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biochemistry Flashcards

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1
Q

what are the functions of protein?

A 
enzyme catalysts- e.g endonuclease
.transport and storage e.g.heamoglobin
.movement e.g.cytoskeleton
.mechanical support e.g.collagen
.immune protection
.signalling and receptors
.ion channels e.g. integral proteins in plasma membrane
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2
Q

what are proteins built from?

A

amino acids are the bricks that build protein.

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3
Q

what is the structure of amino acids?

A

central carbon that has 4 single covalent bonds to
.amine group -NH2
.carboxyl group- COOH
.H atom
.R group which varies and determines type of amino acid

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4
Q

how many amino acids are there?

A

there are 20 standard amino acids

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5
Q

what determines the difference between amino acids?

A

the R group varies between amino acids and determines the difference between these protein monomers.

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6
Q

what does the R group determine?

A 
the R group determines the chemical nature of amino acids and their physical properties 
e.g.- the chemical nature
.acidic- glutamate
.basic- serine, tyrosine
.non-polar- alanine, valine, leucine
.polar- lysine, histidine, arginine
physical nature
-size
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7
Q

what is proline?

A

the R group covalently binds the carbon to the nitrgogen atom (amine group) folding back the amino acid forming a ring.

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8
Q

what is the property of proline?

A

proline has strong rigidity compared to other amino acids the rigidity of proline helps to stabilize folded proteins.

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9
Q

what is proline usually found?

A

often found in very tight turns in protein structures , where polypeptide chain must change direction.

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10
Q

what is the specialised property to proline?

A

proline can induce kinks into alpha helices due to its configuraation , since it is unable to adopt a normal helical conformation.

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11
Q

what is a peptide bond?

A

is it when the carboxyl group of one amino acid and the amine group of another amino acid covalently bind in a condensation reaction with water being formed

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12
Q

how is the protein shape dictated?

A

the protein shape will be dictated by the amino acid sequence

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13
Q

how is the polypeptide chain formed and stabilized?

A

the polypeptide chain folds into a shape (3D) which is stabilized by several non-covalent interaction.
.e.g hydrophobic so the chain would then twist inside and hide from the aqeuous environment outside .

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14
Q

what is the structure of amino acid in an aqueous environment?

A

polar amino acids tend to be located on the outside of the protein in an aqueous environment with non-polar amino acids on the inside

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15
Q

what are the types of bonds/non-covalent interactions to be aware of?

A

.ionic bonds
.hydrogen bonds
.van der waals interactions

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16
Q

what is a disulphide bond?

A

it is a covalent bond between a sulphur and sulphur.

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17
Q

what is unique about the disulphide bond?

A

R groups only covalentally bond if its sulphur

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18
Q

what is the folding pattern of proteins known as?

A

conformation

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19
Q

what are the two patterns that are predominate in proteins?

A

α-helix
β-pleated sheet
they are predominate in proteins because they efficiently fill space

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20
Q

what is the structure of an α-helix?

A

.rod like structure tightly coiled around a single polypeptide chain
. 4 amino acids to every 1 turn
.tightly coiled backbone forms the inner part of the rod and the R group extends outwards.
.stabilised by hydrogen bonds between NH2 and COOH group of main chain

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21
Q

what is the structure of β-pleated sheet ?

A

. formed by the linking of two or more beta strands (linear polypeptide chains)
.poly peptide chain fully extended allowing for more hydrogen bonds.
.adjacent stands can run parallel or anti parallel
.also stabilised by hydrogen bonds
and proline which creates a kink and then goes back on itself

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22
Q

what is a primary protein structure?

A

sequence of amino acid

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23
Q

what is a secondary protein structure?

A

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

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24
Q

what is a tertiary protein structure?

A

3D conformation- folding of the poly peptide chain

- disulphide bonds form between the R group of α-helix and β-pleated sheet.

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25
what is a quaternary protein structure.
complex of several polypeptide chain
26
what is an example of a quaternary structure?
haemoglobin - functions to transport o2 around body 4 polypeptide chain react all interact with eachother in the haem there is iron which binds to oxygen
27
what do carbohydrates contain?
carbohydrates contain carbon hydrogen and oxygen occasionally nitrogen make most of the organic matter on earth
28
How do carbohydrates make up the most organic matter on the earth?
-polysaccharides serve as compact energy storage molecules e.g. glycogen or starch Or structural elements in plant cell walls (cellulose) -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
29
what is a monosaccharides?
composed of one simple sugar like glucose and fructose
30
what is a disaccharide?
composed of 2 monosaccharides
31
what is a oligosaccharides?
composed of small number of monosaccharides | less than 15 sugars.
32
what is polysaccharides?
polymeric carbohydrate molecule | -composed of long chains of monosaccharides.
33
what is the properties of monosaccharides?
colourless water-soluble .crystalline solids
34
how many carbons does a monosaccharide contain?
contains 3-6 carbons c3= trioses c5= pentoses c6 = hexoses
35
what can a monosaccharide contain?
. aldehyde group C=O at the end- aldose . ketone group C=O in the middle - ketose this means that monosaccharides can have structural isomers
36
how does a ring structure form in monosaccharides?
in aqueous solution the aldehyde or ketone tend to react with oh group of same molecule , thereby closing the molecule into a ring.
37
how do sugar derivatives arise?
the OH group can be replaced with other groups to form a range of sugar derivatives. monosaccharides can bind to other things due to OH group
38
what are some examples of sugar derivatives?
-attach Nitrogen/amine group to sugars -phosphate groups (glycolysis) bound to ribose ring sugars and nitrogenous rings also bound to them- phosphorylated sugars .OH group can be replaced by an amine group these are common components of glycoprotein
39
what is the structure of disaccharides?
.two monosaccharides join via a condensation reaction | . the covalent bond formed is called glycosidic bond
40
what are the glycosidic bonds formed?
C1 binds to oxygen = O-glycosidic C1 binds to nitrogen= N-glycosidic C1 binds to sulphur= S-glycosidic C1 binds to carbon= C-glycosidic
41
what are some common disaccharides?
sucrose (glucose and fructose) lactose-(galactose and glucose) maltose-(glucose+glucose) forms backbone of starch- the primary sugar we need for energy in our body.
42
what are oligosaccharides?
polymers containing a small number of component monosaccharides <15 are covalently linked to proteins or to membrane lipids
43
what is the function of oligosaccharides?
commonly found in the plasma membrane of animal cells where they play role in cell-cell recognition-glycocalyx
44
what bonds do oligosaccharides make?
they either make O-glycosidic bonds or N-glycosidic bonds with amino acid R groups or to lipids to make glycoprotein or glycolipids
45
what is the structure of oligosaccharides that are covalently linked to proteins or lipids?
they may be linear or branched
46
what is a O-glycosidic link?
link to a protein via a glycosidic bond between sugar residue and OH group of serine amino acid o-linked glycoproteins could either be single or branched N-linked glycoproteins all contain 3 mannose sugars- branched always
47
what is glycocalyx made of?
carb could be added to lipid or protein
48
what are the functions of glycocalyx?
.cell recognition .cell adhesion .protection .permeability barrier
49
what is the difference between proteoglycans and glycoproteins?
.proteoglycans represent a subclass of glycoproteins .proteoglycans the structure is more complicated and much larger .proteoglycans form ground substances of connective tissue .glycoprotein is an oligosaccharide .they are both composed of proteins and carbohydrates
50
what is the function of proteoglycans?
.proteoglycans play important roleas they trap water in the extracellular space to create a hydrated space around the cell- key component of wound healing, withstand compression - they also regulate fluid and can bind cations ( zinc , iron ,copper) to form electrochemical gradient
51
what is the structure of proteoglycans?
GAGS are chains of repeating disaccharide units. GAGS extend perpendicular from the core protein to form proteoglycans - bottle brush structure there is a protein chord with carbohydrates sticking out.
52
what are GAGS?
chain of repeating disaccharide s
53
what are some examples of proteoglycans?
hyaluronic acid - vitreous which is the jelly like substance in the eye. keratan sulphate- basement membrane / cornea stroma dermatan sulphate- skin chondroitin sulphate- cartilage
54
how are polysaccharides bound?
they are bound together by glycosidic linkages
55
what happens to polysaccharides during hydrolysis?
upon hydrolysis they give constituent monosaccharides or oligosaccharides.
56
what is the structure of polysaccharides?
linear or highly branched.
57
what are the 4 biological roles of lipids?
1. they are components of membrane e.g. phospholipids ,cholesterol. 2. several proteins are covalently modified by fatty acids 3. act as energy store and fuel molecule 4. fatty acid derivatives serve as hormones e.g. steroids
58
where are lipids found?
fats oils waxes phospholipids
59
what are types of lipids?
``` .fatty acids .phospholipids .steroids .glycolipids .triglycerides ```
60
what is the structure of fatty acids?
.these are carboxylic acids with long hydrocarbon chains .some fatty acids are saturated and have a linear shape .some fatty acids are unsaturated(lost 2 H and get a double bond) and now have a kink/bend in their structure/tail- not linear now
61
what is the structure of triglycerides?
3 fatty acids joined together through ester linkage to a glycerol
62
what is the function of triglycerides?
main energy store
63
where are triglycerides found?
in hypo dermis have inclusion in them packed of lipids= triglycerides
64
how do triglycerides release fatty acids?
triglycerides must be hydrolysed to release fatty acids
65
what are adipocytes?
-is a fat-storage -fatty acids are stored in adipocytes as triglycerides -adipocytes are metabolically very active. stored triglyceride is constantly hydrolysed and re-synthesised
66
where are adipocytes found?
they are found mostly in the abdominal cavity and subcutaneous tissue.
67
what is the structure of phospholipids?
.contains 2 fatty acids (unsaturated which means it has a kink) bound through an ester linkage to glycerol. .hydrophilic head has a glycerol bound to a phosphate .hydrophobic tail contains one saturated and one unsaturated fatty acid
68
where are steroids derived from?
all steroids are derived from cholesterol(type of lipid) except retinoic acid
69
what is the function of cholesterol?
cholesterol is a major component of cell membrane | cholesterol impacts fluidity and maintains the integrity of the membrane.
70
how does cholesterol travel around the body?
lipoproteins
71
what is the role of cholesterol in the membrane?
.cholesterol binds to fatty acid near polar head this -immobilises the first few groups of hydrocarbon chain closest to the polar head- less deformable bilayer .cholesterol decreases lipid fluidity by preventing motion of hydrocarbon chain. .cholesterol enhances the permeability-barrier properties of the bilayer.- imprpoves selective permeability of plasma membrane
72
what are glycolipids?
.complex lipids that contain a sugar .the sugar is either glucose or galactose .they are structural lipids.
73
what is the structure of glycolipids?
in the hydrophilic head glycerol is bound to a sugar residue instead of phosphate. hydrophobic tail contains 2 fatty acids one is saturated and other is unsaturated
74
how are lipids carried around the body?
lipids are not soluble in water so are carried around in lipoproteins around the body.
75
what is the function of lipoproteins?
lipoproteins carry lipids and cholesterol in the body.
76
what is HDL?
high density lipoprotein carry 20% plasma cholesterol highest in density
77
what is LDL?
low density lipoprotein highest in cholesterol carry 60% plasma cholesterol
78
what is VLDL?
very low density lipoprotein | carry triglycerides
79
What is another word for condensation reaction?
deyhdration synthesis
80
Where are the R groups of an amino acid chain?
the R -groups are in different conformations such as on the opposite sides on a chain.
81
What would further peptide bonding form?
oligopeptide (less than 25 amino acids) or a polypeptide more than 25
82
What can R groups do?
form different bonds with each other such as ionic, hydrogen etc This is the intermediate/weak interactions.
83
What bond does R-group not usually form?
Covalent unless you have R-groups that contain sulfur.
84
What are the uniform structures in proteins structures?
Alpha helix | Beta pleated sheet
85
What is glycogen?
acts as an energy store of carbohydrates in our body for energy. starch is a classic intake we use as carbs in our body
86
What do carbs do plants use for energy / energy storage?
use cellulose in cell walls
87
How do carbohydrates act as intermediates in metabolism in our bodies?
we break it down and produce glucose, glucose is broke down to extract as much energy out so we can use that to power the proteins in our body
88
What do phosphorylated sugars do?
forms the structural framework for backbones of DNA and RNA
89
What do glycoproteins do?
Each cell of our body has glycocalyx and glycoproteins are found on our cell surfaces for cell recognition
90
How do carbohydrates make up most of the organic matter on earth?
polysaccharides such as glycogen and starch or structural elements such as cellulose glucose (monomeric sugars) phosphorylaed sugrars glycoproteins and glycocalyx
91
What are isomers?
when you could have different monosaccharides/have same component parts but have different structures so they are structural isomers of each other.
92
What can happen to these sugar derivative?
body can change the nature of these sugars to change the amount of energy being released. use sugar to build other things in our body such as nucleotides to form ATP, DNA, RNA
93
What are the 3 different Lipoproteins?
HDL LDL VLDL

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