Group 8/14/19 Flashcards
Learning issues and look ups
Here are our learning issues for Friday:
Biochemistry of amino acids (Marks’ Ch6)
Biochemistry of protein structure (Marks’ Ch7)
Innervation from the wrist down
functions of proteins in the body
transport hydrophobic compounds attach cells to each other and ECM hormones that carry signals ion channels in lipid membranes enzymes to speed up reactions
primary structure
linear sequence of amino acids that determines the unique characteristics of a protein
genetic code
sequence of 3 bases (nucleotides) in DNA that contains the information for the linear sequence of amino acids in the polypeptide chain (its primary structure)
mutations
changes in the nucleotides of a gene that result in a change in the products of that gene that might be inherited
general structure of an amino acid parts
carboxylic acid group: COO-
amino group: H3N+
hydrogen atom
side chain
what configuration is the alpha carbon of an amino acid in?
L-configuration, characteristic of all mammalian proteins’ amino group
what is the name for a free amino acid at physiological pH? Characteristic?
zwitterion, has positively charged amino group and negative carboxylate
zwitterion
ion in which the amino acid is positively charged and the carboxylate group is negatively charged
what joins amino acids?
amino acids are joined by peptide bonds to form polypeptide chains.
how are amino acids grouped by the polarity of the side chain?
charged, nonpolar hydrophobic, or uncharged polar
how are amino acids grouped by structural features?
aliphatic, cyclic, aromatic
what characteristic do nonpolar hydrophobic proteins share?
they’ll cluster together and exclude water
what characteristic do the uncharged polar amino acids share?
participate in hydrogen bonding
which amino acid forms disulfide bonds?
cysteine, contains a sulfhydrl group
which amino acids are acidic, what characteristic do they share?
aspartate and glutamate are negatively charged and acidic
which amino acids are basic, what characteristic do they share?
lysine, arginine, and histidine, are positively charged and they are basic (arginine most basic)
what determines the charge on the amino acid?
the pKa (- log of the Ka, the dissociation constant)
polymorphism and example
a polymorphism is a genetically determined variation in primary structure
example is hemoglobin in humans
what is the relationship between pKa and the acidity
the pKa will be low for things that are acidic
what is the connection between pKa and pH?
if the pH is lower than the pKa, the acidic groups will be protonated, meaning they’ll have a positive charge
name the two terminals of the side chains
carboxyl terminal: last amino acid in chain, has free carboxylate group
amino terminal: first amino acid in the chain, has free amino group
hydropathic index and interpretation
a scale used to denote the hydrophobicity of the side chain
more positive means more hydrophobic
nonpolar, aliphatic amino acids names
glycine, alanine, proline, valine, leucine, isoleucine
aromatic amino acids names, and their polarity
phenylalanine (nonpolar hydrophobic), tyrosine (polar), tryptophan (polar)
polar, uncharged amino acids names
asparagine, glutamine, serine, threonine
sulfur-containing amino acids names
methionine, cysteine
charged amino acids names
aspartate, glutamate, arginine, lysine, histidine
glyine structure and function
R: H
not a lot of steric hindrance, usually in bends or chains
structure of aliphatic, polar, uncharged amino acids
contains amide group: asparagine, gluatmine
contains hydroxyl group: serine and threonine
hydrogen bonding, with each other or other polar compounds
usually found on surface of water-soluble globular proteins
cysteine structure
R: CH2-SH (sulfhydryl group)
can form disulfide bonds with each other
methionine structure
R: CH2-CH2-S-CH3
nonpolar, bulky hydrophobic side chain, doesn’t form disulfide bonds. Important metabolic role is to transfer terminal methyl group to other compounds.
isoelectric point (pI) and significance in testing
pH at which the net charge on the molecules in the solution is 0
molecules will not migrate in an electric field toward the positive pole (cathode) or negative pole (anode)
electrophoresis
technique used to separate proteins on the basis of charge
variant regions
regions of the primary structure that are noncritical and thus variations are tolerated
hypervariable
region of primary structure where different amino acid residues are all tolerated at one position
invariant regions
regions that form binding sites or are critical for forming a 3D structure. Will have exactly the same amino acid sequences between individuals.
polymorphism
variation of an allele (alternate forms of gene at same place on chromosome) that occur with a significant frequency in the population
paralogs
divisions of a protein family that are considered to be different proteins and have different names, because they have different functions
isoforms/isozymes
different forms of a protein/enzyme that have different properties of the amino acid structure, and may have different locations in the body.
They all have the same function (isoforms) or catalyze the same reactions (isozymes)
Hemoglobin (Hb) isoforms
Good example of protein that has isoforms. Expressed as fetal isozyme HbF during development, then replaced with HbA.
Proteins have different structures, making functions different, HbF has higher affinity for O2
posttranslational modification
after protein synthesis, usually when the protein is folded, amino acid residues in primary structure may be further modified by reactions that add a chemical group, oxidize, etc.
examples are trimming and covalent alternations (phoshorylation, glycosylation, hydroxylation, methylation, acetylation, ubiquitination)
glycosylation and types
the addition of carbohydrates to a molecule
types: O-glycosylation and N-glycosylation
fatty acylation
the addition of lipids to a molecule
usually for membrane proteins, lipid group will interact hydrophobically with the other membrane lipids
phosphorylation
protein kinase takes a phosphate group from an ATP to phosphorylate a hydroxyl group
introduces large, negatively charged group that can alter structure and protein activity
ADP-ribosylation
transfer of an ADP-ribose from NAD+ to arginine, glutamine, or cysteine residues on target protein in membrane
regulates the activity of the proteins
secondary structure of proteins
local regions of polypeptide chains formed into structures that are stabilized by repeating patterns of hydrogen bonds, e.g. alpha-helices and beta-sheets
what determines the types of secondary structure that can occur?
rigidity of the peptide backbone
tertiary structure of proteins
involves folding of the secondary structural elements into an overall 3D conformation.
Can allow ligands to bind, allow diffusion of elements in and out, flexibility, changing positions, and puts important residues on surface
quaternary structure
only some proteins have this. Involves a combination of two or more subunits, each composed of a polypeptide chain.
These can allow cooperative binding of ligands, binding sites for other molecules, or increase the stability of a molecule
General examples include dimers, tetramers, oligomers (refers to number of subunits that make up protein)
quaternary structure of fibrous proteins
their polypeptide chains are aligned along an axis, have repeating elements, and are linked to each other through hydrogen and covalent bonds
what conformation does a protein fold into for tertiary structure?
folds into its stable/native conformation
chaperonins*
helps the protein fold into its stable conformation by helping to overcome kinetic and thermodynamic barriers
prion proteins
act as a template for protein misfolding and cause neurodegenerative diseases. Can get prion diseases through infection, or may be a normal protein that was misfolded.
denaturation, and common causes
denaturation is when the protein unfolds, or refolds and loses their native 3D conformation
can be caused by heat, acid, or other agents
globular proteins
small irregular balls, usually soluble in aqueous medium. Usually has a densely packed hydrophobic core with polar amino acid side chains on the outside facing the aqueous environment.
fibrous proteins
linear proteins arranged in single axis, have repeating unit structure
transmembrane proteins
have one or more regions aligned to cross the lipid membrane
alpha helix
maximizes hydrogen bonding, highly compact rigid structure
peptide backbone has hydrogen bonding within the same strand. H bonds form between each carbonyl oxygen atom and amide hydrogen of further-down amino acid residue
Beta sheets
maximizes hydrogen bonding between peptide backbones while maintaining allowed torsion angles
hydrogen bonding between neighboring polypeptide chains arranged parallel to each other, optimal when the sheet is bent/pleated
nonrepetitive secondary structures
bends, loops and turns of secondary structure do not have a repeating element of hydrogen bond formation.
Usually more flexible than alpha helices and beta sheets, sometimes form hinge regions. Characterized by abrupt change of direction, usually on the protein surface.
motifs
relatively small arrangements of secondary structure that are recognized in many different proteins
structural domains
physically independent regions of tertiary structure, usually can be identified visually in large complex proteins, because they can have different structures
solubility of globular proteins in aqueous environment
most globular proteins are cell-soluble. Usually have hydrophobic core, and charged or polar uncharged amino acids are on the surface/outside.
protomer
unit structure composed of nonidentical subunits
what is Ka vs. Kd in the context of ligand binding?
Ka is the association constant for the reaction between the ligand and the protein. Calculated by [LP]/[L][P]
Kd is the dissociation constant, which is reciprocal of Ka
how does Ka indicate the binding site’s affinity for the ligand?
tighter binding of the ligand to the protein means higher Ka and lower Kd
myoglobin vs. hemoglobin structure
both oxygen binding proteins with similar primary structure, have heme in hydrophobic pocket, binds to Fe2+
myoglobin is globular protein with single polypeptide chain with one oxygen binding site
hemoglobin is tetramer with 2 different subunit types with oxygen binding sites
differences in myoglobin and hemoglobin at different PO2’s
when partial pressure of oxygen (PO2) is high, both myoglobin and hemoglobin saturated with oxygen
at low levels of PO2 in oxygen-using tissues, myoglobin binds better than hemoglobin, so myoglobin is more saturated with oxygen at lower PO2
heme
planar porphyrin ring composed of 4 pyrrole rings linked by methenyl bridges that lie with their nitrogen atoms in the center, and bind to the Fe2+ atom
prosthetic group
organic ligands that are bound tightly to proteins, such as the heme of myoglobin
holoprotein vs. apoprotein
holoprotein- protein with its attached prosthetic group
apoprotein- protein without prosthetic group
cooperativity of O2 binding in hemoglobin
conformational changes take pace in tertiary structure when O2 binds to hemoglobin. Changes from tense to relaxed state when O2 binds, and increases affinity for more O2. Called positive cooperativity, creates sigmoidal oxygen saturation curve of hemoglobin.
what degree of structure will determine the folding of a protein?
primary structure determines protein folding
collagen structure*
made from a precursor procollagen, a triple helix with 3 polypeptide chains twisted around each other to form a ropelike structure. They’re linked by hydrogen bonds, and glycine (lacks side chain) is present when the strands come in close contact with each other.
Has lots of hydroxylated residues
denaturation through nonenzymatic modifications of proteins
Examples are nonenzymatic oxidation or glycosylation. In glycosylation, glucose binds and acculumates advanced glycosylation end products (AGEs)
protein denaturation by temperature, pH and solvent
proteins can be denatured by changes of pH, temperature, or solvent that disrupt ionic, hydrogen, or hydrophobic bonds
steps of protein synthesis*
initiation, elongation, and termination
initiation*
eukaryotic initiation factors (eIFs) find either the 5’ cap or an internal ribosome entry site (IRES)
eIFs help combine the 40s subunit with the initiator tRNA
mRNA and 60s subunit will assemble with the complex
eukaryotic vs prokaryotic ribosomal subunits in initiation*
eukaryotes: 40S and 60S -> 80S
prokaryotes: 30s and 50s -> 70s
which processes of initiation are ATP vs GTP used for?*
ATP is used for tRNA activation (charging)
GTP is used for tRNA translocation (gripping and going places)
what are the different elongation sites and their function?*
A site holds the incoming Aminoacyl-tRNA
P site accomodates the growing Peptide
E site holds the Empty tRNA as it Exits
steps of elongation*
- aminoacyl-tRNA binds to the A site, requiring an elongation factor and GTP
- rRNA (ribozyme) catalyzes peptide bond formation, transfer growing polypeptide to amino acid in A site
- Ribosome advances 3 nucleotides toward the 3’ end of mRNA, translocation moves the peptidyl tRNA to P site
termination process of protein synthesis*
a release factor recognizes the stop codon and halts translation. The completed polypeptide is released from the ribosome. Requires GTP.
trimming*
a posttranslational modification where the N- or C- terminal propeptides are removed from zymogen to generate a mature protein (example: trypsinogen t trypsin)
collagen and types*
organizes and strengthens the extracellular matrix
type 1, type 2, type 3 and type 4
mnemonic to remember the different collagen types*
[Be So Totally] Cool, Read Books corresponds to the 4 types of collagen
type 1 collagen*
Be So Totally: in the Bone, Skin and Tendons, as well as dentin, fascia, cornea, late wound repair
type 2 collagen*
Cool: located in Cartilage, especially hyaline; also found in vitreous body, nucleus pulposus
type 3 collagen*
Read: Reticulin, found in the skin, blood vessels, uterus, fetal tissue, granulation tissue
type 4 collagen*
Books: found in the Basement membrane (type 4 under the floor)
collagen synthesis process*
- synthesis: collagen alpha chains are translated (preprocollagen), usually has Gly-X-Y structure
- hydroxylation of some proline and lysine residues, requires vitamin C
- glycosylation of pro-alpha-chain hydroxylysine residues and formation of procollagen via hydrogen and disulfide bonds, to form triple helix of collagen alpha chains
- exocytosis of procollagen into extracellular space
- disulfide-rich terminal regions of procollagen are cleaved to form insoluble tropocollagen
- covalent lysine-hydroxylysine cross-linkages reinforce tropocollagen molecules to make collagen fibrils
what are the essential amino acids?*
PVT TIM HaLL: Phenylalanine, Valine, Tyrosine, Threonine, Isoleucine, Methionine, Histidine, Leucine, Lysine
what are the glucogenic amino acids?*
I MET HIS VAlentine, she is so sweet: Methionine, histidine, valine
glucogenic/ketogenic amino acids?*
isoleucine, phenylalanine, threonine, tyrosine
ketogenic amino acids?*
the onLy pureLy ketogenic amino acids: leucine, lysine
elastin location*
a stretchy protein within skin, lungs, large arteries, elastic ligaments, vocal cords, ligaments flava (connect vertebrae)
elastin structure*
rich in nonhydroxylated proline, glycine, and lysine residues
cross-linkage takes place extracellularly, has tropoelastin with fibrillin scaffolding
