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BIOSCI 107 > Section 3: Special Topics > Flashcards

Section 3: Special Topics Flashcards

(84 cards)

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1
Q

Second law of thermodynamics

A

Entropy will increase over time

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2
Q

Early human dev. - three main techniques

A

Ability to dissociate multi-cellular organisms into single cells
Ability to barcode those cells
Sequence every cell - make a map of where those cells are being derived from

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3
Q

What happens in embryogenesis

A

Patterning
Major axis laid down
3 germ layers form
Rudiments of major organs

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4
Q

Embryogenesis - patterning

A

Development process where cells acquire diff identities depending on their relative positions in their embryos
Pattern laid down on a small scale, typically <1cm
Lay down the 3 main germ layers to allow further differentiation to take place

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5
Q

Embryogenesis - major axis

A

Anterior - head
Posterior - tail
Dorsal - back
Ventral - tummy

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6
Q

Embryogenesis - 3 germ layers

A

Broad brushstrokes of development
Further differentiation takes place within those germ layers

Ectodermal layer
Mesodermal layer
Endodermal layer

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7
Q

Fate map

A

Tells you what a cell is likely to become if development continues normally

Ectodermal layer (outside, blue)
Mesodermal layer (between, red)
Endodermal layer (inside, yellow)
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8
Q

Sperm vs egg size

A

Sperm quite small in size compared to egg

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9
Q

Sperm - major components

A

Genetic material
Tail to help it swim towards egg
Sac of enzymes (acrosome) on head - helps the sperm burrow through the layers surrounding the egg (corona radiata)

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10
Q

When is meiosis completed

A

Post-fertilisation, where 2 nuclei become pronuclei

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11
Q

Placenta is a combination of…

A

The maternal tissues and tissues from the embryo itself

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12
Q

Types of proteins

A

Digestive enzyme/catalytic - break down nutrients in food into small pieces that can be readily absorbed
Transport - carry substances throughout the body in blood or lymph
Structural - build diff structures, e.g. cytoskeleton
Hormone signalling - co-ordinate activity of diff body systems
Immunological - protect body from foreign pathogens
Contractile - muscle contraction
Storage - provide food for early development of embryo
Toxins - used by pathogens or other organisms to cause disease

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13
Q

Peptides

A 
Short polypeptides (~less than 50 amino acids)
Very short peptides can be referred to as dipeptides, tripeptides or tetrapeptides
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14
Q

Residues

A

Individual amino acids in a polypeptide/protein

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15
Q

Forms of amino acids

A

Un-ionised/deionised form

Zwitterionic (doubly ionised) form - dominant form, at physiological pH ~7.4, +ve and -ve charge on either side)

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16
Q

Peptide (amide) bond formation

A

Condensation / dehydration synthesis reaction

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17
Q

Peptide bond properties

A

Bonds are rigid and can’t rotate due to resonance
O-C-N-H of peptide bonds are essentially co-planar
Rotation can occur at the single bonds between the α-carbon and its neighbouring atoms
R amino acid side chains can be cis (same side) or trans (one up one down) - typically trans as cis is less stable due to steric repulsion

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18
Q

N and C terminus

A

N (amino) terminus
C (carboxyl) terminus
Proteins always drawn N to C i.e. the direction they come off the ribosome

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19
Q

Protein structures - complex

A

To facilitate all varied functions proteins provide, they can adopt complex structures

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20
Q

Shape and function of proteins

A

Shape of a protein is critical to its function

Shape is driven by chemical properties and sequences of amino acids in the protein

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21
Q

Binding of substrates to an active site can cause…

A

Conformation changes, which provide a function or strengthen the interaction

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22
Q

Proteins - primary structure

A

The unique sequence of amino acids of a protein
Entirely driven by DNA sequence of gene encoding protein - can deduce the primary structure of a protein by the DNA sequence of a gene

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23
Q

Proteins - secondary structure

A

Localised folding of the polypeptide driven by H bonding interactions within the polypeptide backbone
Two common types: β (pleated) sheet, α helix
Diff amino acids have a tendency to favour structures
Can fairly accurately predict regions of secondary structure in a protein by the sequence

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24
Q

β sheets

A

Can be parallel or anti-parallel
Driven by H bonding between a backbone amine (N-H) group on one strand and a backbone carbonyl (C=O) group on other strand

Large aromatic residues and β-branched amino acids are favoured in β strands

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25
α helices
Right-handed helix Normally each turn is 3.6 amino acids with a pitch of 5.4Å Driven by H bonding between a backbone amine or backbone carbonyl group 3 or 4 residues earlier Tightly packed with almost no free space within the helix Side chains protrude from helix
26
Helices - amino acid examples
Methionine, alanine, leucine, glutamate and lysine like to form helices Proline and glycine don't Proline may create unique conformations in polypeptide, and often referred to as a helix breaker as it's always at the end of a helix
27
Proteins - tertiary structure
Where secondary structures fold in on themselves The 3D shape of a protein - primarily driven by the chemistry of side chains and interactions between them Range of non-covalent interactions - H bonding, ionic bonding, d-d interactions, Van der Walls forces Ionic: opposite charged R groups attract and like charges can repel
28
Tertiary structures - hydrophobic interactions
R groups of non-polar amino acids orient themselves towards the center of the polypeptide and cluster to avoid water In membrane spanning proteins, hydrophobic R groups may be outside interacting with lipid tails
29
Tertiary structures - disulphide bridge
Amino acid cysteine forms a covalent bond with another cysteine through its R group --> disulfide bond Thiol (S-H) groups are oxidised, removing the H and forming a covalent linkage between the 2 sulfur atoms
30
Tertiary structures - H bonds
Polar 'R' groups on the amino acids form bonds with other polar R groups
31
Tertiary structures - hydrophilic interactions
R groups of amino acids orient themselves outward to interact with water and maintain solubility of protein
32
Tertiary structures - ionic bonds
Positively charged R groups bond together
33
Relative strength of bonds
Disulfide > Ionic > Hydrogen > Van der Waals
34
Tertiary structure - co-factors
``` Some proteins (particularly enzymes) can co-ordinate a co-factor or 'prosthetic groups' within the protein using R groups May be essential for function/structure of protein Metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules (heme) or vitamins ```
35
Proteins - quaternary structure
Multiple folded protein subunits Driven by ionic interactions, H bonding and hydrophobic interactions Often dynamic - may have one protein coming on and off another protein or moving around Homooligomers or heterooligomers Not all proteins form quaternary structures
36
Types of proteins
Globular Fibrous Membrane proteins
37
Globular proteins
``` Typically soluble in water Often enzymes, transport, immune Often irregular sequence and secondary structure Moderate or no quaternary structure Lower stability ```
38
Fibrous proteins
``` Typically insoluble in water Often structural Often repetitive primary and secondary structure High level of quaternary structure Highly stable Keratin, actin, collagen, silk ```
39
Membrane proteins
Transverse through a lipid bilayer (membrane) Transport, receptors, signalling, adhesion Transmembrane region - single α-helix or a α-helical bundle Generally high degree of non-polar (hydrophobic) amino acids, which face membrane Polar (hydrophilic) side chains face inwards Quite abundant
40
Levinthal's paradox
Very large number of degrees of freedom in an unfolded polypeptide chain 100 amino acid proteins will have 3^198 diff conformations Most protein correctly fold in the ms - μs time scale
41
Protein folding
Need help to fold correctly - correct environment: solute, salt conc, pH, temp, macromolecular crowding etc Temporal - co-translational folding as the polypeptide is coming off the ribosome i.e. N folds before C terminus Chaperones Enzymes involved in disulfide bond formation
42
Methods for structure determination
X-ray crystallography NMR Cryo-electron microscopy
43
Resolution
The distance corresponding to the smallest observable feature - if two objects are closer than this distance, they appear as one combined blob rather than two separate objects Units: 1 Å (angstrom) = 0.1nm
44
Protein structure representations
Backbone model Ribbon model Wire model Space-filling model
45
Homooligomers
A protein where there are two or more subunits of the same protein
46
Heterooligomers
A protein where there are multiple polypeptides coming together to form one functional group
47
Abbe's diffraction limit
If we have a perfect microscope, we can still only resolve objects sized half the wavelength of the imaging light - can't see viruses or proteins
48
Chaperones
Dedicated proteins which bind to folding proteins, e.g. binding to a patch that is particularly prone to misfolding, or encircling the whole protein to create a localised environment that favours a particular type of folding
49
Skin - total body surface area and body weight
Average 2 m^2 | 7 - 16% of total body weight
50
Skin - thinnest and thickest
Thinnest: eyelids - 0.5mm | Thickest - palms and soles of feet - 4mm or more
51
Human skin functions
Protection/barrier, e.g. from pathogens and UV Blood reservoir - can hold 8-10% of total blood volume Thermoregulation - sweat glands and blood vessels Sensation - touch/pressure, pain, temp Vitamin D synthesis - Vit D precursor require modification by UV before active form can be made in liver
52
Thermoregulation - blood vessels
Vessel constriction in dermis reduces blood flow --> reduced heat loss Vasodilation in dermis increases blood flow --> increased heat loss
53
Epidermis
Provides a barrier and continued renewal No structural strength Mainly consists of layers of keratinocytes
54
Epidermis - layers of thin and thick skin
Thin skin has 4 layers of keratinocytes | Thick skin has 5 layers; 5th layer is stratum lucidum
55
Epidermis - vasculature
No vasculature - all nutrient supply and waste removal occur by diffusion to vascular system of dermis
56
Stratification
Crucial for barrier function and continued renewal of epidermis ``` Stratum basale Stratum spinosum Stratum granulosum Stratum lucidum Stratum corneum ```
57
Stratification process
Proliferating keratinocytes on bottom of epidermis push cells up and away from dermis Undergo programmed cell death Complete epidermal turnover approx once a month
58
Basement membrane
Interface between dermis and epidermis | Important for epidermal attachment to dermis
59
Basement membrane contains...
Collagen IV Perlecan Nidogen Laminin 332
60
Mutation in basement membrane proteins can result in...
Epidermolysis Bullosa (epidermis easily detached by shear forces)
61
Rete ridges
AKA Dermal papillae Contour provides resistance to shear forces Wave-like pattern strengthens attachment between epidermis and dermis
62
Pigmentation - Melanocytes
Reside at epidermal side of BM - spaced out as their dendrites allow single melanocytes to contact and transfer melanosomes to an average of 36 diff keratinocytes Make melanosomes which contain melanin
63
Pigmentation - Melanin
``` Pigment that gives skin its colour Pheomelanin - red Eumelanin - brown/black Protects from UV Nuclear cap protects keratinocyte DNA ```
64
Langerhan's cells
Immune cells Surveil the epidermis for foreign organisms - if barrier if broken, Langerhan cells move into dermis and go find help from immune system to destroy bacteria in epidermis
65
Dermis
Dense matrix made up of collagen and elastin fibres Strong and supple - provides structural strength Thickness varies - thickest on soles and palms Very stable, cellular turnover minimal
66
Dermis - fibroblasts
Produce collagen and elastin Collagens - strength Elastin - elasticity
67
Dermis layers
Papillary dermis - high cell density, loose CT | Reticular dermis - low cell density, dense CT
68
Dermis - vasculature
Supply nutrients and remove waste for both dermis and epidermis Laminin 1+2 lines vessels of vascular system in dermis Alpha SMA - contractile protein
69
Classifications of wound types
Superficial Partial thickness Full thickness
70
Superficial wounds
Damage to epidermis only
71
Superficial wound healing
Healing occurs by migration of keratinocyte from wound edges and dermal appendages (sweat glands, hair follicles, sebaceous glands) Once all keratinocytes are in contact on all sides, stratification can occur to reform epidermis
72
Partial thickness wounds
All epidermis and some of dermis is destroyed
73
Partial thickness wound healing (phases)
Inflammatory phase - immune cells migrate into clot and clean up the wound/pathogens Migratory phase - keratinocytes migrate from wound edge and appendages, and fibroblasts migrate into the clot to make collagen fibres Proliferative phase - keratinocytes proliferate Maturation phase - epidermal stratification, scab falls off
74
Full thickness wounds
All of epidermis and dermis is destroyed Hypodermis can be destroyed too, exposing bone and muscle Wound repair is difficult since all reservoirs of epidermal stem cells have been destroyed Keratinocytes have to migrate from wound edges Heals as scar tissue Intervention required to improve patient outcomes
75
Full thickness wound treatment
Split thickness skin graft: Removes all of epidermis, part of dermis Donor site - patient's own undamaged skin so it doesn't get rejected Covers wound Donor site becomes a partial thickness wound and heals in 10-14 days
76
Burn wound treatment - engineered skin
Reduces time to complete wound coverage Start with a small sample of undamaged patient skin Isolate and expand skin cells in laboratory Grow enough skin to cover all wounds Digest sample of patient skin Isolate and grow fibroblasts and keratinocytes Grow large sheets of autologous, full thickness skin Permanent wound coverage solution
77
Engineered skin limitations
``` No pigmentation No hair follicles No sweat glands No sebaceous glands Still a long way to go before being able to grow fully functional skin in laboratory ```
78
Hypodermis generally in contact with...
Muscle and bone
79
Keratinocytes produce...
Produce keratin
80
Transit amplifying keratinocyte - division
Can divide rapidly to make layers of epidermis above stratum basale Only capable of a limited number of cell divisions before they die
81
Primitive endoderm and ectoderm tissues
Endoderm: hypoblast Ectoderm: epiblast
82
Purpose of extra-embryonic structures
Transport of nutrients and waste to and from embryo
83
Zygote created by process of...
Syngamy
84
Stomoderm gives rise to the...
Oral cavity

BIOSCI 107 (7 decks)

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