Chapter 2 Flashcards
1
Q
How many amino acids are most proteins made of
A
20
2
Q
Amino acids are composed of a central carbon atom bonded to
A
– H—a hydrogen atom
– NH2—an amino functional group
– COOH—a carboxyl functional group
– R group—a variable “side chain”
3
Q
What do all amino acids have in common
A
they all have the same core structure
4
Q
What happens to the amino and carboxyl groups in water
A
- In water, the amino and carboxyl groups ionize
- The amino group acts as a base and attracts a proton
- The carboxyl group acts as an acid and donates a proton
- This helps the amino acids stay in solution, make the amino acids more reactive
5
Q
The 20 amino acids differ only in the unique
A
R- group, or side chain, attached to the central carbon
6
Q
The properties of amino acids are determined by their
A
R-groups
7
Q
Side chains can be grouped into three types, they are:
A
- Charged—includes both acidic (−) and basic (+)
- Uncharged polar
- Nonpolar
8
Q
What type of molecules are proteins
A
Macromolecules
9
Q
What are macromolecules
A
– Large molecules made of smaller subunits
– Subunits are called monomers (“one-part”)
– Monomers link together (polymerize) to form
polymers (“many-parts”)
10
Q
What are the monomers that make up proteins
A
Amino acids
11
Q
Monomers are the building blocks of
A
Polymers
12
Q
Monomers polymerize through which method
A
condensation (dehydration) reactions, which results in the loss of a water molecule. Monomer in, water out
13
Q
What is the reverse reaction of condensation
A
Hydrolysis, which breaks polymers apart by adding a water molecule. Water in, monomer out.
14
Q
When do peptide bonds form
A
- When the Carboxyl Group of One Amino Acid Reacts with the Amino
Group of a Second Amino Acid. - The resulting C–N bond is called a peptide bond
15
Q
Describe the characteristics of a peptide bond
A
Unusually stable because a pair of valence electrons on nitrogen are
partially shared in the C–N bond
Causes peptide bonds to have characteristics of double bonds
16
Q
What does polymerization require
A
Energy
– Monomers would not self-assemble into a polymer
– Polymerization decreases the entropy of the molecule
17
Q
What do peptide bonds form a backbone with
A
- R-group orientation such that side chains extend out and can interact with each other or water
- Directionality
The end with the free amino group is the N-terminus
The end with the free carboxyl group is the C-terminus
By convention, written with N-terminus on the left - Flexibility—Single bonds on either side of the peptide bond can rotate
18
Q
Amino acids polymerize to form
A
Chains
19
Q
A chain of fewer than 50 amino acids is an
A
oligopeptide (“few-peptides”) or a peptide
20
Q
A chain of more than 50 amino acids is a
A
polypeptide (“many-peptides”)
21
Q
The complete, functional form of the
molecule is known as
A
A protein. (Sometimes used to describe any chain of amino acid residues)
22
Q
Proteins have unparalleled diversity of
A
size, shape, and chemical properties
23
Q
Proteins serve diverse functions in cells because
A
structure gives rise to function
24
Q
All proteins have just four basic structures, they are
A
- Primary
- Secondary
- Tertiary
- Quaternary
25
Protein primary structure is
its unique sequence of amino acids
26
The number of primary structures is practically limitless because
– 20 types of amino acids are available
– Lengths range from two amino acid residues to tens of
thousands
27
Primary structure is fundamental to
the higher levels of protein structure
– Secondary, tertiary, and quaternary
28
Which group on the amino acid affect a polypeptide’s properties and function
The amino acid R-groups. A single amino acid change can radically alter protein function. e.g single amino acid change within people with sickle cell disease causes the red blood cells to change from their normal disk shape to a sickle shape when oxygen concentrations are low.
29
Protein secondary structure is formed by
hydrogen bonds between
– The carbonyl group of one amino acid
– The amino group of another amino acid
30
Secondary strucuture of a protein can only occur when
A polypeptide bends so that
C=O and N–H groups are close together
31
What are the types of secondary structure
- Alpha-helixes
- Beta-pleated sheets
32
Describe the beta pleated sheets structure
The arrowheads point towards the carboxyl end of the primary structure
33
The tertiary structure of a polypeptide results from
– Interactions between R-groups
– Or between R-groups and the peptide backbone
* These contacts cause the backbone to bend and fold
* Bending and folding contribute to the distinctive three-dimensional shape of the polypeptide
34
What are the 5 important types of R-group interactions which occur in the tertiary structure
1. hydrogen bonds
2. Hydrophobic interactions
3. Van der waals interactions
4. covalent disulphide bonds
5. Ionic bonds
35
what are hydrogen bonds
form between polar side chains and
opposite partial charges
36
Hydrophobic interactions are when
water forces hydrophobic side chains together
37
Van der Waals interactions are
weak electrical interactions between hydrophobic side chains
38
Covalent disulfide bonds
form bridges between two sulfhydryl groups
39
Ionic bonds
form between groups with full and
opposing charges
40
Many proteins contain several distinct polypeptide subunits that
interact to form a single structure
41
The bonding of two or more distinct polypeptide subunits produces
quaternary structure
42
Some cells contain groups of multiple proteins that carry out a particular function, known as
molecular machines
43
The cro protein is a dimer consisting of
two identical polypeptide subunits
44
Hemoglobin is a tetramer consisting of
Four polypeptide subunits, two identical alpha subunits, and two identical beta subunits
45
Why is protein folding often spontaneous
– Because of the hydrogen bonds and van der Waals interactions
– The folded molecule is more energetically stable than the unfolded molecule
46
A denatured (unfolded) protein is
unable to function normally
47
What proteins help other proteins fold correctly in cells
molecular chaperones
48
What happens when the hydrogen and disulphide bonds are broken in ribonuclease
Ribonuclease is functional when the hydrogen and disulphide bonds are intact. When broken, ribonuclease is no longer able to function. However, in this case, the process is reversible.
49
Proteins are crucial to most tasks required by cells, such as
– Catalysis—speed up chemical reactions
– Defence—antibodies attack pathogens
– Movement—move cells or molecules within cells
– Signalling—convey signals between cells
– Structure—shape cells and comprise body structures
– Transport—allow molecules to enter and exit cells or carry them throughout the body
50
What is regarded as one of the most important protein function
Catalysis
51
A protein that functions as a catalyst is known as
An Enzyme
52
The reactants in enzyme-catalyzed
reactions are
Substrates
53
The location on an enzyme where substrates bind and react is the
Active site
54
What is the function of the plasma membrane (also cell membrane)
- It separates life from nonlife
- separates the cell’s interior from the external environment
55
Membranes function to
– Keep damaging materials out of the cell
– Allow entry of materials needed by the cell
– Facilitate the chemical reactions necessary for life
56
What are lipids
– Carbon-containing compounds
– Found in organisms
– Largely non-polar and hydrophobic
57
Molecules that are hydrophobic and contain primarily carbon and hydrogen bonds in which electrons are shared equally are
Hydrocarbons
58
An isoprenoid is a
- hydrocarbon chain
– Function as pigments, scents, vitamins, sex hormone
precursors
– Building blocks for more complex lipids
59
A hydrocarbon chain that is bonded to a carboxyl (–COOH) functional group that contains 14–20 carbon atoms and can be saturated or unsaturated is a
Fatty acid
60
The Fluidity of Lipids Depends on
the
Length and Saturation of Their
Hydrocarbon Chains. e.g butter consists of primarily saturated ipids, waxes are lipids with extremely long saturated hydrocarbon chains, and oils are dominated by polyunsaturates which are lipids with hydrocarbon chains containing multiple C=C double bonds
61
Lipid structure varies
Widely
62
The three most important types of lipids found in cells:
Fats, steroids, and phospholipids
63
What are fats
Fats are composed of three fatty acids linked to glycerol.
Also called triaylglycerols or triglycerides
64
What are steroids
A family of lipids with a distinctive four-ring structure. Cholesterol is an important steroid in mammals
65
What are Phospholipids
Phospholipids consist of a glycerol linked to a phosphate group (PO42−) and to either two chains of isoprene or two fatty acids.
66
Steroids differ from one
another by
The functional groups attached to
carbons in the rings. Examples: Hormones such as estrogen and testosterone. Cholesterol, a component of plasma membranes which has a polar hydroxyl group and an isoprenoid chain attached to its rings
67
When their fatty acids are
polyunsaturated, they
are liquid and form oils
68
The primary role of fats is
energy
storage
69
Fats form by
dehydration reactions between a hydroxyl group of glycerol and the carboxyl group of a fatty acid (ester linkage)
70
Phospholipids consist of a glycerol
linked to
A phosphate group bonded to a
charged or polar molecule
71
Two hydrocarbon chains are
Fatty acids in Bacteria and
Eukarya
Isoprenoids in Archaea
72
The primary role of phospholipids is to
form cell membranes
73
Phospholipids are amphipathic meaning
They have both hydrophilic and
hydrophobic regions
74
When amphipathic lipids are placed in water, what happens
– The hydrophilic heads interact with water
– The hydrophobic tails interact with each other, away from the water
- they form micelles or lipid bilayers
75
Phospholipid bilayers form
spontaneously, meaning that no inside input of energy is required
76
Phospholipid bilayers
have
selective
permeability
77
What is selective permeability
- only certain substances cross lipid bilayers readily
– Small or nonpolar
molecules move
across phospholipid
bilayers quickly
– Charged or large
polar substances
cross slowly, if at all
78
Phospholipids in plasma membranes move
Laterally within the bilayer
79
How does Membrane fluidity change as temperature drops
Membrane fluidity decreases.
– Molecules in the bilayer move more slowly
– Hydrophobic tails pack together more tightly
– Decreased membrane fluidity causes decreased
permeability
80
Phospholipids are in constant lateral motion, but rarely
Flip to the other side of the bilayer.
Membranes are in part dynamic since phospholipid molecules randomly move laterally within each layer of the structure
81
What are the characteristics of membranes made from lipids
– Flexible
Cells can change shape
– Repairable
Lipids move to reform a continuous surface
– Expandable
Cells increase surface area by adding new membrane
lipids
82
How do Substances Move Across Lipid
Bilayers:
Diffusion and osmosis
83
Small molecules and ions in a solution, called solutes:
– Have thermal energy
– Are in constant, random motion
84
The spontaneous movement of solutes is called
Diffusion
85
A concentration gradient is created by
a difference in solute concentrations
86
When a concentration gradient exists, what happens
There is a net movement from high-concentration regions to low-concentration regions
87
Diffusion along a concentration gradient creates
–Increased entropy
– Is spontaneous
88
Equilibrium occurs when the molecules or ions are
Randomly distributed
– Molecules are still moving randomly
– But there is no more net movement
89
Passive transport occurs when
substances
diffuse across a membrane in the absence of an
outside energy source
90
Water moves quickly across lipid bilayers. This is a special case of diffusion that occurs across selectively permeable membranes when the solute cannot cross the membrane
Osmosis
91
For osmosis water moves from regions of
low solute concentration to regions of high solute concentration
– This dilutes the higher concentration of solute
– It equalizes the concentration on both sides of the bilayer
92
The concentration of a solution outside a cell may differ from the concentration
Inside the cell
93
An outside solution with a higher concentration is said to be
Hypertonic to the inside of a cell
94
A solution with a lower concentration is
hypotonic to the cell
95
If solute concentrations are equal on the outside and inside of a cell, solutions are
isotonic to each other
96
When an outside solution is hypertonic to the inside
There is a net flow of water out of the vesicle, and the vesicle shrinks
97
When an outside solution is hypotonic to the inside
There is a net flow of water into the vesicle, causing the vesicle to swell and burst
98
When the inside and outside solutions are isotonic to each other
There is no change
99
The basic membrane structure is provided by
Phospholipids
100
What other structure contains as much protein as the phospholipid
Plasma membrane
101
Proteins can insert into a
- membrane
– They can be amphipathic, since their side chains can
be polar, charged, or nonpolar
– They can fold into shapes
102
The Hydrophobic Region of an
Amphipathic Protein Can Be
Anchored into
a Lipid Bilayer
103
The fluid-mosaic model of membrane structure suggests
– Some proteins are inserted into the lipid bilayer
– Thus making the membrane a fluid, dynamic mosaic of
phospholipids and proteins
104
Proteins that span the membrane are
Integral membrane proteins or transmembrane
proteins
105
Integral membranes or transmembrane proteins:
– They have segments facing both its interior and exterior surfaces
– Portions that pass through the hydrophobic tails in the
bilayer have hydrophobic side chains
106
Which proteins bind to the
membrane without passing through it
and may be found on interior or exterior of the cell
Peripheral membrane proteins
107
Ion channels are
specialized membrane proteins
– Form pores, or openings, in a membrane
– Ions diffuse through
108
Electrochemical gradients occur when
- ions build up on one side of a plasma membrane
– They establish both a concentration gradient and a charge gradient
– Ions diffuse down their electrochemical gradients
109
Channel proteins are selective because
– The residues facing inside the pore are hydrophilic
– Each channel protein permits only a particular type of ion or small molecule to pass through it
110
Aquaporins (“water-pores”) permit
water to cross the plasma membrane
111
Gated channels
- open or close in response to a
signal
– Binding of a particular molecule
– Change in the electrical voltage across the membrane
112
The flow of ions and small molecules through membrane channels is carefully
controlled
113
Movement of substances through channels does not require
energy
114
When transmembrane proteins assist passive transport, the process is called
facilitated
diffusion
115
Facilitated diffusion can also occur through carrier proteins that
– Change shape to transport solutes across a membrane
– Transport larger molecules, such as glucose
116
Describe the hypothesis for how the GLUT-1 molecule facilitates glucose diffusion
1. Unbound protein: GLUT-1 is a transmembrane transport protein, shown with its binding site facing outside the cell
2. Glucose binding: glucose binds to GLUT-1 from outside the cell
3. Conformational change: the protein shifts to face the inside of the cell
4. Release: glucose moves inside the cell. Steps may repeat or reverse, depending on the concentration gradient
117
Pumps and Coupled Transporters Perform
Active transport
118
Facilitated diffusion through channels or carriers is passive transport, which
– It moves substances with their concentration gradient
– It does not require an input of energy
119
Active transport
– Moves substances against their gradient
– Requires an input of energy
– ATP often provides the energy in cells
120
Membrane proteins that provide active
transport of molecules across the membrane are
Pumps
121
The sodium–potassium pump
– Uses ATP
– Transports Na+ and K+ against their concentration gradients
122
The Sodium–Potassium Pump Depends on
an Input of Chemical Energy Stored in ATP
123
Describe the process of the sodium-potassium pump
1. Unbound protein: three binding sites within the protein have a high affinity for sodium ions
2. Sodium binding: three sodium ions from the inside of the cell bind to these sites
3. Shape change: a phosphate group from ATP binds to the protein. In response, the protein changes shape
4. Release: the sodium ions leave the protein and move to the exterior of the cell
5. Unbound protein: in this conformation, the protein has binding sites with a high affinity for potassium ions
6. Potassium binding: two potassium ions bind to the pump
7. Shape change: the phosphate group is cleaved from the protein, allowing the pump to return to its original shape
8. Release: the potassium ions leave the protein and diffuse to the interior of the cell. These 8 steps repeat
124
By moving materials against their concentration gradients, pumps set up
electrochemical gradients
– These gradients represent potential energy
ATP is not directly used to power transport
125
To bring in glucose, the pumps use a
coupled transporter.
– These membrane proteins use the gradient of one molecule, in this case sodium ions, to power the movement of another molecule, glucose
126
The three mechanisms of membrane transport are
1. Diffusion
2. Facilitated diffusion through channels or carriers
Active transport:
3. Primary and secondary active transport
127
Carbohydrates, or sugars, are macromolecules that
– Play an important role in energy
– Contribute to cell structure
– Are involved with cell recognition and identity
128
Carbohydrates include
– Monosaccharide (“one-sugar”) monomers
– Oligosaccharide (“few-sugars”) small polymers
– Polysaccharide (“many-sugars”) large polymers
129
Carbohydrates have the molecular formula
- (CH 2O)n
– “carbo” refers to carbon; “hydrate” refers to water
– “n” can vary from 3 to over a thousand
-
130
What structural groups do carbohydrates have
Contain a carbonyl group (C=O), hydroxyl groups (O–H), and many carbon–hydrogen bonds (C–H)
131
Why are carbohydrates hydrophilic
Since carbonyl and hydroxyl groups are polar, carbohydrates are hydrophilic
132
Monosaccharide monomers are simple sugars that structurally vary in four primary ways:
1. Location of the carbonyl group
- At the end= aldose
- In the middle= ketose
2. Number of carbon atoms presents
- Three = triose
- Five = pentose
- Six = hectose
3. Spatial arrangement of their atoms
- Different arrangement of the hydroxyl groups
- The two six-carbon sugars shown here vary only in the spatial orientation of the hydroxyl groups on carbon number 4. Linear and alternative ring forms
- Sugars typically form ring structures in aqueous solution
(a) the linear form of glucose is rare
(b) In solution, almost all glucose molecules spontaneously react to form one of two ring structures, called the alpha and beta forms of glucose
133
Distinct monosaccharides exist because
so many aspects of their structure are variable
– Aldose or ketose placement of the carbonyl group
– Variation in carbon number
– Different arrangements of hydroxyl groups in space
– Alternative ring forms
134
Each monosaccharide has a unique structure and
Function
135
Two sugars linked together form a
Disaccharide (maltose, lactose)
136
Monosaccharides polymerize when
a condensation reaction occurs between two hydroxyl groups
– A covalent bond called a glycosidic linkage forms. The linkages can be broken by hydrolysis reactions
137
two of the most important glycosidic linkages which are between the C-1 and C-4 carbons are
alpha-1,4-glycosidic linkage
beta-1,4-glycosidic linkage
However, their geometry is different
– C-1 hydroxyl groups are on opposite sides of the plane
of the glucose rings
138
Polysaccharides, or complex carbohydrates are
polymers of monosaccharide monomers
139
The most common polysaccharides found in organisms today
starch, glycogen, cellulose, and chitin, along with a modified polysaccharide called peptidoglycan
140
Plants store sugar as
Starch
141
Starch is a polysaccharide which
– Composed of α-glucose monomers
– Forms a helix
– Amylose—unbranched starch with only α-1,4-glycosidic linkages
– Amylopectin—branched starch with some α-1,6-glycosidic
linkages
Branches occur about once in every 30 monomers
142
Animals store sugar as
Glycogen
143
Glycogen is a polysaccharide which
– Stored in liver and muscle cells
– Can be broken into glucose monomers for energy
– Highly branched alpha-glucose polymer, nearly identical to starch
Branches occur in about 1 out of 10 monomers
144
The structural polymer in plants is
Cellulose
145
The structural polysaccharide cellulose is
– Forms a protective layer around plant cells called the cell wall
– Made of β-glucose monomers joined by β-1,4-glycosidic linkages
– Every other glucose is flipped, so it
Generates a linear molecule rather than a helix
Permits hydrogen bonds to form between adjacent, parallel
strands
146
The structural polymer found in cell walls of fungi and exoskeletons of insects and crustaceans
Chitin
147
The structural polymer chitin is
– Monomer is N-acetylglucosamine (NAG)
– Structure is similar to cellulose:
β-1,4-glycosidic linkages with every other monomer flipped
Linear strands with hydrogen bonds between them
148
Polysaccharides Differ in
structure
149
The structural polymer found in
bacterial cell walls
Peptidoglycan
150
The structural polymer Peptidoglycan contains
– Long backbones of alternating monosaccharides
– Joined by β-1,4-glycosidic linkages
– Short amino acid chains form peptide bonds between
adjacent strands
151
Carbohydrates have diverse functions in cells, including
– Serve as precursors to larger molecules, such as
nucleotides and amino acids
– Provide fibrous structural materials
– Indicate cell identity
– Store chemical energy
152
Cellulose, chitin, and peptidoglycan form
long strands with bonds between adjacent strands
– Strands may be organized into fibres or sheets
153
β-1,4-glycosidic linkages are not easy to hydrolyze because
– Most organisms lack enzymes to hydrolyze them
– These fibres exclude water, making hydrolysis difficult
154
Carbohydrates form dietary fibre, which is
important for
digestive health
155
Cell identity is indicated by
Carbohydrates. which display information on the outer surface of cells
156
Glycoproteins are
carbohydrates attached to proteins
157
Glycolipids are
carbohydrates attached to lipids
158
Glycoproteins and glycolipids are key molecules in
– Cell–cell recognition: Identify cells as “self”
– Cell–cell signalling: Communication between cells
159
Explain how carbohydrates are an identification badge for cells
- Glycolipids and glycoproteins contain carbohydrates that project outside the cell from the surface of the plasma membrane enclosing the cell.
- These sugar groups have distinctive structures that identify the type or species of the cell
160
Different human cells have different sets of
glycoproteins on the surface
161
Human blood cells glycoproteins and glycolipids can display one of three different oligosaccharides, they are
A, B and H antigen
Antigens are molecules that can potentially provoke an
immune system response
162
Your blood type depends upon what combination of these three antigens you possess
– Blood type A cells: Display A and H antigens
– Blood type B cells: Display B and H antigens
– Blood type AB cells: Display A, B and H antigens
– Blood type O cells: Display H antigens
163
Patients cannot receive blood that has
antigens they do not make
164
Carbohydrates store
chemical energy
165
In photosynthesis, plants harvest energy from
plants harvest energy from
sunlight and store it in the bonds of carbohydrates
166
Carbohydrates have more energy than CO2 because
– Electrons in C–O bonds are held more tightly and have low potential energy
– Electrons in C–H and C–C bonds are shared more equally and have higher potential energy
167
Fatty acids hold even more energy because
they have more C–C and C–H bonds
168
In Organisms, Potential Energy
Is Stored in the
Bonds of Molecules
169
Starch and glycogen are easily hydrolyzed because they have
alpha-glycosidic linkages
170
Glycogen is hydrolyzed by the enzyme
- phosphorylase
– Most animal cells contain phosphorylase
– They can break down glycogen to provide glucose
171
Starch is hydrolyzed by
amylase enzymes
– Amylases play a key role in carbohydrate digestion
172
Energy Stored in Glucose Is Used to Make
ATP
173
When a cell needs energy, it
breaks down glucose. Captured energy is used to make ATP
