BMS527 Lecture 2: Protein Structure and Function

Flashcards covering protein structural levels, fibrous vs. globular distinctions, specific protein mechanisms (keratin, collagen, elastin, actin, hemoglobin, GPCRs), and analytical techniques.

The __________ structure of a protein is defined as the linear sequence of covalent bonded AA.

1°

The __________ structure is the local arrangement of the polypeptide backbone in space, which is very dependent on H-bonding.

2°

The __________ structure describes the overall 3D structure and global fold of a polypeptide.

3°

The __________ structure refers to the arrangement of proteins made up 1+ subunit or polypeptide chain.

4°

Proteins such as collagen and keratin are categorized as __________ proteins based on their elongated, filamentous structure.

Fibrous

Proteins like haemoglobin and immunoglobulins are classified as __________ proteins because they are round and spherical.

Globular

Fibrous proteins typically have __________ AA sequences and low solubility in water.

Repetitive

Globular proteins are more sensitive to changes in __________ and pH compared to fibrous proteins.

heat

The dominant structural motifs in fibrous proteins are __________ structures.

secondary

__________ is the predominant type of keratin found in humans, occurring in hair and fingernails.

$\alpha$-keratin

The keratin predominant in birds and reptiles, which adopts beta sheets, is __________.

$\beta$-keratin

In $\alpha$-keratin, large hydrophobic residues occur every __________ AA, creating a hydrophobic side on the helix.

4

The structure resulting from two $\alpha$-keratin molecules interacting is known as a __________.

coiled-coil

Crosslinking in keratin by __________ bonds b/w adjacent polypeptide chains increases the rigidity of the protein.

disulfide

The most abundant protein in the human body is __________.

Collagen

The basic unit of collagen is a triple-strand left-handed helix called __________.

tropocollagen

The collagen helix has __________ AA/helical turn.

3.3

Collagen contains the repetitive tripeptide motif __________, where X and Y are often proline or hydroxyproline.

Gly-X-Y

The enzyme prolyl hydroxylase requires __________ and $Fe^{2+}$ to convert proline to hydroxyproline in collagen.

Ascorbate

__________ is a post-translationally modified AA in collagen that serves as a site for carbohydrate modification.

Hydroxylysine

In collagen, __________ and regular lysine can crosslink across chains to stabilize the structure.

Allysine

In contrast to collagen, __________ is a connective tissue protein with rubber-like properties that lacks a regular secondary structure.

Elastin

Elastin forms __________ cross links b/w strands via 4 lysine side chains.

desmosine

The desmosine ring in elastin is formed when 3 epsilon amino groups of lysine are oxidized to produce __________.

allysine

Elastin is degraded by a protease called __________, which is released by neutrophils.

elastase

The protein __________ is primarily produced in hepatocytes and serves to inhibit proteases like elastase.

$\alpha 1$-antitrypsin

In inherited AAT deficiency, a substitution of __________ for K leads to protein polymerization and reduced secretion from hepatocytes.

E342

Globular monomers of actin are referred to as __________.

G actin

Filamentous actin, or __________, is formed when globular monomers bind with ATP.

F actin

F-actin assembly involves the hydrolysis of __________ followed by the slow release of Pi.

ATP

Adaptive immune response includes __________ (antibody) and cellular components.

humoral

An IgG antibody is composed of two identical heavy chains and two identical __________ chains.

light

Specificity to antigenic determinants in antibodies is conferred by the __________ domains.

variable

Proteolytic separation of an IgG antibody yields two $F_{ab}$ fragments and one __________ fragment.

$F_c$

The __________ fold consists of two antiparallel $\beta$ sheets stacked face to face.

immunoglobulin

Hypervariable sites in antibody sequences are also known as __________.

CDR loops

A hallmark of __________ is a dramatic increase in serum IgG containing "incorrect" sugar residues.

rheumatoid arthritis

Membrane-spanning regions of proteins are typically rich in __________ aa.

hydrophobic

A __________ is a non-polypeptide unit required for the biological function of proteins like hemoglobin.

prosthetic group

The heme group contains an iron atom in the __________ state held in the center of a porphyrin ring.

$$Fe^{2+}$$

In myoglobin, the __________ histidine binds directly to heme.

proximal

In myoglobin, the __________ histidine helps stabilize oxygen binding.

distal

Myoglobin consists of __________ alpha helices and serves as an oxygen reservoir in muscle.

8

Hemoglobin is a $65\text{-kD}$ heterotetramer characterized by the subunit composition __________.

$$\alpha_2\beta_2$$

In the __________ form of hemoglobin, the dimers are constrained and have a low affinity for oxygen.

T

In the __________ form of hemoglobin, the dimers are relaxed and have a higher affinity for oxygen.

R

Oxygen acts as a positive __________ effector, increasing hemoglobin's affinity for more oxygen binding.

homotropic

The oxygen dissociation curve for hemoglobin is __________, indicating cooperative binding.

sigmoidal

The metabolite __________ binds to an allosteric site in hemoglobin, decreasing its affinity for oxygen.

2,3-bisphosphoglycerate

At high altitudes, the expression of __________ is elevated to allow greater unloading of oxygen in tissues.

2,3-BPG

Carbon dioxide binds to the __________ of the hemoglobin polypeptide chain.

N terminus

Carbon monoxide binds tightly to Fe in heme and shifts hemoglobin to the __________ state.

R

Fetal hemoglobin (HbF) is a tetramer composed of two alpha chains and two __________ chains.

$\gamma$

Sickle cell anaemia is caused by a mutation of __________ for V in the beta strand of hemoglobin.

E6

G protein-coupled receptors (GPCRs) contain __________ transmembrane alpha-helices.

7

G proteins are heterotrimers consisting of the subunits __________.

$G\alpha$, $G\beta$, and $G\gamma$

Activation of the $G\alpha$ subunit occurs when __________ is swapped for GTP.

GDP

__________ ion channels are regulated by changes in membrane potential near the channel.

Voltage-gated

Receptor tyrosine kinases (RTKs) are examples of __________ receptors.

Enzyme linked

In electrophoresis, the __________ gel acts as a sieve, allowing smaller molecules to pass through faster.

polyacrylamide

__________ is a method for analyzing proteins in their native, non-denatured conformation.

Native PAGE

In isoelectric focusing, proteins migrate through a pH gradient until they reach a point where pH = __________.

pI

__________ electrophoresis separates proteins based only on size by denaturing them and masking their charge.

SDS PAGE

The reagent __________ adds a negative charge to the entire protein molecule for denaturing gel electrophoresis.

SDS

In __________ chromatography, larger proteins elute from the column first.

size exclusion

__________ chromatography uses beads with a specific charge to retain proteins of the opposite charge.

Ion exchange

To remove retained proteins from an ion exchange column, a wash with __________ or a pH gradient is used.

salt

__________ chromatography uses stationary phase beads with a specific ligand or antibody that the protein of interest binds to.

Affinity

The __________ assay is an absorbance-based colorimetric method used to determine protein concentration.

Bradford

The Bradford assay uses the dye __________, which turns blue upon binding to protein.

Coomassie brilliant blue

In the Bradford assay, protein binding causes a shift in absorbance from $465\,nm$ to __________.

$$595\,nm$$

Over 75% of protein structures have been solved using __________.

X-ray crystallography

A major downside of X-ray crystallography is that the conditions for protein __________ may not be physiologically relevant.

crystallization

NMR spectroscopy typically involves labeling proteins with isotopes such as __________ and $^{15}N$.

$$^{13}C$$

Unlike crystallography, __________ is primarily performed with proteins in solution, allowing for the study of dynamic conformations.

NMR spectroscopy

A limitation of NMR is that it is virtually impossible to study __________ proteins due to their hydrophobic nature.

membrane

Collagen polypeptide chains are __________ and glycosylated to aid fibril formation.

crosslinked

The affinity of hemoglobin for the last oxygen molecule is __________ times greater than for the first.

300

In the absence of __________, hemoglobin functions like myoglobin and refuses to release oxygen in peripheral tissues.

2,3-BPG

The $F_{ab}$ region of an antibody contains __________ immunoglobulin folds.

4

Actin filaments remodel the cellular architecture using __________ contractility.

myosin-II

Elastin is composed primarily of small, __________ aa.

non-polar

Proline acts as a secondary structure breaker but supports the helical conformation of collagen by putting regular __________ in the structure.

kinks

The conversion of prolyl residues to hydroxyprolyl residues in collagen is an example of a __________ modification.

post-translational

In GPCR signaling, the activated $G\alpha$ subunit separates from the __________ dimer to act on second messenger pathways.

$$G\beta/\gamma$$