Quiz 3- Biochem Flashcards
4 types of protein structure
Globular proteins, fibrous proteins, transmembrane proteins, DNA binding proteins
Aldose
a monosaccharide that contains an aldehyde group
Aliphatic
A compound containing carbon and hydrogen joined together in straight chains, branched chains or non-aromatic rings
Amines
- 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
Amino acid in proteins
- 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
Anomeric
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.
Anomers of Cyclic Glucose
- 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
Aromatic amino acids
- phenylalanine (nonpolar), tyrosine and tryptophan (more polar)
- ring structures are similar but their polarity is different
Aromatic ring
- 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
Blood coagulation
- 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
Carboxylic acids
weak acids; they have a conjugate base that exists in equilibrium with the acid
Central Dogma
DNA → RNA → protein
Charged amino acids
- aspartate, glutamate, lysine, arginine, histidine
- aspartate and glutamate are the negatively charged amino acids
- arginine, lysine and histidine carry a positive charge
Consequences of non-conservative change
- because glutamate, with a negatively charged group has been replaced by the hydrophobic valine, it can interact with a hydrophobic pocket on another hemoglobin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
Cysteine
very important in protein structure because S-S bonds can be formed stabilizing the shape of a protein
D- and L- sugars
- 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
Denaturation
- 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
Deprotonation
- process of losing a proton
- occurs at high pH
- low hydrogen concentration
Dissociation of histidine groups
histidine is special because it can accept and donate at a low pH
Disulfide bonds
- 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
DNA binding proteins
members of the protein globular family; stabilize separated strands
Electronegativity
- 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
Esters and amides
- 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)
Fibrous proteins
geometrically linear, arranged around a single axis, and have a repeating unit structure
Free radicals
- 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
Functional groups
- 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
General amino acid structure
- 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
Globular proteins
these are compact, generally rounded, and soluble in water
Glycation
The covalent binding of a protein or lipid molecule to a glucose molecule
Glycine
simplest, smallest amino acid, and the only non-chiral one
Hemoglobin HbA1c
- 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”
Homologs
- 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
How is a molecule named?
Based on where the functional group is
How many bonds can carbon form?
4
Hydrogen bond
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.
Immunoglobulins
- 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
Ionic bond
A chemical bond resulting from the attraction between oppositely charged ions; formed when one or more electrons are transferred from one atom to another
“ISO”
A prefix meaning equal; when two carbons are bonded to another carbon, forming a branch
Isoelectric point (pI)
the pH at which the molecule is electrically neutral; there is no net charge on the molecule
Ketose
a monosaccharide that contains a ketone group
Levels of protein structure
primary, secondary, tertiary, quaternary
Methylation
- 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
Monosaccharides
- 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
Non-polar aliphatic amino acids
- glycine, alanine, proline, valine, leucine, isoleucine
- hydrophobic since their electrons are shared and there are no charges to interact with the polar water molecules
Oxidation
Loss of electrons (loss of H or gain of O)
Oxidized and reduced groups
C-C groups and C-O groups are “oxidized” or “reduced” depending on the electrons around the carbon atom
Peptide bond
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
Phenylalanine
- phenyl ring of phenylalanine the carbons and hydrogens equally share electrons, making this group nonpolar and hydrophobic
Phosphate
- very important and common functional group
- makes a molecule for water soluble, hydrophilic
- oxygen atoms make molecules more polar
Phosphoric acid
- H3PO4
- weak acid
- one proton lost at low pH, but H2PO4 ↔ HPO4 2- has pKa of 6.8
Polar uncharged amino acids
- 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
Polymorphisms
- 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
Post-translational modification
- 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
Primary structure
linear sequence of amino acid residues joined through peptide bonds to form a polypeptide chain
Proline
- unique because of its ring structure; much less flexible than other amino acids
- known as the helix breaker
Protein Modification
- 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
Protein structure
- the shape of a protein determines its function
- proteins are held in their shape by non-covalent bonds
Protein structure rules
- 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
Protonation
- process of gaining a proton
- occurs at low pH
- high hydrogen concentration
Protonation and deprotonation
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
Quaternary structure
association of multiple polypeptides, forming a functional protein; will occur if it has multiple subunits that come together
Reactivity of Polar Molecules
- 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
Reduction
Gain of electrons (gain of H or loss of O)
Retinol-binding protein (RBP)
the specific protein responsible for transporting retinol (nonpolar) through the blood
Ring structures
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”
Secondary structure
recurring structures that form in short, localized regions of the polypeptide chains; consists of alpha helixes or beta sheets
Sickle cell anemia
- 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
Side chain interactions
- 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
Structure of amino acids in proteins
- 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
Suffix denoting double bonds
ene
Suffix denoting single bonds
ane
Suffix for a sugar
ose
Suffix for a negatively charged
ate
Sulfur containing amino acids
- cysteine and methionine
- sulfur can form double bonds to keep proteins together
- disulfide is strong and covalent
Tertiary structure
- finished structure of a protein, contains an alpha helix
- many proteins stop at tertiary
- three dimensional shape of protein
Transmembrane proteins
consists of one or more proteins that have one or more regions aligned to cross the lipid membrane
Triglycerides
- 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
Tryptophan and tyrosine
- contain an N and an O that are slightly more electronegative and make these molecules slightly more polar
- tryptophan contains double bonds
What forms the backbone of the polypeptide?
- peptide bonds
- carbons and nitrogens of the amino acids
What happens when insulin is released in to the pancreas?
- 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
What is nomenclature?
naming system
When do acidic groups dissociate?
at physiological pH and exist as anions
Where is the amino acid located?
- Beginning; n-terminus
Which atoms make up organic compounds?
Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Sulfur (S), Phosphorus (P)
Which carbon is considered number 1?
the carbon in the group that is most oxidized
Why is it the “alpha” carbon?
- 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
Will peptide bonds break on their own?
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
“yl”
- suffix: a monovalent hydrocarbon radical e.g. ethyl
- implies that it is a group attached to a compound
Zwitterions
- 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
𝞪-Helices
- 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
β- Sheets
- 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
