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Biological Sciences > Lecture 5 Part 1. Biochemistry > Flashcards

Lecture 5 Part 1. Biochemistry Flashcards

1
Q

What are the functions of proteins

A
  • Enzyme Catalysts ie endonuclease = speed up reactions - pull 2 molecules together, put them in the right orientation that will make reaction more likely to occur
  • Transport and Storage ie Heamoglobin
  • Co-ordinate Movement ie cytoskeletal actin… tubulin
  • Mechanical Support ie collagen
  • Immune Protection ie Immunoglobins - tag microbes
  • Signaling and Receptors ie toll like receptors
  • Ion Channels/pores ie Integral proteins in plasma membrane
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2
Q

What does an amino acid contain - structure

A
  • A central C
  • amino group (NH2)
  • carboxyl group (COOH)
  • H atom
  • R group
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3
Q

What varies and determines type of amino acid

A

R group

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4
Q

How many standard amino acids are there

A

20

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5
Q

What does R group determine

A

Differences between amino acids and the chemical nature of it
Different electrochemical properties of amino acid

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6
Q

What are the different chemical properties of amino acids

A
  • Acidic – Glutamate/Aspartate
  • Basic - Serine, Tyrosine
  • Non-Polar – Alanine, Valine,
  • Polar
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7
Q

Proline

A
  • The R group covalently binds to the NH2+ group of the central Carbon ‘folding back’ the amino acid
  • Can function to induce kinks into alpha helices, since it is unable to adopt a normal helical conformation
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8
Q

How is proline different to other amino acids

A

Conformational rigidity

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9
Q

What does rigidity of proline help

A

Stabilize folded proteins

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10
Q

Where is proline often found

A

In very tight turns in protein structures, where the polypeptide chain must change direction

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11
Q

What is it unable to do

A

Adopt a normal helical conformation

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12
Q

What are proteins

A

Linear sequences of amino acids held together by peptide bonds

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13
Q

What forms when proteins join

A

Dipeptide

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14
Q

What does either end of dipeptide have that allows further bonding

A

Has an amino and carboxyl group free

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15
Q

What would further peptide bonding create

A

oligopeptide (<25 aa) or polypeptide (>25aa).

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16
Q

What happens during a condensation reaction

A

When 2 molecules join together with the formation of a new chemical bond, forming a water molecule

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17
Q

What is formed during condensation reaction

A

H20

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18
Q

How do R groups stick out in sequence

A

Do not stick out from the same backbone in the same orientation as each other.
R groups opposite side on 2 amino acids - one r group sticks out on one side, other R group sticks out other side

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19
Q

What determines protein shape

A

Amino acid sequence

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20
Q

Where are polar amino acids located

A

Outside of the protein in an aqueous environment

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21
Q

Where are non polar amino acids located

A

Inside

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22
Q

What does polypeptide chain fold into

A

A shape which is stabilized by several non-covalent interactions.

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23
Q

What are the 4 types of bonds and what do they do

A
  • Ionic bond
  • Hydrogen bond
  • van der Waals interactions
  • Covalent bonds
    Stabilise new 3D structure
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24
Q

What bond doesnt form between R groups at different points along protein sequence

A

Covalent bonds

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25
Q

What stabilises new 3D structure

A

Non - covalent interactions

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26
Q

Disulphide bond

A
  • Stabilising cross link between Sulphur and Sulphur (covalent bond)
  • S-S bond between cysteine residues
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27
Q

What is confirmation

A

Folding pattern of a protein

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28
Q

What can polypeptide chains fold into

A

Regular structure ( 3D) - stabilise itself with interactions

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29
Q

What two patters predominate in proteins and why

A
  • α-helix
  • β-‘pleated’ sheet
  • Because they efficiently fill space
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30
Q

What are the secondary protein structures

A
  • α-helix

- β-‘pleated’ sheet

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31
Q

α-helix

A
  • Rod like structure or coil)
    single polypeptide chain
  • Tightly coiled backbone forms the inner part of the rod and the R groups extend outward
  • Stabilised by hydrogen bonds between NH to CO groups of the main chain.
  • Roughly 4 amino acids to every 1 turn of chain
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32
Q

β-‘pleated’ sheet

A
  • Extended polypeptide chains that fold back over each other - more H bonding
  • Formed by linking two or more β-strands - adjacent - parallel or anti parallel
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33
Q

What are the levels of organisation of protein structure

A
  • Primary
  • Secondary
  • Tertiary
  • Quaternary
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34
Q

What is primary structure

A

Sequence of amino acids

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35
Q

What is secondary structure

A

α helix and β sheet formation with folding as a result of hydrogen bonding between peptides

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36
Q

What is tertiary structure

A

3D conformation – folding of the polypeptide chain – disulphide bonds form between the R groups of the α helices and β sheets

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37
Q

What is Quaternary structure

A

Complex of several polypeptide chains

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38
Q

Example of Quaternary structure

A

Haemoglobin

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39
Q

What are carbohydrates

A
  • Compounds containing C , H , O
  • Carbo = carbon
    hydrate = water, which contains hydrogen and oxygen
  • Essentially hydrated Carbon (C + H2O)
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40
Q

What elements do carbs contain

A

C , H , O

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41
Q

What is role of carbohydrates

A

Make up most organic matter on Earth:

  • Polysaccharides serve as compact energy storage molecules (glycogen or starch) - breaks down = glucose = energy Or structural elements in plant cell walls (cellulose) - humans cant use - cant break down in body
  • Monomeric sugars act as intermediates in metabolism (glucose and other molecules in the glycolytic pathway
  • Phosphorylated sugars form the structural framework of DNA and RNA (ribose)
  • Glycoproteins and glycolipids are found on cell surfaces – cell recognition - glycocalyx
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42
Q

What are monosaccharides

A

Composed of one simple sugar like glucose and fructose

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43
Q

What are disaccharides

A

Composed of two monosaccharides

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44
Q

What are oligosacchharides

A

Composed of a small number of monosaccharides

few sugars < 15

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45
Q

What are polysaccharides

A

Polymeric carbohydrate molecule composed of long chains of monosaccharides

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46
Q

Monosaccharides

A
  • The building bocks of carbohydrates:
  • Simplest form of carbohydrates
  • Usually colourless, water-soluble, crystalline solids
  • General formula (CH20)n n ≥ 3
  • Contain 3-6 carbon atoms - form backbone of molecule
    C3= trioses
    C5= pentoses
    C6= hexoses
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47
Q

What do monosaccharides contain

A

An aldehyde group (called aldose)

Or ketone group (called ketose)

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48
Q

Ring structure formation:

A

In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of same molecule, thereby closing molecule into a ring

49
Q

How are sugar derivatives formed

A

The hydroxyl group (OH) can be replaced with other groups

50
Q

Examples of sugar derivatives

A
  • Phosphorylated sugars (i.e glucose-6-phosphate)
    are used in glycolysis.
  • Sugars can also form a covalent bonds with nitrogenous bases - change amount of energy released
  • The hydroxyl group could be replaced by an amine group (NH2). These are common components of glycoproteins.
51
Q

What are disaccharides

A

2 monosaccharides join via a condensation reaction

52
Q

What’s the covalent bond in a disaccharide

A

Glycosidic bond

53
Q

O - glycosidic bond

A

C1 binds to Oxygen

54
Q

N - glycosidic bond

A

C1 binds to Nitrogen

55
Q

S - glycosidic bond

A

C1 binds to Sulphur

56
Q

C - glycosidic bond

A

C1 binds to Carbon

57
Q

What are the common saccharides

A

Sucrose - glucose and fructose
Lactose - glucose and galactose
Maltose - glucose and glucsoe

58
Q

What are oligosaccharides

A

Polymer containing a small number of component monosaccharides (<15)

59
Q

Functions of oligosaccharides

A

commonly found on the plasma membrane of animal cells where they play a role in cell-cell recognition - glycocalyx

60
Q

Is branching possible for oligosaccharides

A

Yes

61
Q

What can you make with oligosaccharides

A

Either make O-glycosidic bonds or N-glycosodic bounds with amino acid R groups or to lipids to make glycoporteins or glycolipids

62
Q

Which oligosaccharides may be linear or branched chains

A

covalently linked to proteins or to membrane lipids

branched - reacting through hydroxyl groups

63
Q

What do oligosaccharies of glycoproteins and glycolipids often include

A

Modified sugars

e.g. acetlyglucosamine

64
Q

What monosaccharides do oligosaccharies of glycoproteins and glycolipids often include

A

glucose
galactose
mannose
fructose

65
Q

What happens in O glycosidic linked oligosaccharide

A

link to a protein via a glycosidic bond between a sugar residue and an hydroxyl group (OH) on serine or threonine amino acids

66
Q

What happens in N glycosidic linked oligosaccharide

A

complex and branched

67
Q

What do N - linked glycoproteins all contain

A

Common core of 3 mannose sugars attached to protein - make these branched

68
Q

Whats attached to common core of N linked glycoproteins

A

Variety of sugars

69
Q

O - linked glycoproteins

A

Either single chain or branched

70
Q

What’s glycocalyx

A

Outer layer – bound polysaccharides on the cell surface and superficial layer of unbound proteoglycans and glycoproteins

71
Q

What are the functions of glycocalyx

A

Cell recognition
Cell adhesion
Protection
Permeability barrier

72
Q

Whats the difference between glycoproteins and proteoglycans

A
  • Proteoglycans represent a subclass of glycoproteins
  • Both composed of protein and carbohydrate
  • In a glycoprotein the complexity and length of the oligosaccharide is limited to <15 sugars
  • In a proteoglycan the structure is more complicated and much larger
  • Proteoglycans form ground substance of connective tissues
73
Q

Proteoglycans role

A
  • Proteoglycans play an important role in connective tissues (ground substance ie cartilage, vitreous), extracellular matrix - wound healing
  • Proportion of collagen and proteoglycans varies between different connective tissues
  • Proteoglycans create hydrated spaces around cells and withstand compression
  • Regulate fluid and can bind cations (Zinc, Iron, Copper) to form electrochemical gradients + wound healing
74
Q

What do proteoglycans play an important role in

A

Connective tissue

75
Q

Proteoglycan structure: glycosaminoglycans (GAGS)- what are they

A

Repeating disaccharide units
Held together by another carbon and hydrogen chain = make up ground susbtance - density of ground susbtance based on ratio of collagen fibres and hydrogen

76
Q

Structure of GAGS

A

Extend perpendicular from the core protein to form a proteoglycan – bottlebrush structure
GAGS sticking on outside, protein chain in middle

77
Q

Examples of proteoglycans

A

Hyaluronic acid – vitreous
Dermatan sulphate- skin
Chondroitin sulphate- cartilage
Keratan sulphate –basement membrane/cornea stroma

78
Q

What are polysaccharides

A

Polymeric carbohydrate molecule composed of long chains of monosaccharide units

79
Q

What are polysaccharides bound together by

A

Glycosidic linkages

80
Q

How do polysaccharides break down into constituent monosaccharides or oligosaccharides

A

Hydrolysis

81
Q

Structure of polysaccharides

A

Linear or highly branched

82
Q

Types of polysaccharides

A

Storage or Structural

83
Q

What are lipids

A

Naturally occurring molecules

84
Q

Role of lipids

A
  • Components of membranes (phospholipids and sphingolipids, cholesterol)
  • Several proteins are covalently modified by fatty acids
  • Act as energy stores (triacylglycerols) and fuel molecules
  • Fatty acid derivatives serve as hormones (i.e steroids) and intracellular second messangers
85
Q

What are the types of lipids

A 
Fatty acids
Triglycerides
Phospholipids
Steroids
Glycolipids
86
Q

Structure of fatty acid

A

Carboxylic acids with long hydrocarbon chain ‘tails’

Carboxyl group attached to a long hydrocarbon chain and a methyl group: CH3(CH)nCOOH

87
Q

Saturated

A

No double bonds between carbons in hydrocarbon tail

Straight

88
Q

Unsaturated

A

One or more double bonds = shape into fatty acids

Bends or kinks in tail

89
Q

What are triglycerides

A

3 fatty acids joined together through ester linkage to Glycerol (carbohydrate).

90
Q

Role of triglycerides

A

Energy store

91
Q

Where are fatty acids stored

A

Adipocytes as triglyceride (lipid inclusions in cells)

92
Q

How is fatty acid released from triglyceride

A

Its hydrolysed

93
Q

Where are adipocytes mostly found

A

In the abdominal cavity and subcutaneous tissue

94
Q

Property of adipocyte

A

Metabolically very active; stored triglyceride is constantly hydrolyzed and resynthesised

95
Q

What is a phospholipid

A

Contains 2 fatty acids bound through ester linkage to glycerol, but where the third fatty acid would bind in a triglyceride, you have a link to phosphoric acid . The phosphate is also bound to a polar head group (alcohol)

96
Q

What are phospholipids major constituents of

A

Cell membranes

97
Q

Where are steroid hormones derived from

A

Cholestrol except retinoic acid

98
Q

Role of cholestrol

A

Major component of cell membranes – imparts fluidity and maintains the integrity of the membrane

99
Q

How does cholestrol travel around in body

A

in lipoproteins

100
Q

Cholestrol in membrane

A
  • Cholesterol hydroxyl group aligns with the polar head phosphate group of the phospholipid
  • Steroid ring interacts with the hydrocarbon chain closest to the polar head group of the phospholipid
  • Cholesterol immobilises the first few CH2 groups of the hydrocarbon chain closest to the polar head groups – less deformable bilayer
  • Decreases lipid fluidity by preventing motion of hydrocarbon chains
  • Enhances permeability-barrier properties of the bilayer
101
Q

What are glycolipids

A
  • Complex lipid that contains a sugar.
  • They are structural lipids
  • Sugar and fatty acid - between phospholipids
102
Q

What is the sugar in glycolipids

A

Glucose or galactose

103
Q

Structure of glycolipids

A

Composed of a hydrophobic region
(the two long hydrocarbon chains) and polar region, which in this lipid consists of one or more sugar residues
(No phosphate).

104
Q

What are Lipoproteins

A

Core of triglycerides and/or cholesterol and a surface monolayer of phospholipid, unesterified cholesterol and proteins

105
Q

Role of lipoproteins

A

Transport of lipids and cholesterol in the blood

106
Q

How do lipoproteins differ

A

In the ratio of protein to lipids - classified according to their density:

107
Q

HDL - High density lipoprotein

A

Highest in density due to high protein:lipid ratio, carry 20% plasma cholesterol

108
Q

LDL - Low density lipoprotein

A

Highest in cholesterol as % of weight, carry 60% plasma cholesterol

109
Q

VLDL - Very Low density lipoprotein

A

Carry triglycerides

110
Q

What is amino acid

A

Monomer of protein

111
Q

How do amino acids have different physical properties

A

Affects physical space of it and how other amino acids can fit around it e.g size

112
Q

What is a kink

A

point in the helix where there is a sharp change in the direction of the helix axis
A sharp twist or curve in something that is otherwise straight

113
Q

What is peptide bond

A

Covalent bond between C in COOH and N in NH2

114
Q

Is amino acid chain functional on its own and why

A

No

It hasn’t developed specialised regions to do specific functions

115
Q

How is R group hydrophobic

A

Doesn’t like aqueous environment - polypeptide chain in water in cells - hide, rest of chain twist around it = hydrophobic region hidden inside protein

116
Q

How is each R group specific

A

Specific interaction with another R group = specific shape and function

117
Q

What environment does ring structure form

A

Aqueous

118
Q

What happens in N - glycosidic bond

A

Sugar reacting with nitrogenous ring = hydroxyl ring displaced

119
Q

What is proteoglycan

A

Type of protein carb mix - secreted into extracellular place = form part of ground susbtance of connective tissues

Biological Sciences (27 decks)

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