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BLG 143 Chapter 1 > Chapter 2 > Flashcards

Chapter 2 Flashcards

1
Q

How many amino acids are most proteins made of

A

20

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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”

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3
Q

What do all amino acids have in common

A

they all have the same core structure

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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
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5
Q

The 20 amino acids differ only in the unique

A

R- group, or side chain, attached to the central carbon

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6
Q

The properties of amino acids are determined by their

A

R-groups

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7
Q

Side chains can be grouped into three types, they are:

A
  1. Charged—includes both acidic (−) and basic (+)
  2. Uncharged polar
  3. Nonpolar
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8
Q

What type of molecules are proteins

A

Macromolecules

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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”)

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10
Q

What are the monomers that make up proteins

A

Amino acids

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11
Q

Monomers are the building blocks of

A

Polymers

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12
Q

Monomers polymerize through which method

A

condensation (dehydration) reactions, which results in the loss of a water molecule. Monomer in, water out

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13
Q

What is the reverse reaction of condensation

A

Hydrolysis, which breaks polymers apart by adding a water molecule. Water in, monomer out.

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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
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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

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16
Q

What does polymerization require

A

Energy
– Monomers would not self-assemble into a polymer
– Polymerization decreases the entropy of the molecule

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17
Q

What do peptide bonds form a backbone with

A
  1. R-group orientation such that side chains extend out and can interact with each other or water
  2. 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
  3. Flexibility—Single bonds on either side of the peptide bond can rotate
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18
Q

Amino acids polymerize to form

A

Chains

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19
Q

A chain of fewer than 50 amino acids is an

A

oligopeptide (“few-peptides”) or a peptide

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20
Q

A chain of more than 50 amino acids is a

A

polypeptide (“many-peptides”)

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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)

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22
Q

Proteins have unparalleled diversity of

A

size, shape, and chemical properties

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23
Q

Proteins serve diverse functions in cells because

A

structure gives rise to function

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24
Q

All proteins have just four basic structures, they are

A
  1. Primary
  2. Secondary
  3. Tertiary
  4. Quaternary
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25
Q

Protein primary structure is

A

its unique sequence of amino acids

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26
Q

The number of primary structures is practically limitless because

A

– 20 types of amino acids are available
– Lengths range from two amino acid residues to tens of
thousands

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27
Q

Primary structure is fundamental to

A

the higher levels of protein structure
– Secondary, tertiary, and quaternary

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28
Q

Which group on the amino acid affect a polypeptide’s properties and function

A

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.

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29
Q

Protein secondary structure is formed by

A

hydrogen bonds between
– The carbonyl group of one amino acid
– The amino group of another amino acid

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30
Q

Secondary strucuture of a protein can only occur when

A

A polypeptide bends so that
C=O and N–H groups are close together

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31
Q

What are the types of secondary structure

A
  • Alpha-helixes
  • Beta-pleated sheets
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32
Q

Describe the beta pleated sheets structure

A

The arrowheads point towards the carboxyl end of the primary structure

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33
Q

The tertiary structure of a polypeptide results from

A

– 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

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34
Q

What are the 5 important types of R-group interactions which occur in the tertiary structure

A
  1. hydrogen bonds
  2. Hydrophobic interactions
  3. Van der waals interactions
  4. covalent disulphide bonds
  5. Ionic bonds
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35
Q

what are hydrogen bonds

A

form between polar side chains and
opposite partial charges

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36
Q

Hydrophobic interactions are when

A

water forces hydrophobic side chains together

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37
Q

Van der Waals interactions are

A

weak electrical interactions between hydrophobic side chains

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38
Q

Covalent disulfide bonds

A

form bridges between two sulfhydryl groups

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39
Q

Ionic bonds

A

form between groups with full and
opposing charges

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40
Q

Many proteins contain several distinct polypeptide subunits that

A

interact to form a single structure

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41
Q

The bonding of two or more distinct polypeptide subunits produces

A

quaternary structure

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42
Q

Some cells contain groups of multiple proteins that carry out a particular function, known as

A

molecular machines

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43
Q

The cro protein is a dimer consisting of

A

two identical polypeptide subunits

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44
Q

Hemoglobin is a tetramer consisting of

A

Four polypeptide subunits, two identical alpha subunits, and two identical beta subunits

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45
Q

Why is protein folding often spontaneous

A

– Because of the hydrogen bonds and van der Waals interactions
– The folded molecule is more energetically stable than the unfolded molecule

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46
Q

A denatured (unfolded) protein is

A

unable to function normally

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47
Q

What proteins help other proteins fold correctly in cells

A

molecular chaperones

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48
Q

What happens when the hydrogen and disulphide bonds are broken in ribonuclease

A

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.

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49
Q

Proteins are crucial to most tasks required by cells, such as

A

– 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

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50
Q

What is regarded as one of the most important protein function

A

Catalysis

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51
Q

A protein that functions as a catalyst is known as

A

An Enzyme

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52
Q

The reactants in enzyme-catalyzed
reactions are

A

Substrates

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53
Q

The location on an enzyme where substrates bind and react is the

A

Active site

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54
Q

What is the function of the plasma membrane (also cell membrane)

A
  • It separates life from nonlife
  • separates the cell’s interior from the external environment
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55
Q

Membranes function to

A

– Keep damaging materials out of the cell
– Allow entry of materials needed by the cell
– Facilitate the chemical reactions necessary for life

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56
Q

What are lipids

A

– Carbon-containing compounds
– Found in organisms
– Largely non-polar and hydrophobic

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57
Q

Molecules that are hydrophobic and contain primarily carbon and hydrogen bonds in which electrons are shared equally are

A

Hydrocarbons

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58
Q

An isoprenoid is a

A
  • hydrocarbon chain
    – Function as pigments, scents, vitamins, sex hormone
    precursors
    – Building blocks for more complex lipids
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59
Q

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

A

Fatty acid

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60
Q

The Fluidity of Lipids Depends on
the

A

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

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61
Q

Lipid structure varies

A

Widely

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62
Q

The three most important types of lipids found in cells:

A

Fats, steroids, and phospholipids

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63
Q

What are fats

A

Fats are composed of three fatty acids linked to glycerol.
 Also called triaylglycerols or triglycerides

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64
Q

What are steroids

A

A family of lipids with a distinctive four-ring structure. Cholesterol is an important steroid in mammals

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65
Q

What are Phospholipids

A

Phospholipids consist of a glycerol linked to a phosphate group (PO42−) and to either two chains of isoprene or two fatty acids.

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66
Q

Steroids differ from one
another by

A

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

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67
Q

When their fatty acids are
polyunsaturated, they

A

are liquid and form oils

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68
Q

The primary role of fats is

A

energy
storage

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69
Q

Fats form by

A

dehydration reactions between a hydroxyl group of glycerol and the carboxyl group of a fatty acid (ester linkage)

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70
Q

Phospholipids consist of a glycerol
linked to

A

A phosphate group bonded to a
charged or polar molecule

71
Q

Two hydrocarbon chains are

A

 Fatty acids in Bacteria and
Eukarya
 Isoprenoids in Archaea

72
Q

The primary role of phospholipids is to

A

form cell membranes

73
Q

Phospholipids are amphipathic meaning

A

They have both hydrophilic and
hydrophobic regions

74
Q

When amphipathic lipids are placed in water, what happens

A

– The hydrophilic heads interact with water
– The hydrophobic tails interact with each other, away from the water
- they form micelles or lipid bilayers

75
Q

Phospholipid bilayers form

A

spontaneously, meaning that no inside input of energy is required

76
Q

Phospholipid bilayers
have

A

selective
permeability

77
Q

What is selective permeability

A
  • 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
Q

Phospholipids in plasma membranes move

A

Laterally within the bilayer

79
Q

How does Membrane fluidity change as temperature drops

A

Membrane fluidity decreases.
– Molecules in the bilayer move more slowly
– Hydrophobic tails pack together more tightly
– Decreased membrane fluidity causes decreased
permeability

80
Q

Phospholipids are in constant lateral motion, but rarely

A

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
Q

What are the characteristics of membranes made from lipids

A

– Flexible
 Cells can change shape
– Repairable
 Lipids move to reform a continuous surface
– Expandable
 Cells increase surface area by adding new membrane
lipids

82
Q

How do Substances Move Across Lipid
Bilayers:

A

Diffusion and osmosis

83
Q

Small molecules and ions in a solution, called solutes:

A

– Have thermal energy
– Are in constant, random motion

84
Q

The spontaneous movement of solutes is called

A

Diffusion

85
Q

A concentration gradient is created by

A

a difference in solute concentrations

86
Q

When a concentration gradient exists, what happens

A

There is a net movement from high-concentration regions to low-concentration regions

87
Q

Diffusion along a concentration gradient creates

A

–Increased entropy
– Is spontaneous

88
Q

Equilibrium occurs when the molecules or ions are

A

Randomly distributed
– Molecules are still moving randomly
– But there is no more net movement

89
Q

Passive transport occurs when

A

substances
diffuse across a membrane in the absence of an
outside energy source

90
Q

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

A

Osmosis

91
Q

For osmosis water moves from regions of

A

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
Q

The concentration of a solution outside a cell may differ from the concentration

A

Inside the cell

93
Q

An outside solution with a higher concentration is said to be

A

Hypertonic to the inside of a cell

94
Q

A solution with a lower concentration is

A

hypotonic to the cell

95
Q

If solute concentrations are equal on the outside and inside of a cell, solutions are

A

isotonic to each other

96
Q

When an outside solution is hypertonic to the inside

A

There is a net flow of water out of the vesicle, and the vesicle shrinks

97
Q

When an outside solution is hypotonic to the inside

A

There is a net flow of water into the vesicle, causing the vesicle to swell and burst

98
Q

When the inside and outside solutions are isotonic to each other

A

There is no change

99
Q

The basic membrane structure is provided by

A

Phospholipids

100
Q

What other structure contains as much protein as the phospholipid

A

Plasma membrane

101
Q

Proteins can insert into a

A
  • membrane
    – They can be amphipathic, since their side chains can
    be polar, charged, or nonpolar
    – They can fold into shapes
102
Q

The Hydrophobic Region of an
Amphipathic Protein Can Be

A

Anchored into
a Lipid Bilayer

103
Q

The fluid-mosaic model of membrane structure suggests

A

– Some proteins are inserted into the lipid bilayer
– Thus making the membrane a fluid, dynamic mosaic of
phospholipids and proteins

104
Q

Proteins that span the membrane are

A

Integral membrane proteins or transmembrane
proteins

105
Q

Integral membranes or transmembrane proteins:

A

– 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
Q

Which proteins bind to the
membrane without passing through it
and may be found on interior or exterior of the cell

A

Peripheral membrane proteins

107
Q

Ion channels are

A

specialized membrane proteins
– Form pores, or openings, in a membrane
– Ions diffuse through

108
Q

Electrochemical gradients occur when

A
  • 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
Q

Channel proteins are selective because

A

– 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
Q

Aquaporins (“water-pores”) permit

A

water to cross the plasma membrane

111
Q

Gated channels

A
  • open or close in response to a
    signal
    – Binding of a particular molecule
    – Change in the electrical voltage across the membrane
112
Q

The flow of ions and small molecules through membrane channels is carefully

A

controlled

113
Q

Movement of substances through channels does not require

A

energy

114
Q

When transmembrane proteins assist passive transport, the process is called

A

facilitated
diffusion

115
Q

Facilitated diffusion can also occur through carrier proteins that

A

– Change shape to transport solutes across a membrane
– Transport larger molecules, such as glucose

116
Q

Describe the hypothesis for how the GLUT-1 molecule facilitates glucose diffusion

A
  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
Q

Pumps and Coupled Transporters Perform

A

Active transport

118
Q

Facilitated diffusion through channels or carriers is passive transport, which

A

– It moves substances with their concentration gradient
– It does not require an input of energy

119
Q

Active transport

A

– Moves substances against their gradient
– Requires an input of energy
– ATP often provides the energy in cells

120
Q

Membrane proteins that provide active
transport of molecules across the membrane are

A

Pumps

121
Q

The sodium–potassium pump

A

– Uses ATP
– Transports Na+ and K+ against their concentration gradients

122
Q

The Sodium–Potassium Pump Depends on

A

an Input of Chemical Energy Stored in ATP

123
Q

Describe the process of the sodium-potassium pump

A
  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
Q

By moving materials against their concentration gradients, pumps set up

A

electrochemical gradients
– These gradients represent potential energy
 ATP is not directly used to power transport

125
Q

To bring in glucose, the pumps use a

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
Q

The three mechanisms of membrane transport are

A
  1. Diffusion
  2. Facilitated diffusion through channels or carriers
    Active transport:
  3. Primary and secondary active transport
127
Q

Carbohydrates, or sugars, are macromolecules that

A

– Play an important role in energy
– Contribute to cell structure
– Are involved with cell recognition and identity

128
Q

Carbohydrates include

A

– Monosaccharide (“one-sugar”) monomers
– Oligosaccharide (“few-sugars”) small polymers
– Polysaccharide (“many-sugars”) large polymers

129
Q

Carbohydrates have the molecular formula

A
  • (CH 2O)n
    – “carbo” refers to carbon; “hydrate” refers to water
    – “n” can vary from 3 to over a thousand
    -
130
Q

What structural groups do carbohydrates have

A

Contain a carbonyl group (C=O), hydroxyl groups (O–H), and many carbon–hydrogen bonds (C–H)

131
Q

Why are carbohydrates hydrophilic

A

Since carbonyl and hydroxyl groups are polar, carbohydrates are hydrophilic

132
Q

Monosaccharide monomers are simple sugars that structurally vary in four primary ways:

A
  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
Q

Distinct monosaccharides exist because

A

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
Q

Each monosaccharide has a unique structure and

A

Function

135
Q

Two sugars linked together form a

A

Disaccharide (maltose, lactose)

136
Q

Monosaccharides polymerize when

A

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
Q

two of the most important glycosidic linkages which are between the C-1 and C-4 carbons are

A

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
Q

Polysaccharides, or complex carbohydrates are

A

polymers of monosaccharide monomers

139
Q

The most common polysaccharides found in organisms today

A

starch, glycogen, cellulose, and chitin, along with a modified polysaccharide called peptidoglycan

140
Q

Plants store sugar as

A

Starch

141
Q

Starch is a polysaccharide which

A

– 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
Q

Animals store sugar as

A

Glycogen

143
Q

Glycogen is a polysaccharide which

A

– 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
Q

The structural polymer in plants is

A

Cellulose

145
Q

The structural polysaccharide cellulose is

A

– 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
Q

The structural polymer found in cell walls of fungi and exoskeletons of insects and crustaceans

A

Chitin

147
Q

The structural polymer chitin is

A

– 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
Q

Polysaccharides Differ in

A

structure

149
Q

The structural polymer found in
bacterial cell walls

A

Peptidoglycan

150
Q

The structural polymer Peptidoglycan contains

A

– Long backbones of alternating monosaccharides
– Joined by β-1,4-glycosidic linkages
– Short amino acid chains form peptide bonds between
adjacent strands

151
Q

Carbohydrates have diverse functions in cells, including

A

– Serve as precursors to larger molecules, such as
nucleotides and amino acids
– Provide fibrous structural materials
– Indicate cell identity
– Store chemical energy

152
Q

Cellulose, chitin, and peptidoglycan form

A

long strands with bonds between adjacent strands
– Strands may be organized into fibres or sheets

153
Q

β-1,4-glycosidic linkages are not easy to hydrolyze because

A

– Most organisms lack enzymes to hydrolyze them
– These fibres exclude water, making hydrolysis difficult

154
Q

Carbohydrates form dietary fibre, which is

A

important for
digestive health

155
Q

Cell identity is indicated by

A

Carbohydrates. which display information on the outer surface of cells

156
Q

Glycoproteins are

A

carbohydrates attached to proteins

157
Q

Glycolipids are

A

carbohydrates attached to lipids

158
Q

Glycoproteins and glycolipids are key molecules in

A

– Cell–cell recognition: Identify cells as “self”
– Cell–cell signalling: Communication between cells

159
Q

Explain how carbohydrates are an identification badge for cells

A
  • 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
Q

Different human cells have different sets of

A

glycoproteins on the surface

161
Q

Human blood cells glycoproteins and glycolipids can display one of three different oligosaccharides, they are

A

 A, B and H antigen
 Antigens are molecules that can potentially provoke an
immune system response

162
Q

Your blood type depends upon what combination of these three antigens you possess

A

– 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
Q

Patients cannot receive blood that has

A

antigens they do not make

164
Q

Carbohydrates store

A

chemical energy

165
Q

In photosynthesis, plants harvest energy from

A

plants harvest energy from
sunlight and store it in the bonds of carbohydrates

166
Q

Carbohydrates have more energy than CO2 because

A

– 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
Q

Fatty acids hold even more energy because

A

they have more C–C and C–H bonds

168
Q

In Organisms, Potential Energy
Is Stored in the

A

Bonds of Molecules

169
Q

Starch and glycogen are easily hydrolyzed because they have

A

alpha-glycosidic linkages

170
Q

Glycogen is hydrolyzed by the enzyme

A
  • phosphorylase
    – Most animal cells contain phosphorylase
    – They can break down glycogen to provide glucose
171
Q

Starch is hydrolyzed by

A

amylase enzymes
– Amylases play a key role in carbohydrate digestion

172
Q

Energy Stored in Glucose Is Used to Make

A

ATP

173
Q

When a cell needs energy, it

A

breaks down glucose. Captured energy is used to make ATP

BLG 143 Chapter 1 (5 decks)

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