane
As rotor rotates, flagella rotates –> propels cell along

(cilia also involved in helping cells move but don’t have a hook and motor structure)

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30
Q

Prokaryotic cells - nucleoid

A

DNA concentrated here but not enclosed by membrane

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31
Q

Prokaryotic cells - ribosomes

A

Complexes that synthesize proteins

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32
Q

Prokaryotic cells - plasma membrane

A

Encloses cytoplasm

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33
Q

Prokaryotic cells - cell wall

A

Rigid structure

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34
Q

Prokaryotic cells - glycocalyx

A

Outer coating consisting of a capsule or slime layer

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35
Q

Prokaryotic cells - fimbriae

A

Attachment to other bacteria

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36
Q

Eukaryotic cells - nucleus

A

Have a membrane bound nucleus which contains most of cell’s DNA

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37
Q

What structures are present in plant cells but not in animal cells

A

Cellulose cell wall - protects cell and maintains shape
Central vacuole - storage and breakdown of waste products
Chloroplasts - photosynthetic organelle (also present in eukaryotic algae)

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38
Q

Organelles / components of eukaryotic cells

A 
Endomembrane system
Mitochondria
Chloroplasts (plastids)
Cytoskeleton
Cilia and flagella
Plasma membrane (PM)
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39
Q

Endomembrane system

A

Nucleus
ER
Golgi apparatus
Lysosomes

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40
Q

Nuclear envelope

A 
2 layers (inner and outer membrane) that enclose nucleus
Fuse tgt to form pores within the nuclear envelope
Lined with proteins - molecules can move into and out of nucleus
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41
Q

Nucleus - what is chromatin

A

Found within nucleus and is the DNA with histone proteins

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42
Q

Nucleus - chromatin structure

A

When cell is between cell division, chromatin forms a wispy white structure
When cell is about to divide, chromatin is organised into chromosomes

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43
Q

Nucleus - nucleolus

A

Dense region in middle of nucleus
Usually only seen when between cell division
Involved in synthesis of rRNA

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44
Q

Outer membrane of nuclear envelope is continuous with…

A

Membrane of ER

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45
Q

What is the endoplasmic reticulum (ER)

A

An interconnecting network of membranes in the cytoplasm

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46
Q

Rough ER (RER)

A

Ribosomes attached

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47
Q

What are ribosomes

A

Protein-making complexes

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48
Q

What are ribosomes composed of

A

A large subunit and a small subunit

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49
Q

Where are ribosomes found

A

On RER or free in cytosol

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50
Q

As ribosomes on surface of RER make proteins…

A

They insert them into inside of RER

These proteins are destined to either be secreted by cell or used by membrane-enclosed organelles within the cell

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51
Q

Smooth ER - structure

A

More tubular than RER

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52
Q

Smooth ER - function

A

Involved in synthesis and transport of lipids

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53
Q

Relationships among organelles of endomembrane system

A

Proteins inserted into RER move toward outer layers ER and bud off into a vesicle
These proteins aren’t complete and need to be modified –> taken from RER to Golgi apparatus

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54
Q

Golgi - structure

A

A flattened stack of membranous sacs

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55
Q

Golgi apparatus - process/steps

A

Membrane of vesicle fuses with membrane of Golgi, emptying proteins into Golgi apparatus
Proteins can now be modified in several ways - addition of molecules (e.g. carbohydrates, phosphorylated, lipids) that enable them to carry out their functions
Once protein is completed, it’s sorted into a particular area of Golgi so it can bud off into a new vesicle
Finished protein can now leave Golgi apparatus

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56
Q

Golgi apparatus - where do vesicles fuse

A

Always fuse at cis side of Golgi, and as proteins move through Golgi, they move to the trans face

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57
Q

Golgi apparatus - finished protein - destined to be?

A

Destined to either by secreted by cell - vesicle buds off and vesicle membrane fuses with outer PM and contents are secreted to outside of cell
OR may be used by other members of endomembrane system - proteins trapped and trafficked back to ER or to earlier regions of Golgi where they may be required to facilitate modifications of proteins

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58
Q

What are found in lysosomes

A

Hydrolytic enzymes made by RER and modified in Golgi, which were then budded off into a lysosome
Hydrolytic enzymes must be enclosed within lysosomes to keep them away from and protect other areas of cell

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59
Q

Lysosomes - functions

A

Digestion of food

Recycling molecules

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60
Q

Lysosomes - digestion of food

A

Food is taken up into a food vacuole by cell
Membrane of lysosome fuses with membrane of food vacuole and empties its hydrolytic enzymes into food vacuole –> digests food into molecules that can be used by cell

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61
Q

Lysosomes - recycling molecules

A

Enables cells to break down damaged organelles by emptying its hydrolytic enzymes into vesicle –> liberates the molecules which are in those organelles –> enables cell to use and recycle those molecules

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62
Q

What are mitochondria

A

Respiratory enzymes (Kreb’s cycle) located in inner membrane and matrix

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63
Q

What do mitochondria contain

A

Own mitochondrial DNA and free ribosomes - potential to produce own proteins

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64
Q

Mitochondria - membranes

A

2 membranous structures - outer and inner membrane

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65
Q

Mitochondria - inner membrane

A

Folds in and out of mitochondria to form cristae

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66
Q

Mitochondria - what occurs here

A

Site of cellular respiration and where oxygen and food molecules are combined to make ATP for cell

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67
Q

Mitochondria - importance of cristae

A

Important because lots of enzymes involved in respiration processes are embedded in cristae
Folds = increased SA = increased no of enzymes present in mitochondria

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68
Q

Mitochondria - where are enzymes found

A

Not all enzymes embedded in cristae, some found in matrix (region between cristae)

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69
Q

Where are chloroplasts found

A

Only in plants and algae

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70
Q

Chloroplasts - what occurs here

A

Photosynthesis

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71
Q

Chloroplasts - membranes

A

Bound by an outer and inner membrane

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72
Q

Chloroplasts - thylakoids

A

A 3rd internal membrane network containing photosynthetic apparatus

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73
Q

What do chloroplasts contain

A

Own DNA and ribosomes

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74
Q

Chloroplasts belong to a family called ____

A

Plastids

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75
Q

What are thylakoids

A

Interconnected flattened sacs stacked on top of each other

Contains chlorophyll

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76
Q

Cytoskeleton - functions

A

Maintain cell shape (all)
Facilitate cell movement
Facilitate movement of components within cell (e.g. vesicles)

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77
Q

What is the cytoskeleton

A

Interconnecting protein structures within cytoplasm

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78
Q

Types of cytoskeletal filaments

A

Microtubules
Microfilaments
Intermediate filaments

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79
Q

Cytoskeleton: Microfilaments (actin)

A

Cell motility - enable formation of pseudopodia (cell ‘foot’) and to extend out and crawl along

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80
Q

Cytoskeleton: Intermediate filaments

A

Involved in helping anchor organelles in position inside cell

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81
Q

Cytoskeleton: Microtubules

A

Provides a network for vesicles to move along using microproteins attached to bottom of vesicle
ATP enables motor protein to change in shape –> walks along microtubule, taking with it the vesicle containing the protein to Golgi to be modified

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82
Q

Cilia and flagellae contain…

A

Microtubules

Help flagella bend and cilia waft

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83
Q

Cilia and flagellae - similarity of structure

A

Similar internal structure

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84
Q

Cilia and flagellae - microtubules

A

9 pairs around the edge and 1 pair in the middle
Outer microtubules linked by motor proteins called dimes
Allows it to bend to an extent (using ATP), then goes back because of cross-linking proteins in between

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85
Q

Cell membrane - function

A

Forms a barrier that selectively regulates movement into and out of cell (PM)
Also membranes surrounding organelles - have similar structure to outer PM

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86
Q

What cells have membrane-bound organelles

A

Eukaryotic cells

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87
Q

Lipid bilayer thickness

A

7-8nm thick

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88
Q

Phospholipid bilayer - structure

A

Each layer contains lots of phospholipids

Each phospholipid consists of a hydrophilic head and 2 hydrophobic tails

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89
Q

Phospholipid bilayer: Head - structure

A 
From top to bottom:
Choline (or other small molecule)
Phosphate
Glycerol
(then tail)
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90
Q

Phospholipid bilayer: What are the tails attached to

A

2 Cs of glycerol molecule

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91
Q

Phospholipid bilayer: Tail

A

Hydrophobic

Fatty acid chain

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92
Q

Phospholipid bilayer: Tail - saturation

A

If structure is saturated –> straight

If structure is unsaturated (has double bond between 2Cs) –> kink in tail

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93
Q

For proteins to be embedded in the membrane…

A

They must have both hydrophobic and hydrophilic regions
Hydrophobic regions to associate with fatty acid tails in middle of membrane
Hydrophilic regions to associate with hydrophilic heads and aqueous environment either inside or outside of cell

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94
Q

Amphipathic

A

Have both hydrophilic and hydrophobic properties

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95
Q

Types of proteins in cell membrane

A

Integral proteins

Peripheral proteins

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96
Q

Integral proteins

A

Can span entire membrane - called transmembrane proteins

Or, can only partially protrude into cell membrane

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97
Q

Peripheral proteins

A

Can associate with phospholipids themselves or with integral proteins

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98
Q

Glycoproteins

A

Proteins attached to carbohydrate structures

Many receptors and docking proteins embedded in cell membranes are glycoproteins

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99
Q

Proteins anchored to cytoskeleton

A

Some proteins embedded in membrane can be anchored to cytoskeleton inside cell
Anchors cytoskeleton in position –> helps maintain cell shape and size

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100
Q

In animal cells, instead of having a cell wall like plants, they have…

A

ECM - a network of fibres outside the matrix

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101
Q

ECM components

A

Proteins and carbohydrates

Made by the cell themselves (makes its own)

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102
Q

ECM - collagen fibres

A

Main component of ECM
Long strong protein fibres
Intertwined with a proteoglycan complex

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103
Q

Proteoglycan complex

A

Consists of a core protein with numerous carbohydrates radiating off the side

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104
Q

ECM - fibronectin

A

Links proteins embedded in cell membrane with collagen proteins
Can anchor cell in a particular position within the tissue
Enables cell to follow collagen fibres and navigate its way through the tissue

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105
Q

ECM components can interact with…

A

Integrins, which can detect changes in ECM and communicate these changes to inside of cell through a signalling cascade

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106
Q

Functions of membrane proteins

A 
Enzymatic activity
Signal transduction
Cell-cell recognition
Attachment to cytoskeleton and ECM
Intercellular joining (cell junctions)
Transport
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107
Q

Functions of membrane proteins: enzymatic activity

A

e.g. protein enzymes embedded in cristae which carry out respiration
Enzymes are embedded in sequence - enables to catalyse sequential reactions

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108
Q

Functions of membrane proteins: signal transduction

A

Act as receptors to detect signalling molecules in extracellular environment
Once receptor bound to signalling molecule, it can communicate inside cell via signal transduction

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109
Q

Functions of membrane proteins: cell-cell recognition

A

Glycoprotein attached to a small carbohydrate and another protein can recognise this specific glycoprotein –> enables cells to dock with each other briefly –> enables other proteins in membrane to communicate with each other while they are docked tgt

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110
Q

Functions of membrane proteins: attachment to cytoskeleton and ECM

A

Anchors cytoskeletal fibres in place and helps maintain cell structure and place
Or can associate with collagen fibres of ECM
Or may move through tissue by following collagen fibres

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111
Q

Phospholipids are synthesised in association with…

A

The ER

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112
Q

Synthesis of membrane components and their orientation - steps

A

At each transition with ER and Golgi, the blue layer (hydrophobic) of phospholipid remains facing inside of those organelles
Orange layer always faces outer cytoplasm of vesicles and Golgi
As membrane of vesicle fuses with outer PM, orange layer remains facing inside of cytoplasm, but blue layer now faces outside of cell

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113
Q

For a protein to be embedded in the membrane and conduct its function correctly…

A

It must be correctly orientated in the membrane

Thus, its important when the protein is first made in the ER, it is orientated correctly

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114
Q

Where can proteins throughout cell be embedded

A

Some embedded in inner membrane to carry out their functions, but others need to be embedded in outer PM of cell (e.g. receptors and docking proteins)

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115
Q

Fluidity of phospholipids

A

Phospholipids move very rapidly within their monolayer - lateral movement occurs ~10^7 times per second
Phospholipids rarely flip-flop from one side of PM to the other because hydrophilic head would have to cross hydrophobic tail - ~once per month

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116
Q

Fluidity of membrane - double bond

A

Helps maintain fluidity as it can push away neighbouring phospholipids –> creates more space

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117
Q

Fluidity of membrane - if all phospholipids had fully saturated fatty acid tails..

A

They would pack tightly tgt and end up with a very viscous membrane (not much space for phospholipids to move)

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118
Q

Fluidity of membranes - animal and plants living in very cold temp

A

Have lots of unsaturated fats in phospholipids because otherwise they would stick to each other and solidify - helps retain fluidity of membrane

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119
Q

What cells is cholesterol found in

A

Only found in animal cell membrane - not plants

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120
Q

Fluidity of membranes: Cholesterol

A

Acts as a fluidity buffer (in animal cell membranes)

A steroid which can squeeze between fatty acids of phospholipids

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121
Q

Fluidity of membranes: Cholesterol - temp

A

At cold temp, stops neighbouring phospholipids from sticking tgt and solidifying - helps maintain fluidity
At moderate temp, reduces amount of space between phospholipids and reduces membrane fluidity

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122
Q

Cell fusion - process

A

Mouse + human cell with membrane proteins joined tgt to form a hybrid cell
Leave for one hour, resulting in mixed proteins
Indicated proteins were able to move laterally around the membrane - membranes aren’t static!

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123
Q

Cell junctions in animal tissues

A

Tight junction
Desmosome
Gap junction

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124
Q

Cell junctions in plant tissues

A

Plasmodesmata

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125
Q

Cell junctions: Tight junction

A

Mesh of proteins knitting 2 neighbouring cells tightly tgt –> fluid unable to pass between cells
Primarily composed of occludins and claudins

e.g. skin cells - makes us water-tight

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126
Q

Cell junctions: Desmosomes

A

Anchor is extremely strong between 2 neighbouring cells
Anchored in position by intermediate filaments (keratin) that radiate into cell
e.g. muscle cells

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127
Q

Cell junctions: Gap junctions

A

Each junction made of 6 cylindrical proteins called connexins, which form a tube that runs from one cell to a neighbour cell
Tube is ~2nm in diameter, so small molecules can move from cytoplasm of one cell to cytoplasm of neighbouring cell –> allows communication
Types of molecules that can move through are iron, sugars and amino acids
e.g. found in lots of tissues; heart muscle, liver, embryos

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128
Q

Cell junctions: Plasmodesmata

A

Little tubes that run from one cell to another
Similar to gap junctions; facilitate movement of molecules from one plant cell to another
Through these tubes, small proteins and RNA can move
Cytoplasm of 2 neighbouring plant cells connected –> communication

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129
Q

Types of transport for small molecule across cell membrane

A

Passive transport

  • Diffusion
  • Facilitated diffusion
  • – Channel proteins
  • – Carrier proteins

Active transport
- Na/K pump

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130
Q

Passive membrane transport

A

Molecules move passively from high to low conc

Spontaneous - no energy expenditure by cell required

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131
Q

Passive membrane transport: Diffusion

A

No protein required

Small, non-polar molecules (e.g. CO2 and lipids) are hydrophobic, so can easily diffuse through cell membrane

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132
Q

Passive membrane transport: Facilitated diffusion

A 
Polar molecules (e.g. water, ions and glucose) are hydrophilic, hence require transport proteins to diffuse through membrane
Most transport proteins are specific --> selectivity
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133
Q

Osmosis

A

Diffusion of water across membrane

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134
Q

Passive membrane transport: Facilitated diffusion - channel protein

A

Provides a channel through which specific molecules can move from a high to low conc
e.g. aquaporin - facilitates movement of water from one side of molecule to the other

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135
Q

Passive membrane transport: Facilitated diffusion - carrier protein

A

Highly selective
Has a receptor that enables binding of a specific molecule
When that molecule binds, it induces a change in shape –> molecule has access to other side of cell membrane
As molecule dissociates from protein, protein quickly reverts back to original shape so it can move another molecule
e.g. glucose transporter

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136
Q

Active membrane transport

A

Molecules move across membrane against conc gradient
Usually require energy in form of ATP
All carrier proteins

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137
Q

Active membrane transport: Na/K pump - purpose

A

Allows cell to maintain a low conc of Na+ and high conc of K+ –> cell is able to maintain its resting potential

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138
Q

Active membrane transport: Na/K pump - steps

A

Na/K pump has a carrier protein which has 3 binding sites for Na+
As the 3rd Na+ binds, it enables ATP to donate a phosphate group –> carrier protein now phosphorylated
This induces a change in shape, and 3 Na+ now have access to outside of cell
Simultaneously, the 3 binding sites for Na+ reduce their affinity to bind Na+, so Na+ is quickly released to outside of cell
Phosphate group that was bound to carrier protein dissociates from carrier protein, enabling K+ binding sites to develop a higher affinity for K+
This induces a change in shape and K+ now have access to inside of cell
Simultaneously, affinity of K+ binding sites are reduced to K+ quickly released
Cycle repeats

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139
Q

How much ATP made by a cell is used to run the Na/K pump when resting?

A

~30%

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140
Q

Membrane transport proteins - advantage(s) and disadvantage(s)

A

Provide selectivity
Can increase rate of transport
Continuously recycled

Rate of transport limited by no of proteins

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141
Q

Types of transport for large molecules across cell membrane

A

Exocytosis

Endocytosis

  • Phagocytosis - cell ‘eating’
  • Pinocytosis - cell ‘drinking’
  • Receptor mediated endocytosis
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142
Q

Exocytosis

A

Where contents of a cell vacuole are released to the exterior through fusion of the vacuole membrane with the cell membrane

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143
Q

Endocytosis: Phagocytosis

A

Cell rearranges to cytoskeleton to send out 2 pseudopodia on either side of the food particle to engulf it into a food vacuole

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144
Q

Endocytosis: Pinocytosis

A

Where cell takes little ‘gulps’ of ECF containing some molecules - non-selective
As it takes a ‘gulp’, it pinches the ECF and encloses it within a vesicle
Once vesicle is formed, it is coated with proteins –> coated vesicle

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145
Q

Endocytosis: Receptor-mediated endocytosis

A

Receptors on cell surface recognise and bind to molecules and cluster tgt on membrane –> pinched off into a vesicle
A few other molecules in ECM are also engulfed within the vesicle, i.e. both specific and non-specific uptake
Eventually buds off into a vesicle and is coated with proteins –> enables it to be trafficked to right place of cell
Empty receptor moves back to outer cell membrane

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146
Q

Reuse of receptors?

A

Receptors are recycled - not just used once

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147
Q

Functions of proteins

A 
Enzymes
Defensive
Storage
Transport
Hormones
Receptors
Contractile/motor proteins
Structural proteins
Gene regulatory proteins
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148
Q

How much of the dry weight of most cells is protein?

A

> 50%

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149
Q

Functions of proteins - enzymes

A

Majority of enzymes are proteins

Selective catalysts that can accelerate rate of specific metabolic reactions

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150
Q

Functions of proteins - defense

A

Immune system - protects against disease

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151
Q

Functions of proteins - transport

A

e.g. Haemoglobin - transports O2 from lungs to other tissue in body

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152
Q

Functions of proteins - hormones

A

Majority of hormones in our body are made of proteins

Hormones coordinate an organism’s activity

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153
Q

Functions of proteins - receptors

A

Proteins embedded in cell membrane

Detect specific molecules outside cell and communicates to inside of cell

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154
Q

Functions of proteins - contractile/motor proteins

A

e.g. flagella - a motor protein is anchored to one pair of the microtubules, and the other side of the motor protein walks along a neighbouring pair of microtubules –> enables flagella to bend

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155
Q

Functions of proteins - structural proteins

A

e.g. cytoskeleton

Also have outside cell in ECM, e.g. collagen

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156
Q

Functions of proteins - gene regulatory proteins

A

Combine with specific regions of DNA and control whether certain genes will be expressed
Allows cells to respond to changes in environment
Allows cells to differentiate into particular cell types with specialised functions

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157
Q

Parts of an amino acid

A 
α-carbon
Amino group (NH2)
Carboxyl group (COOH)
H attached to α-carbon
R side chain
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158
Q

Amino acids - types of side chains

A

Non-polar: hydrophobic
Polar: hydrophilic
Electrically charged: hydrophilic

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159
Q

Polypeptides are built up with…

A

Monomers called amino acids

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160
Q

Amino acid side chains

A

Each amino acid has a distinct side chain / R group
Determines how the amino acid behaves in polypeptide
Can be simple or complex

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161
Q

Number of amino acids

A

20 diff amino acids with diff side chains

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162
Q

Amino acids: Non-polar side chains

A

Hydrophobic

9 types

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163
Q

Amino acids: Polar side chains

A

Hydrophilic
6 types
Cysteine is only weakly polar

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164
Q

Amino acids: Electrically charged side chains

A 
Hydrophilic
2 acidic (-vely charged)
3 basic (+vely charged)
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165
Q

Peptide bonds

A

Link carboxyl group of one amino acid to amino group of next
Dehydration reaction
Form one at a time
Forms a repetitive backbone

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166
Q

What do amino acid side chains determine

A

How final peptide folds and ultimately its 3D structure and final function

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167
Q

Proteins: Primary structure

A

Linear arrangement of amino acids in polypeptide chain
Sequence of amino acid is unique to each protein
Dictates secondary, tertiary, and quaternary structure

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168
Q

Primary structure: Polypeptide synthesis

A

Amino acid sequence specified by sequence of nucleotides in DNA
Info in DNA copied into mRNA (transcription)
Info in mRNA determines amino acid sequence (translation)

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169
Q

Proteins: Secondary structure - types

A

Alpha helix - regions with repeated coiling
Beta-pleated sheet - diff sheets with repeated folding associate with each other

Particular amino acid sequences form alpha helices, while others have a propensity to form beta-pleated sheets

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170
Q

Proteins: Secondary structure - H bonds

A

Form between repetitive regions of polypeptide backbones
Stabilise secondary structre
O in C=O has -ve charge, which is attracted to H in N-H with +ve charge –> H bond

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171
Q

Proteins: Secondary structure - H bonds - strength

A

Individually are relatively weak, but numerous of them form between regions of polypeptide backbone –> relatively strong

172
Q

Proteins: Secondary structure - H bonds - R groups

A

Formation of H bonds can be influenced by R groups
If R group is v large, can push away neighbouring polypeptides –> interferes with formation of H bonds - known as steric hindrance
Or, R group could carry a charge - interferes with neighbouring H bonds

173
Q

Proteins: Secondary structure - alpha helix

A

Delicate coil held tgt by H-bonding between every 4th amino acid
Often found in regions of transmembrane proteins that cross the lipid bilayer

174
Q

Proteins: Secondary structure - alpha helix - transmembrane proteins

A

Each alpha helices region is connected by a non-folded region
Transmembrane proteins often have the C-terminus facing inside the cell and N-terminus facing outside

175
Q

Proteins: Secondary structure - beta-pleated sheet

A

Two or more strands of same polypeptide chain lay side by side
H bonds form between O and H of neighbouring polypeptide backbones
Make up the core of many globular proteins
Many H bonds = lots of strength

176
Q

Proteins: Tertiary structure

A

Describes the overall 3D conformation of the polypeptide chain
Stabilised by interactions between side chains

177
Q

Proteins: Tertiary structure - types of weak interaction(s) between side chains

A

H bonds: between polar side chains
Hydrophobic interactions and vdW: between non-polar side chains
Ionic bonds: between oppositely charged side chains

Individually weak, but tgt strong

178
Q

Proteins: Tertiary structure - types of strong interaction(s) between side chains

A

Disulphide bridge: type of covalent bond between 2 cysteine amino acids
- Sulfhydryl groups associate with each other, Hs lost and S atoms form a disulphide bridge

179
Q

Proteins: Quaternary structure

A

The entire protein structure, i.e. all polypeptides

Consist of two or more polypeptides, which can be the same or diff

180
Q

Proteins: Quaternary structure - Collagen

A

Consists of 3 identical coiled polypeptides that intertwine with each other

181
Q

Proteins: Quaternary structure - haemoglobin

A

Consists of 4 polypeptides; 2 identical alpha subunits and 2 beta subunits, which come tgt with 4 haeme groups

182
Q

Chaperonins

A

Assists folding of proteins (provides optimal environment)

  • protects polypeptide from degradation
  • polypeptides fold spontaneously into proteins

Some chaperonins tgt with associated systems check correct folding has occured

  • refold
  • mark for destruction
183
Q

If proteins are misfolded…

A

It can give rise to various disease states

Thus important they fold correctly

184
Q

Chaperonins - steps

A
  1. Cap detaches and an unfolded polypeptide enters the cylinder
  2. Cap attaches, causing cylinder to change shape –> creates a hydrophilic environment for folding of polypeptide
  3. Cap comes off, and the properly folded protein is released
185
Q

Denaturation of a protein

A

Destruction of the secondary, tertiary and quaternary structure (i.e. 3D shape)
Breakage of H bonds, Ionic bonds, hydrophobic interactions and S-S bonds

186
Q

Causes of denaturation of a protein

A

Heat - breaks weak bonds (increase in temp –> proteins move further from each other –> bonds break)
pH - changes ionisation patterns of R groups
Reducing agents - reduce S-S bonds to SH
Organic solvents - disturb hydrophobic and hydrophilic interactions
Detergents - disrupt hydrophobic interactions

187
Q

Hydrolysis vs denaturation

A

NOT the same

Hydrolysis breaks primary structure, denaturation doesn’t affect primary structure

188
Q

Denaturation and renaturation of a protein

A

In vitro, some denatured proteins can return to their functional shape if denaturing agent is removed and still function
Provides evidence that all info required for a polypeptide to fold into its correct 3D shape is in sequence of side chains

189
Q

Exergonic reactions

A

Reactants contain more energy than products
Free energy released
Usually catabolic; large molecules –> small molecules + energy

190
Q

Endergonic reactions

A

Reactants contain less energy than products
Free energy required
Usually anabolic; small molecules + energy –> large molecules

191
Q

Exergonic reactions with enzymes

A

Ea is lowered

Change in free energy is unaffected (energy released is same)

192
Q

Activation energy

A

Energy needed to break/distort bonds to reach transitions state

193
Q

Enzymes

A

Act as catalysts that lower the Ea, thus increasing rate of rxn
Not consumed by rxn and can be used again
Almost all enzymes are proteins with complex 3D structures which determine its activity (some are RNA)

194
Q

Catalytic cycle of an enzyme - steps

A
  1. Substrates enter active site
  2. Substrates are held in active site by weak interactions (usually H and ionic bonds)
  3. Substrates are converted to products
  4. Products are released
  5. Active site available for new substrates
195
Q

Induced fit

A

Overall shape of enzyme enables it to clasp down on substrate once it binds to amino acids in active site
After being clasped down, additional ionic and H bonds can form

196
Q

The overall shape, size and structure of enzymes ensures…

A

The amino acid in active sites are able to bind to the substrate and are correctly aligned

197
Q

Catalytic cycle of an enzyme - general equation

A

Enzyme + substrate(s) –>
Enzyme substrate complex –>
Enzyme + product(s)

198
Q

Enzyme names end in..

A

-ase

199
Q

Enzyme names: Isomerase

A

Catalyse intramolecular rearrangements

200
Q

What enzymes hydrolyse RNA and DNA

A

Ribonuclease

Deoxyribonuclease

201
Q

What enzymes synthesise RNA and DNA

A

RNA and DNA polymerase

202
Q

How many reactions can each enzyme typically catalyse in a second

A

~1000

Very quickly - each cycle is v brief

203
Q

Enzyme names can indicate…

A

What the substrate is

204
Q

How are enzymes classified

A

According to how tightly they bind to the substrate

205
Q

Co-factors

A

Non-protein helpers for catalytic activity

206
Q

Types of co-factors

A

Some permanently bound, some bind reversibly with substrate

Prosthetic groups
Coenzymes

207
Q

Co-factors: Prosthetic groups

A

Organic or inorganic molecules tightly bound to the protein

208
Q

Co-factors: Co-enzymes

A

Small organic molecules, non-covalently bound to protein

209
Q

Enzyme and substrate conc

A

Enzyme conc directly proportional to reaction rate (so long as sufficient substrate) - linear relationship

Available enzyme can become saturated with substrate - increases steeply then plateaus at a max

210
Q

How do cells regulate metabolic pathways

A

By controlling when are where certain enzymes are active

211
Q

How do cells control when/where certain enzymes are active

A

Switching on and off genes that encode particular enzymes
Regulating enzyme activity once they are made
- conversion of an inactive enzyme precursor to an active form (usually first enzyme made is not active)
- cellular localisation (enzymes may be locked inside organelles in a cell)
- allosteric regulation (inhibition or activation)

212
Q

Allosteric regulation of enzyme activity - oscillation

A

There is oscillation between the active form and inactive form

213
Q

Allosteric regulation of enzyme activity - active vs inactive form

A

Active form:
Active sites are open

Inactive form:
Active sites are non-functional / closed off

214
Q

Enzymes - human body

A

Majority of enzymes in human body have optimal temp of 37°C

215
Q

Enzymes - temp

A

As temp increases, ROR increases until a max, where the enzymes break and denature (for humans this is 37°C)

216
Q

Trypsin

A

Involved in breaking down peptides and polypeptides into amino acids

217
Q

Allosteric regulation of enzyme activity - activating an enzyme

A

If a cell wants an enzyme to be active, it can produce an activator which binds to a site away from the active site and stabilises one of the sub-units within the enzyme in its active state
This active subunit then communicates to other sub-units within enzyme to remain in active states - only need one activator to bind

218
Q

Allosteric regulation of enzyme activity - deactivating an enzyme

A

If cell wants enzyme to be inactive, it produces an inhibitor which binds to a site away from active site and stabilises one of the sub-units in its inactive form, which communicates to other sub-units to remain inactive

219
Q

Allosteric regulation of enzyme activity - binding of activator and inhibitor

A

Only binds weakly - can quickly dissociate to enable enzyme to go back to oscillation stage

220
Q

Allosteric regulation of enzyme activity - Regulatory molecules bind to the enzyme via…

A

Non-covalent interactions

221
Q

Allosteric regulation of enzyme activity: Feedback inhibition

A

Multi-step pathway, where each reaction is catalysed by a diff enzyme
Metabolic pathway is switched off by the end product (when in excess) binding to and inhibiting an enzyme that acts early in the pathway (usually binds to allosteric regulatory site on first enzyme –> induces change in shape of active site so it’s no longer functional)

222
Q

Types of nucleic acids

A

DNA and RNA - involved in all informational processes in cell
ATP - stores and transports chemical energy within cell
cAMP - involved in intracellular signalling

223
Q

ATP and RNA

A

ATP is one of the building blocks used to make RNA

224
Q

cAMP is derived from…

A

ATP

225
Q

Structure of a nucleotide

A

Phosphate group
Sugar (pentose)
Nitrogenous base

226
Q

Nucleic acids

A

A polymer of nucleotides

227
Q

How are nucleotides bound tgt

A

By covalent bonds called phosphodiester bonds - gives rise to a repetitive sugar-phosphate backbone

228
Q

Types of nitrogenous bases

A

Pyrimidines:
Cytosine (C)
Thymine (T) or Uracil (U)

Purines:
Adenine (A)
Guanine (G)

229
Q

How can nucleic acid structure be stabilised

A

By H bonds between nitrogenous bases

230
Q

DNA vs RNA - strands

A

DNA - double-stranded helix

RNA - usually single strand, but can bend back on themselves - helps form their unique 3D structures

231
Q

What is DNA

A

The major hereditary material of the cell

232
Q

DNA: Polynucleotide - directionality

A

From 5’ (phosphate group) to 3’ (with -OH of sugar)

233
Q

What provides genetic info

A

Sequence of nitrogenous bases in DNA

234
Q

DNA: 5’ vs 3’ end

A

5’ is bound to a phosphate group, so no new nucleotides can be added to the 5’ end
3’ end C is bound to an OH, which is available to bind to a phosphate group of a new nucleotide,
So, can only add a new nucleotide to the 3’ end

235
Q

Complementary base pairing

A

H bonds form between specific base pairs
A-T (or U)
C-G

236
Q

DNA: Anti-parallel

A

One nucleic acid runs from 5’ to 3’ in one direction, and other runs from 5’ to 3’ in opp direction

237
Q

DNA: Nitrogenous bases in middle of helix

A

Tightly stacked on each other

Hydrophobic - start to interact with each other through vdW - helps stabilise double helix

238
Q

Chromosomes: Packing of DNA

A

DNA starts off 2nm in diameter and starts packing with histones
Nucleosome forms

Histone tails radiate out of nucleosomes, which associate with neighbouring DNA strands and nucleosomes –> gives rise to a 30nm fibre

Protein scaffold used to anchor 30nm fibre as it loops round and round to form a 300nm fibre

Chromosomes are highly organised - genes always end up in the same position in the chromatid (700nm)
Not much known about the last step

239
Q

Nucleosomes

A

Beads on a string

Where 8 histones (proteins) cluster tgt and DNA molecule wraps around the histone cluster twice –> forms a nucleosome

240
Q

DNA vs RNA - structure

A

Unlike DNA, structure of RNA molecules is more variable

241
Q

DNA and RNA - sequence of bases

A

Sequence of bases in DNA specifies the sequence of bases in RNA

242
Q

Types of RNA

A

Ribosomal (rRNA)
Messenger (mRNA)
Transfer (tRNA)

243
Q

What is rRNA

A

The RNA component of the ribosome

244
Q

rRNA - function

A

Helps support structure of ribosome
Involved in protein synthesis
Stable RNA which comprises the bulk of the cellular RNA

245
Q

Where is rRNA synthesised

A

In nucleolus from highly repetitive DNA

246
Q

What % of ribosomes are made of rRNA

A

~60% of ribosomes are made of rRNA and 40% made of protein

247
Q

mRNA - function

A

Conveys info from DNA in nucleus to ribosome, where it specifies the amino acid sequence of the polypeptide

248
Q

mRNA - speed

A

Synthesised at a fast rate, degraded rapidly, so is present in relatively small amounts

249
Q

Why do we need mRNA

A

Because DNA can’t leave the nucleus, and to get info from DNA to ribosome, need a messenger molecule

250
Q

tRNA - function

A

Translator - translates nucleotide sequence in mRNA into amino acids during protein synthesis

251
Q

What does a tRNA contain

A

4 base-paired regions
3 loops including an anticodon
Amino acid attachment site

252
Q

tRNA - anticodon

A

Anticodon loop binds to codon in mRNA

253
Q

For each of the 20 amino acids, there is at

least one specific ____

A

tRNA molecule in the cell

254
Q

Replication of DNA - the basic concept

A
  1. Parent molecule
  2. Separation of strands
  3. Daughter DNA molecules, each consisting of one parental strand and one new strand
255
Q

Replication - enzymes

A

Replication is an enzymic process; carried out by a multi-enzyme complex
Must be accurate and fast

256
Q

Proposed models of DNA replication

A

Conservative model: 2 parental strands re-associate with each other and 2 new strands associate with each other
Semi-conservative model: Each parental strand forms a double helix with a new strand
Dispersive model: Daughter DNA molecules contain a mix of new DNA and parental DNA

257
Q

Which model is DNA replictaion

A

Semi-conservative

258
Q

Origin of DNA replication in prokaryotes

A

Each chromosome only has 2 origins of replication - one for each strand
Parental strands are separated and new DNA is made
As replication continues, there are 2 replication forks
In the middle of 2 replication forks is a replication bubble
Replication forks eventually meet and end up with 2 daughter DNA molecules

259
Q

DNA: Prokaryotes - chromosome shape

A

Circular

260
Q

Replication forks

A

Where the parental DNA is pulled apart and made available for replication

261
Q

DNA: Eukaryotes - chromosome shape

A

Linear

262
Q

Origin of DNA replication in eukaryotes

A

Each chromosome has multiple origins of replication - can have a few hundred or thousand
Occurs in both directions simultaneously
Each bubble has 2 replication forks
As replication continues, replication bubbles fuse and end up with 2 daughter DNA molecules

263
Q

Proteins involved in initiation of replication: Helicase

A

Enzymes which break H-bonds and untwist double helix at replication fork so DNA strands available for replication
If mutation so helicase doesn’t work, no replication fork will be formed

264
Q

Proteins involved in initiation of replication: Single-strand binding proteins

A

Prevent single strand DNA from re-pairing, bending, or kinking

265
Q

Proteins involved in initiation of replication: Topoisomerase

A

Breaks, swivels and rejoins parental DNA ahead of replication fork
As DNA unwinds, coils get pushed down, causing region ahead of replication fork to become super coiled –> large amount of pressure on DNA molecule in that region, so topoisomerase relieves strain by breaking sugar-phosphate backbone and unwinding the supercoiled region

266
Q

Proteins involved in initiation of replication: Primase

A

Synthesises short RNA primers using the parental DNA as a template

267
Q

First bit of nucleic acid made during DNA replication

A

Is not DNA, but is RNA because DNA polymerase can’t add the first nucleotide in a new nucleic acid strand - needs an existing 3’ end to add a new nucleotide to
3’ end comes from an RNA primer

268
Q

RNA primer - length

A

Usually quite short - between 5-10 nucleotides in length

269
Q

What is DNA replication driven by

A

The energy released from the hydrolysis of bonds between phosphate groups in nucleotide being added
New nucleotide has 3 phosphate groups - the 2 phosphate bonds are hydrolysed –> provides energy required

270
Q

DNA polymerase

A

Catalyses addition of new nucleotide

Can proofread and repair DNA as its made

271
Q

DNA replication: Leading strand

A

Continuous synthesis

DNA polymerase III adds first nucleotide to 3’ end

272
Q

DNA replication: Lagging strand

A

Discontinuous synthesis of fragments in 5’ to 3’ direction

273
Q

DNA replication: Bi-directional

A

Occurs in both directions (left and right) simultaneously

274
Q

DNA replication: Anti-parallel

A

Overall, new DNA strand must be anti-parallel to parental strand

275
Q

DNA replication: Rules

A

All strands when paired to each other, must be anti-parallel to each other
Can only add a nucleotide to a 3’ end

276
Q

DNA replication: Okazaki fragments

A

Fragments in lagging strand

Usually between 100-200 nucleotides long in eukaryotic cells

277
Q

DNA replication: Lagging strand - steps

A
  1. Primase generates RNA primer
  2. DNA pol III adds nucleotides to primer, forming Okazaki fragment 1
  3. Once reaches next RNA primer, DNA pol III detaches
  4. Okazaki fragment 2 is primed
  5. DNA pol III adds nucleotides, detaching when it reaches fragment 1 primer
  6. DNA pol I replaces RNA in primers with DNA
  7. DNA ligase forms bond between DNA fragments
  8. Lagging strand in region is complete
278
Q

Shortening of ends of DNA molecules

A

End primer removed, but can’t be replaced with DNA as no 3’ end available
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

279
Q

What are telomeres

A

Region of repetitive nucleotide sequence at the end of each chromatid

280
Q

Telomeres - function

A

Prevent loss of genes near ends

With each round of replication, gradually get eroded away

281
Q

Telomeres - continuously dividing cells

A

In continuously dividing cells, telomerase replaces lost telomeric sequences

282
Q

Transcription

A

The transfer of info from DNA into (pre) mRNA

283
Q

Translation

A

Nucleotide sequence of mRNA translated into the amino acid sequence of a protein

284
Q

Where does transcription occur

A

Nucleus

285
Q

Where does translation occur

A

Cytoplasm

286
Q

What is translation conducted by

A

Ribosomes

287
Q

Prokaryotic vs eukaryotic cells - RNA processing

A

Process is similar in prokaryotic cells, but mRNA that is first transcribed can directly be translated
i.e. doesn’t need to undergo RNA processing

288
Q

Transcription - basic steps

A

Initiation
Elongation
Termination

289
Q

Transcription - detailed steps

A
  1. RNA polymerase binds to promoter on DNA
  2. DNA strands unwind
  3. RNA polymerase initiates RNA synthesis at start point within promoter of template strand
  4. RNA polymerase joins complementary RNA nucleotides one by one to 3’ end of growing RNA transcript
  5. New RNA peels away from template strand
  6. Transcribed DNA rewinds into double helix
  7. Complete RNA transcript is released
  8. RNA polymerase detaches from DNA
290
Q

What is the promoter

A

A nucleotide sequence that RNA polymerase binds to during transcription
Determines which DNA strand will provide the template for transcription

291
Q

Transcription: Initiation - transcription factors

A

In prokaryotic cells, RNA polymerase can bind directly to promoter itself
In eukaryotic cells, transcription factors facilitate binding of RNA polymerase to promoter and help initiate process of transcription

292
Q

Transcription: Initiation - unwinding of DNA strands

A

Usually pulls apart enough of the DNA to expose 10-20 nucleotides at a time

293
Q

Transcription: Elongation - speed

A

Addition of RNA nucleotides is catalysed by RNA polymerase

~40 nucleotides / sec

294
Q

Transcription: Termination - prokaryotes

A

Proceeds through a terminator sequence in DNA

Transcribed RNA terminator sequence provides a signal –> polymerase detaches from DNA

295
Q

Transcription: Termination - polyadenylation signal sequence

A

In eukaryotes
A point in the DNA which is transcribed into the RNA polyadenylation signal, which is bound by specific proteins in the nucleus, which cut the RNA free from the polymerase

296
Q

Average length of mRNA molecule

A

900-1200 bases long

Both DNA strands may code for mRNA

297
Q

Genes - overlapping

A

Some genes may overlap

e.g. HIV-1 genome consists of 9 genes, some of which are overlapping

298
Q

Transcription: 5’ cap and 3’ poly-A tail

A

Only in eukaryotic cells

Added by enzymes to pre-mRNA

299
Q

Transcription: 5’ cap and 3’ poly-A tail - functions

A

Promote export of mRNA from nucleus
Protects mRNA from degradation where it may be exposed to hydrolytic enzymes
5’ cap facilitates ribosome attachment

300
Q

Transcription: 5’ cap

A

Added to 5’ end

Consists of a guanine nucleotide that’s linked to the pre-mRNA molecule by a triphosphate linkage

301
Q

Transcription: Poly-A-tail

A

Added to 3’ end

Consists between 50-250 adenine nucleotides

302
Q

Exons

A

Sequence which will leave the nucleus as mRNA (coding segment) –> translated into amino acid sequences

303
Q

Introns

A

Non-coding RNA which lies between exons

304
Q

Splicing

A

Introns are cut out and exons are ligated tgt to form the mature mRNA molecule

305
Q

Where are UTR found

A

In final mRNA, there are 2 UTR

306
Q

What are UTRs

A

Untranslated regions

Not translated into a polypeptide, but info in coding segment is translated into amino acid sequence of polypeptide

307
Q

Introns - functions

A

Although not part of coding region, will have lots of important functions within cell
e.g. regulate processes of transcription and translation

308
Q

When does splicing occur

A

After transcription, where eukaryotic cells modify pre-mRNA

309
Q

Splicing: snRNPs

A

Small nuclear ribonucleoproteins

Along with other proteins, form a spliceosome on pre-mRNA

310
Q

Splicing: Splice sites

A

Within the spliceosome

Where the snRNA pairs with base pairs in the pre-mRNA intron

311
Q

Splicing: Spliceosome

A

Cuts the pre-mRNA releasing the intron for degradation and splices exons tgt
Catalysed by snRNA (ribozyme)

312
Q

Splicing: Spliceosome releases ____

A

mRNA

313
Q

What do snRNPs consist of

A

Proteins and small nuclear RNA, which can pair with splice sites on introns

314
Q

What is a gene

A

A region of DNA which codes for a functional product, either a polypeptide or an RNA molecule

315
Q

What do exons code for

A

When spliced tgt and translated into a protein, the original exons code for particular regions of the protein with specific function

316
Q

Codon

A

A sequence of 3 nucleotides which can be translated into a particular amino acid

317
Q

Some tRNA molecules are bound to..

A

Amino acids or polypeptides

318
Q

Where are codons and anti-codons located

A

Codon: mRNA molecule

Anti-codon: tRNA molecule

319
Q

mRNA specifies…

A

The amino acid sequence

320
Q

tRNA - structure

A

A single strand of nucleotides that fold back on itself
4 regions bound to each other by H bonds, formed between complementary base pairs
Has an amino acid attachment site
Anticodon loop to pair with mRNA codon

321
Q

Why is tRNA important

A

Important for accurate translation to happen

322
Q

Aminoacyl tRNA synthetases

A

Enzymes that attach the correct amino acid to each tRNA molecule
20 diff synthetases
Gets energy from ATP

323
Q

tRNA is ____ bound to amino acid

A

Covalently

324
Q

How many tRNA molecules are amino acids bound to

A

Some only be bound to one, while others can have a few

325
Q

What does every mRNA molecule contain at its 5’ end

A

A ribosomal binding site

326
Q

tRNA binding sites of ribosomes

A

P site: holds the tRNA carrying the growing polypeptide chain
A site: holds the tRNA carrying the next amino acid to be added
E site: where discharged tRNAs leave the ribosome

327
Q

Translation - basic steps

A

Initiation
Elongation
Termination

328
Q

Translation - detailed steps (eukaryotes)

A

Small ribosomal subunit binds to initiator tRNA
5’ cap of mRNA binds to small ribosomal subunit
Initiator tRNA scans mRNA molecule for start codon
Anticodon of initiator tRNA H-bonds to start codon
Large ribosomal subunit binds and initiator tRNA is positioned in P-site of ribosome
Translation begins

Anticodon of an aminoacyl tRNA pairs with complementary mRNA codon in A site
rRNA molecule of large ribosomal subunit catalyses formation of peptide bond between new amino acid and growing peptide
Ribosome moves tRNA into neighbouring sites
mRNA moves along with bound tRNAs, bringing next codon into A site

When ribosome reaches stop codon, A site accepts a release factor, which promotes release of polypeptide from tRNA in P site by hydrolysis
Polypeptide released through exit tunnel
mRNA and ribosomal subunits dissociate

329
Q

Translation: Start codon

A

Always AUG –> initiator tRNA always UAC

Signifies start of translation

330
Q

Energy for translation

A

GTP provides energy for all three stages of translation

331
Q

Translation: Release factor

A

A protein shaped like a tRNA molecule

Can only bind to a stop codon

332
Q

Translation: Stop codons

A

UAA
UAG
UGA

333
Q

Signal mechanism for targeting proteins to ER

A

Signal peptides on newly generated polypeptides can target them to ER
Many polypeptides are modified in the ER or Golgi after they are made, e.g. glycosylation

334
Q

Signal mechanism for targeting proteins to ER - steps

A

Signal peptides combine with a SRP which combines with its receptor on ER –> enables free ribosome to dock with ER
As ribosome translates info on mRNA into amino acid sequence of polypeptide, that polypeptide can be inserted into the RER
Once translation is complete, ribosome and mRNA dissociate and protein is now inside ER

335
Q

SRP

A

Signal recognition particle

336
Q

Polyribosome

A

A single mRNA strand along which many ribosomes are travelling
Each of these ribosomes are synthesising growing polypeptide chains
Enables cell to make proteins quickly

337
Q

Where are polyribosomes found

A

In both eukaryotic and prokaryotic cells

338
Q

Where does coupled transcription and translation occur

A

Only in prokaryotic cells

339
Q

Coupled transcription and translation in bacteria

A

Bacteria can have DNA molecule with RNA polymerase transcribing info in DNA into mRNA
No physical barrier (nuclear membrane) between transcription and in translation and no mRNA processing required

340
Q

Pyrimidines vs purines - structure

A 
Pyrimidines = single-ring structures
Purine = double ring structures
341
Q

Which carbon of a sugar is the nitrogenous base attached to

A

1’ carbon

342
Q

Which carbon of a sugar is the phosphate group attached to

A

5’ sugar

343
Q

Why is complementary base pairing important for replication of DNA

A

Ensures the 2 daughter DNA molecules are exact copies of the parental DNA molecule

344
Q

Genetic code - problem and solution

A

There are only 4 nucleotide bases to specify 20 amino acids

So, the genetic code is a triplet of nucleotides (codon):
Possible combinations = 4^3

345
Q

What is the genetic code

A

A set of rules that controls how the info is translated from the genetic material (e.g. RNA) into the amino acid sequence

346
Q

Transcription and translation - overall pathway

A

DNA strand (template) –transcription–>
mRNA –translation–>
Protein

347
Q

Genetic code: Codon table - organisation

A

Highly organised

348
Q

Genetic code - redundancy

A

Code is redundant - most amino acids are specified by more than one triplet
So, there is >1 RNA for some amino acids

349
Q

Genetic code - wobble

A

Some tRNA molecules require accurate base-pairing only at the first 2 positions of the codon and can tolerate a mis-match at the third

350
Q

Genetic code: Start codon

A

AUG

Initiates translation but also codes for methionine

351
Q

Genetic code: Stop codons

A

UAA, UAG, UGA

Terminate translation - don’t code for amino acids, instead bind to a release factor

352
Q

What happens if a start codon is in the middle of a polypeptide sequence

A

It will just be translated into Met

353
Q

What does ‘wild type’ mean

A

Normal

354
Q

Genetic code - universal

A

Genetic code is shared by most organisms

355
Q

Genetic code: Mutations

A

Changes in one or a few nucleotides in a sequence can affect protein structure and function (small scale mutations)
Can be a permanent, inheritable alteration in the DNA sequence
May arise spontaneously as a result of low frequency random errors, or induced by external agents which damage DNA

356
Q

Point mutations

A

Change in a single base pair

357
Q

Types of point mutations

A

Nucleotide pair substitutions

Nucleotide pair insertions or deletions

358
Q

Point mutations: Nucleotide pair substitutions

A

Can result in:

  • silent; no effect on amino acid sequence
  • missense; an amino acid is changed
  • nonsense; creation of premature termination codon - serious
359
Q

Point mutations: Nucleotide pair insertions or deletions

A

Cause a frameshift, resulting in a missense or nonsense outcome

360
Q

What can point mutations arise from

A

Mistakes in replication by DNA polymerase
Mutagenic agents, e.g. UV light
Spontaneous chemical reactions in cells

361
Q

Missense - severity

A

If occurs later in polypeptide, may not significantly influence how the polypeptide folds and protein may still be able to function
But if happens earlier in polypeptide, more likely to alter how the polypeptide folds and change its 3D structure and impair function
But new amino acid may be similar to previous and not have a significant effect on structure/function

362
Q

Nonsense - severity

A

If occurs toward end of polypeptide, may not have significant effect
If occurs further in, the polypeptide will be incomplete - likely won’t function

363
Q

Frameshift

A

All subsequent codons will also be shifted

364
Q

Point mutation: 3 nucleotide pair deletion

A

All deleted from same codon

No frameshift, but one amino acid missing

365
Q

What can DNA be damaged by

A

Incorrectly paired or altered nucleotides

Chemical changes of DNA bases, e.g. UV damage can cause a covalent bond to form between 2 neighbouring thymine bases

366
Q

Repairing damaged DNA by excision repair - steps

A
  1. A thymine dimer distorts the DNA molecule
  2. A nuclease enzyme cuts the damaged DNA strand at 2 points and the damaged section is removed
  3. Repair synthesis by a DNA polymerase fills in the missing nucleotides
  4. DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete
367
Q

Gene expression: Prokaryotes

A

Prokaryote cell gene expression involves response to changes in available nutrients

368
Q

Gene expression: Eukaryotes

A

Eukaryote cell differentiation is regulated by gene expression
i.e. the genes expressed determine the type of cell it will become

369
Q

Gene expression - totipotent

A

Many specialised cells don’t lose genetic info

The nucleus is totipotent - theoretically able to program the development of a new embryo

370
Q

Cloning a mammal: The mammary cell is ________

A

Totipotent

371
Q

Cloning a mammal: What does it show

A

Nucleus from differentiated mammary cell contains the genetic info required to generate clone of donor animal

372
Q

Cloning a mammal: Dolly - steps

A
  1. Mammary cell donor –> cultured mammary cells
  2. Egg cell donor –> nucleus removed
  3. Cells fused
  4. Grown in culture
  5. Implanted in uterus of a third sheep
  6. Embryonic development - genetically identical to mammary cell donor
373
Q

Cloning a mammal: Dolly - length of chromosome

A

Slightly shorter than original mammary cell

374
Q

How much does of their genes does a cell express

A

Do not express all their genes
Generally only expresses a small % of the possible proteins it can make e.g. a human cell expresses ~20% of its genes at a given time

375
Q

Gene expression - turning on and off

A

Cells continually turn genes on and off in response to signals from their external and internal environments

376
Q

Gene expression: Prokaryotes - nutrients

A

Especially sensitive to nutrients in their environment
When they detect a particular nutrient they can metabolise, they make protein enzymes needed to process the nutrient
When that nutrient is no longer there, they stop making those enzymes

377
Q

Regulation of eukaryotic gene expression: Chromatin modification

A

Genes in tightly packed (condensed) chromatin are usually not transcribed because RNA polymerase can’t access the DNA

378
Q

Highly vs less condensed DNA

A

Highly condensed DNA = heterochromatin

Less condensed DNA = euchromatin

379
Q

Regulation of eukaryotic gene expression: Chromatin modification - acetylation

A

Acetylation of histone tails loosen the chromatin structure –> DNA accessible by RNA for transcription

380
Q

Regulation of eukaryotic gene expression: Chromatin modification - methylation

A

Where methyl groups are added to histone tails –> DNA no longer available to RNA polymerase –> condensation of chromatin and reduced transcription

381
Q

Regulation of eukaryotic gene expression: Epigenetic inheritance

A

The inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself
e.g. the genes in condensed regions of DNA which were methylated will be silenced before and after cell division because remain methylated

382
Q

Regulation of eukaryotic gene expression: Initiation of transcription

A

TFs can bind to specific regions of DNA
Some bind to promoter region and facilitate RNA polymerase binding (transcription initiation complex) - facilitates transcritpion
Some bind to regulatory sequences - can either stimulate or repress transcription

383
Q

What are transcription factors (TF)

A

Proteins that can initiate and regulate transcription in eukaryotic cells

384
Q

What is the most frequent way gene expression is controlled

A

Regulating transcription

385
Q

Transcription initiation complex

A

Where there is RNA polymerase and transcription factors binding, the entire structure is referred to as the transcription initiation complex

386
Q

Regulation of eukaryotic gene expression: RNA processing

A

Alternative RNA splicing - diff mRNA molecules are produced from the same pre-mRNA

387
Q

Regulation of eukaryotic gene expression: Translation

A

Can be controlled by regulating factors which mediate initiation of translation
Initiation of translation for some mRNA can be locked by regulatory proteins which bind to UTRs towards the ends of mRNA –> stops mRNA from binding to ribosome –> translation can’t start

388
Q

Haemogloblin mRNA - stability

A

Highly stable

389
Q

What does lifespan of mRNA in cytoplasm determine

A

How long it can be used for protein synthesis

390
Q

How long does it take for prokaryotic mRNA to degrade

A

Typically within minutes

391
Q

How long does it take for eukaryotic mRNA to degrade

A

Can last from hours to weeks

392
Q

Regulation of eukaryotic gene expression: Protein processing and degradation

A

Protein modification which is required to produce functional proteins is regulated
Protein trafficking to the correct organelle is regulated
Length of time a protein functions regulated by selective degradation

393
Q

Examples of protein modification

A

Glycosylation
Phosphorylation

If a protein is deemed not required, it these processes will stop –> protein incomplete –> can’t conduct final function

394
Q

Regulation of eukaryotic gene expression: Protein processing and degradation - selective degradation

A

If a protein is no longer required, it can be tagged with a ubiquitin protein which marks it for degradation by proteasomes

395
Q

How can non-coding RNAs control gene expression

A

By influencing:

  • chromatin packing
  • translation
  • mRNA degradation
396
Q

Examples of non-coding mRNAs

A

Introns
Micro RNAs
Small interfering RNA molecules

397
Q

Control of gene expression in prokaryotes: Metabolic control

A

Occurs at 2 levels:

  1. Adjust catalytic activities of enzymes already made (rapid response)
  2. Adjust production of enzyme molecules by regulating expression of genes encoding enzymes –> none of the enzymes are made (long-term response)
398
Q

What is the most frequent way prokaryotes regulate metabolic processes

A

Transcriptional control

399
Q

Hydrolysis of lactose

A

β-galactosidase catalyses the hydrolysis of lactose (disaccharide) into glucose and galactose (monosaccharides)

400
Q

β-galactosidase - low lactose conc

A

When lactose is absent, only a few molecules of β-galactosidase are present

401
Q

β-galactosidase - high lactose conc

A

When lactose becomes readily available, the no of β-galactosidase molecules can increase 1000x within 15 mins

402
Q

How can numbers of β-galactosidase increase rapidly

A

Bacterial mRNA only lasts a few mins, so bacteria can rapidly change pattern of protein synthesis in response to a change in food source

403
Q

Growth curve of bacteria grown on lactose alone

A

Lag phase: bacteria start to transcribe β-galactosidase mRNA –> translated into β-galactosidase protein
Exponential bacterial growth: bacteria metabolise lactose and grow
Plateaus

404
Q

Lac operon - structural genes

A

lacZ gene for β-galactosidase
lacY gene for permease
lacA gene for transacetylase

All of which are involved in processing lactose

405
Q

Lac operon - what is an operon

A

A group of genes coding for proteins with related functions

Expression of these genes is under the control of a single promoter and operator

406
Q

lac mRNA - negative regulation

A

A repressor protein binds to the operator to prevent the gene being expressed

407
Q

lac mRNA - positive regulation

A

A transcription factor or activator bind to promoter and enable RNA polymerase to initiate transcription

408
Q

lac mRNA - negative regulation - when lactose is absent

A 
Regulatory gene (lacI) codes for lac repressor protein
lac repressor protein binds to operator and obstructs promoter --> RNA polymerase can't get access
Transcription of lac operon genes can't occur
409
Q

Where is lacI located

A

Next to the operon

410
Q

lac mRNA - negative regulation - when lactose is present

A

Allolactose (inducer) binds to lac repressor protein, inducing it to change shape (allosteric protein) so it can no longer bind to the operator –> RNA polymerase can bind to promoter
Transcription and translation of lac operon genes can occur

411
Q

What happens when bacteria are grown on glucose and lactose (when both are present)

A

E. coli preferentially uses glucose first
When glucose is low and plateaus, E.coli will then generate enzymes for lactose breakdown and use lactose as an energy source

412
Q

How is information that glucose is low conveyed to the lac operon

A

By +ve control of lac operon by activator protein CRP
Low glucose –> cAMP accumulates –> binds to and activates cAMP receptor protein (CRP - allosteric)
Active CRP binds to promoter and facilitates binding of RNA polymerase to promoter –> transcription of lac operon genes

413
Q

What happens when glucose becomes present again (initially just lactose)

A

Level of cAMP falls so it can no longer activate CRP
CRP detaches from lac operon
RNA polymerase binds less efficiently to promoter
Transcription proceeds at low level, even if lactose is present

414
Q

Lac operon: Mutations in structural genes (Z, Y, A)

A

May result in production of a non-functional protein

415
Q

Lac operon: Mutations in repressor gene (lacI), operator, or promoter regions

A

May:
Abolish transcription: e.g. mutation in promoter may destroy RNA polymerase binding site
Permanently turn on transcription: e.g. mutations in lacI may inactivate the repressor (constitutive mutants)

416
Q

If you abolish transcription…

A

The enzymes will never be made

417
Q

What must occur if a new polypeptide is going to be secreted from a eukaryotic cell

A

Its signal peptide must target it to the ER

418
Q

Where would you expect to find tight junctions

A

Between the cells lining an animal’s stomach

419
Q

Eukaryotic cilia and flagella bend because of…

A

A motor protein called dynein

420
Q

A glycosidic linkage corresponds to what protein

A

Peptide bond

421
Q

If the operator is moved to the end of the lac operon, past all the genes in the operon, what would likely occur?

A

Genes of lac operon can be transcribed continuously

422
Q

Why is ATP an important molecule for cellular metabolic processes?

A

It provides energy coupling between exergonic and endergonic reactions

423
Q

A student researcher removes the 5’ cap and poly-A tail from an mRNA molecule and inserts this modified mRNA molecule into the cytosol of a eukaryotic cell. What would you expect the student to find?

A

The mRNA is digested by enzymes in the cytosol

424
Q

What is the most current description of a gene

A

A DNA sequence that is expressed to form a functional product; either RNA or a polypeptide

425
Q

There is a mutation in the lacI regulatory gene that generates a super-repressor protein, which represses the lac operon permanently. What describes this mutant super-repressor protein?

A

It cannot bind to the lactose inducer

BIOSCI 101 (4 decks)

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