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First Year > Quiz 3- Biochem > Flashcards

Quiz 3- Biochem Flashcards

1
Q

4 types of protein structure

A

Globular proteins, fibrous proteins, transmembrane proteins, DNA binding proteins

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2
Q

Aldose

A

a monosaccharide that contains an aldehyde group

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3
Q

Aliphatic

A

A compound containing carbon and hydrogen joined together in straight chains, branched chains or non-aromatic rings

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4
Q

Amines

A
  • compounds with nitrogen are usually basic and can have a positive charge
  • if nitrogen has 3 bonds, there is no charge on the molecule
  • There are two remaining electrons in nitrogen’s valence shell
  • N has a positive charge if the two remaining electrons form a bond with a carbon atom or hydrogen ion
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5
Q

Amino acid in proteins

A
  • all proteins in the body are made from the 20 amino acids coded for by our DNA
  • the unique sequence of amino acids in each protein predicts its shape
  • proteins are not just flat molecules
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6
Q

Anomeric

A

Cyclization of a linear glucose molecule generates a chiral carbon where before there was an achiral one. This new stereocenter is called the anomeric carbon.

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7
Q

Anomers of Cyclic Glucose

A
  • exist in equilibrium with a straight-chain form in solution
  • OH group on the anomeric carbon can react with an OH or an NH on another molecule
  • these are glycosidic bonds and can be 𝛼 or β
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8
Q

Aromatic amino acids

A
  • phenylalanine (nonpolar), tyrosine and tryptophan (more polar)
  • ring structures are similar but their polarity is different
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9
Q

Aromatic ring

A
  • carbons bonded together in a ring with alternating double bonds and saturated with hydrogens; compounds containing 6 C benzene ring
  • electrons are shared equally in these structures so they are non-polar and not very reactive
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10
Q

Blood coagulation

A
  • blood clotting
  • in order for blood to blot, the coagulation enzymes and substrates must assemble on a negative surface
  • calcium bridges between the γ-carboxylated proteins and the membrane surface
  • Vitamin K is required for γ-carboxylation; this is where the drug “warfarin” interferes to prevent clots
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11
Q

Carboxylic acids

A

weak acids; they have a conjugate base that exists in equilibrium with the acid

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12
Q

Central Dogma

A

DNA → RNA → protein

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13
Q

Charged amino acids

A
  • aspartate, glutamate, lysine, arginine, histidine
  • aspartate and glutamate are the negatively charged amino acids
  • arginine, lysine and histidine carry a positive charge
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14
Q

Consequences of non-conservative change

A
  • because glutamate, with a negatively charged group has been replaced by the hydrophobic valine, it can interact with a hydrophobic pocket on another hemoglobin
  • this allows the formation of long strands or polymers of hemoglobin
  • causes RBCs to sickle and prevents it from doing it’s job; delivering oxygen to tissues
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15
Q

Cysteine

A

very important in protein structure because S-S bonds can be formed stabilizing the shape of a protein

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16
Q

D- and L- sugars

A
  • Sugars are named as D “right-handed” or L “left-handed” sugars
  • Sugars with a chiral center (4 different groups attached to the carbon)
  • non-superimposable mirror images of each other
  • named for whether the OH farthest from the carbonyl group is the same as D- or L- glyceraldehyde
  • Most sugars in human tissues are D-sugars
  • Proteins are only composed of L- amino acids
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17
Q

Denaturation

A
  • occurs due to a change in temperature
  • changes in pH cause structural changes due to disruption of the hydrogen and ionic bonds
  • temperature impacts change in shape which impacts function
  • i.e. egg in a hot pan
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18
Q

Deprotonation

A
  • process of losing a proton
  • occurs at high pH
  • low hydrogen concentration
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19
Q

Dissociation of histidine groups

A

histidine is special because it can accept and donate at a low pH

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20
Q

Disulfide bonds

A
  • strong chemical side bonds formed when the sulfur atoms in two adjacent protein chains are joined together
  • groups of two cysteins are oxidized to form cystine
  • important shape stabilizer and often holds different parts of a protein molecule together or two or more chains that make up a protein molecule, i.e. insulin
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21
Q

DNA binding proteins

A

members of the protein globular family; stabilize separated strands

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22
Q

Electronegativity

A
  • oxygen, nitrogen, and sulphur are more electronegative than carbon
  • they form polar bonds and the electrons spend more time around the O, N, S
  • substances with these elements are more hydrophilic
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23
Q

Esters and amides

A
  • formed through condensation reactions
  • if water molecule is lost, it is a condensation reaction
  • CO2 is the anhydride form of carbonic acid H2CO3 (a molecule of water is removed)
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24
Q

Fibrous proteins

A

geometrically linear, arranged around a single axis, and have a repeating unit structure

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25
Q

Free radicals

A
  • have a single electron and exist in solution (or lipid environment) independently
  • many compounds in the body can be turned into free radicals when one of their electrons is removed
  • radiation can also create free radicals
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26
Q

Functional groups

A
  • structures bonded to a carbon chain
  • usually bonds between carbon and oxygen, nitrogen, sulphur and phosphate groups
  • tend to be polar and more reactive
  • infer polarity on the molecule
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27
Q

General amino acid structure

A
  • the alpha carbon is surrounded by a hydrogen atom, amino functional group, carboxyl functional group, R-group
  • chemical properties of the side chains of its amino acids determine how a protein can interact with other molecules
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28
Q

Globular proteins

A

these are compact, generally rounded, and soluble in water

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29
Q

Glycation

A

The covalent binding of a protein or lipid molecule to a glucose molecule

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30
Q

Glycine

A

simplest, smallest amino acid, and the only non-chiral one

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31
Q

Hemoglobin HbA1c

A
  • lifespan of a red blood cell is 120 days
  • measuring HbA1c gives a picture of what kind of conditions the RBCs have been exposed to
  • the higher the blood glucose, the more Hb will be “glycated”
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32
Q

Homologs

A
  • members of a pair of chromosomes
  • different chains of hemoglobin
  • similar in structure but not the same protein
  • similar proteins that have arisen from a common ancestor, often by gene duplication
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33
Q

How is a molecule named?

A

Based on where the functional group is

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34
Q

How many bonds can carbon form?

A

4

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35
Q

Hydrogen bond

A

A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule.

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36
Q

Immunoglobulins

A
  • antibodies that perform important defence functions
  • all have the structure of two light and two heavy chains held together by disulfide bonds
  • antigens are bound at the end of the “Y”, a variable region depending on the specific antibody, alerting the body to invasion
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37
Q

Ionic bond

A

A chemical bond resulting from the attraction between oppositely charged ions; formed when one or more electrons are transferred from one atom to another

38
Q

“ISO”

A

A prefix meaning equal; when two carbons are bonded to another carbon, forming a branch

39
Q

Isoelectric point (pI)

A

the pH at which the molecule is electrically neutral; there is no net charge on the molecule

40
Q

Ketose

A

a monosaccharide that contains a ketone group

41
Q

Levels of protein structure

A

primary, secondary, tertiary, quaternary

42
Q

Methylation

A
  • important in determining whether or not a gene will be expressed
  • makes DNA accessible and less likely that the gene will be transcribed
  • important in whether or not a protein is expressed in our cells
43
Q

Monosaccharides

A
  • glucose, fructose, galactose
  • have three or more carbon atoms, with a ketone or aldehyde group and hydroxyl groups with a general structure of CnH2nOn
  • Fructose is a ketose
  • Glucose is an aldose
44
Q

Non-polar aliphatic amino acids

A
  • glycine, alanine, proline, valine, leucine, isoleucine

- hydrophobic since their electrons are shared and there are no charges to interact with the polar water molecules

45
Q

Oxidation

A

Loss of electrons (loss of H or gain of O)

46
Q

Oxidized and reduced groups

A

C-C groups and C-O groups are “oxidized” or “reduced” depending on the electrons around the carbon atom

47
Q

Peptide bond

A

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid; water is released by the reaction making it a condensation reaction

48
Q

Phenylalanine

A
  • phenyl ring of phenylalanine the carbons and hydrogens equally share electrons, making this group nonpolar and hydrophobic
49
Q

Phosphate

A
  • very important and common functional group
  • makes a molecule for water soluble, hydrophilic
  • oxygen atoms make molecules more polar
50
Q

Phosphoric acid

A
  • H3PO4
  • weak acid
  • one proton lost at low pH, but H2PO4 ↔ HPO4 2- has pKa of 6.8
51
Q

Polar uncharged amino acids

A
  • serine, threonine, cysteine, asparagine, glutamine
  • have side chains containing electronegative O and N atoms
  • side groups are not charged but the electrons are not shared equally, making them polar
  • polarity allows them to interact with polar water molecules, increasing their hydrophilicity
  • water soluble
52
Q

Polymorphisms

A
  • differences in DNA sequences within the human population
  • difference in the primary structure of the beta globin in sickle cell anemia is an example of a polymorphism
  • many genes in the human genome have alternate versions (are polymorphic), and this often has no consequence to the function of the protein
53
Q

Post-translational modification

A
  • changes that occur after proteins are translated
  • ex: gamma-carboxylation
  • some proteins involved in blood coagulation must undergo this in order to bind on the surface of platelets to form a clot
54
Q

Primary structure

A

linear sequence of amino acid residues joined through peptide bonds to form a polypeptide chain

55
Q

Proline

A
  • unique because of its ring structure; much less flexible than other amino acids
  • known as the helix breaker
56
Q

Protein Modification

A
  • the process of affecting enzyme activity by covalently modifying it
  • advanced glycation end-products or “AGEs” result from glycation
  • these are pro-inflammatory molecules that are harmful to cells
57
Q

Protein structure

A
  • the shape of a protein determines its function

- proteins are held in their shape by non-covalent bonds

58
Q

Protein structure rules

A
  • three dimensional structure must be flexible enough to function properly but stable enough that it will not convert to another shape
  • must have amino acids with side groups that are compatible with environments the protein will function in
  • peptide bond that forms the backbone of proteins is that between an amino acid and carboxyl group
  • R-groups are on opposite sides on the bond
59
Q

Protonation

A
  • process of gaining a proton
  • occurs at low pH
  • high hydrogen concentration
60
Q

Protonation and deprotonation

A

when pH < pKa, protonated state

  • when pH>pKa, deprotonated state
  • a large change in pH could cause the addition or dissociation of a proton
  • loss or gain of a proton could cause the breaking of the hydrogen bonds that hold the protein in its proper conformation
  • proteins without the correct tertiary structure cannot perform their function
61
Q

Quaternary structure

A

association of multiple polypeptides, forming a functional protein; will occur if it has multiple subunits that come together

62
Q

Reactivity of Polar Molecules

A
  • partial positive charges on carbon molecules attract negatively charged groups and make reactions more likely
  • carboxylic acids tend to react with a number of compounds, expelling water in a condensation reaction
63
Q

Reduction

A

Gain of electrons (gain of H or loss of O)

64
Q

Retinol-binding protein (RBP)

A

the specific protein responsible for transporting retinol (nonpolar) through the blood

65
Q

Ring structures

A

when most monosaccharides dissolve in water, they form

  • most common form of monosaccharides in solution
  • carbonyl group reacts with a hydroxyl group in the same molecule
  • oxygen from the OH group becomes part of the 5 or 6 C-ring
  • carbonyl carbon has an OH group attached and is “anomeric”
66
Q

Secondary structure

A

recurring structures that form in short, localized regions of the polypeptide chains; consists of alpha helixes or beta sheets

67
Q

Sickle cell anemia

A
  • hereditary disorder of abnormal hemoglobin producing sickle-shaped erythrocytes and hemolysis
  • normal RBCs are flexible and disc-shaped which allows them to travel freely through capillaries
  • sickle cells are crescent shaped and inflexible, causing cells to stick to the inside of capillaries blocking flow to vital organs and tissues
68
Q

Side chain interactions

A
  • charged groups on the amino acids can interact with each other
  • considered an electrostatic interaction or bond (not a hydrogen bond)
  • disulfide bonds are strongest because they are covalent
69
Q

Structure of amino acids in proteins

A
  • properties of side chains on each amino acid dictates the associations between them leading to the shape of the protein
  • shape is very important to function
  • protein cannot maintain their structure if pH or temperature are far out of optimal range
70
Q

Suffix denoting double bonds

A

ene

71
Q

Suffix denoting single bonds

A

ane

72
Q

Suffix for a sugar

A

ose

73
Q

Suffix for a negatively charged

A

ate

74
Q

Sulfur containing amino acids

A
  • cysteine and methionine
  • sulfur can form double bonds to keep proteins together
  • disulfide is strong and covalent
75
Q

Tertiary structure

A
  • finished structure of a protein, contains an alpha helix
  • many proteins stop at tertiary
  • three dimensional shape of protein
76
Q

Transmembrane proteins

A

consists of one or more proteins that have one or more regions aligned to cross the lipid membrane

77
Q

Triglycerides

A
  • also known as triacylglycerols
  • consist of glycerol and three fatty acids
  • fatty acids attached to glycerol are usually different
  • fatty acids are joined to glycerol through ester linkages
  • preference is shown for unsaturated fatty acids
78
Q

Tryptophan and tyrosine

A
  • contain an N and an O that are slightly more electronegative and make these molecules slightly more polar
  • tryptophan contains double bonds
79
Q

What forms the backbone of the polypeptide?

A
  • peptide bonds

- carbons and nitrogens of the amino acids

80
Q

What happens when insulin is released in to the pancreas?

A
  • c-peptide is cut out so if disulfide bonds were not there, they would not work
  • disulfide bonds are crucial in keeping the bond together
  • insulin binds on the outside of the cell which causes a cascade of events inside the cell
81
Q

What is nomenclature?

A

naming system

82
Q

When do acidic groups dissociate?

A

at physiological pH and exist as anions

83
Q

Where is the amino acid located?

A
  • Beginning; n-terminus
84
Q

Which atoms make up organic compounds?

A

Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Sulfur (S), Phosphorus (P)

85
Q

Which carbon is considered number 1?

A

the carbon in the group that is most oxidized

86
Q

Why is it the “alpha” carbon?

A
  • carboxylic acid group is the most oxidized group and alpha carbon is next to it
  • alpha carbon is less oxidized
  • R-side chain is always different
87
Q

Will peptide bonds break on their own?

A

No, peptide bonds are very strong and takes an enzyme to come in and pull it apart; it will not break up on its own

88
Q

“yl”

A
  • suffix: a monovalent hydrocarbon radical e.g. ethyl

- implies that it is a group attached to a compound

89
Q

Zwitterions

A
  • at physiological pH, amino acids are zwitterions where both amino and carboxylic acid groups are charged
  • at this pH the molecule is neutral, this is not the case when pH changes
  • both amino acids cancel each other out
  • depending on pKa of each side chain, the group may be charged or uncharged at physiological pH
90
Q

𝞪-Helices

A
  • common secondary structure in proteins
  • regular repeating structure where the coil is maintained by H-bonds between the H in the N-H bond and the O of the carbonyl group four amino acids away
  • proline is not present
  • maintains it’s structure because hydrogen bonds are forming along the backbone
  • R-groups radiate out from the helix; keeping them far enough apart that the helix is stable
  • more flexible than beta sheets
91
Q

β- Sheets

A
  • maintained by hydrogen bonding between backbone groups
  • has two faces: one side faces polar structure, other faces nonpolar structure
  • can be parallel or antiparallel, depending on orientation
  • more rigid structures than alpha helices
  • can form β-barrels; structures that can transport hydrophobic substances or form pores in membranes

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