Proteins Flashcards
What is a protein?
Linear polymers of amino acids
What is a peptide bond formation?
The creation of an amide bond between the carboxyl group (-COO) of one amino acid and the amino group (-NH3) of another amino acid
What is the structure of the backbone of a protein chain?
Repeated sequence (N-Ca-C)
Three things that create a peptide bond formation
- Amide bond
Between - Carboxyl group (-COO) of amino acid
- Amino group (-NH3) of another amino acid
Most proteins use _____ amino acids
all
What is Ribonuclease?
The enzyme that breaks down RNA molecules
R-side chains (inside) are _____
Hydrophobic
The atoms around the peptide bond (CO-NH) are ____________
Coplanar
Outside of proteins are __________
Hydrophilic
How was the phylogenetic tree constructed?
By comparing the amino acid sequences of the protein cytochrome c
What are the two terminal ends of proteins?
-Amino terminal end (HOOC)
- Carboxyl terminal end (NH2)
What type of bond are disulfide bonds?
Covalent bonds
Do proteins have spaces?
No
What is lysosome?
An extracellular protein
How many disulfide bonds are in a protein?
Any number
List the sizes of proteins from smallest to largest
Insulin, cytochrome, ribonuclease, lysosome, myoglobin, hemoglobin, immunoglobin, glutamine sythetase
Shape of insulin
A + B chain
Shape of cytochrome
Single chain
Shape of ribonuclease
Single chain
Shape of lysozyme
Single chain
Shape of myoglobin
Single chain
Shape of hemoglobin
4 chains
(2 alpha)
(2 beta)
Shape of immunoglobulin
4 chains
Shape of glutamine synthetase
12 chains
Where are the number of amino acid changes listed on the phylogenetic tree?
The number of amino acid changes are given on the branches
What is released during a peptide/amide bond formation?
Water
A phylogentic tree compares amino acid sequences of the protein ______
Cytochrome C
_____ proteins require something bound to them to activate
Conjugated
The binding of nonprotein groups affect protein ____
Folding
Glycoproteins contain ____
Carbohydrates
Lipoproteins contain _____
Lipids
Nucleoprotein complexes contain ___
Nucleic acid
Phosphoproteins contain _____
Phosphate
Metalloproteins contain _____
Metal atoms
Hemoproteins contain _____
Heme
Flavoproteins contain ____
Flavin
Glyco means
Carbohydrate
Lipo means
Lipid
Nucleo means
DNA or RNA
Metallo means
Metal ion
Biological functions of proteins:
Enzymes
Ribonuclease, trypsin
Biological functions of proteins:
Regulatory proteins
Insulin, transcription factor NF -1
Biological functions of proteins:
Transport Proteins
Hemoglobin, glucose transporter
Biological functions of proteins:
Storage Proteins
Casein, ovalbumin
Biological functions of proteins:
Contractile, Motile Proteins
Actin, myosin, tubulin
Biological functions of proteins:
Structural Proteins
Collagen, a-keratin
(Hair & fingernails)
Biological functions of proteins:
Protective Proteins
Immunoglobulins, fibrinogen
(antibodies)
Biological functions of proteins:
Exotic Proteins
antifreeze proteins, glue proteins
Protein Techniques:
Chromatography
- ion exchange chromatography
- size exclusion chromatography
- affinity chromatography
Ion exchange chromatography
Separates proteins on the basis of their overall charge
Size exclusion chromatography
Separates proteins on the basis of size
Affinity chromatography
Separates proteins on the basis of affinity (specific binding to small molecules)
Protein Techniques:
Electrophoresis
- SDS-PAGE
- Isoelectric focusing
- Two dimensional gel electrophoresis
SDS-PAGE electrophoresis
Separates proteins on the basis of molecular weight
Isoelectric focusing
Separates proteins on the basis of Isoelectric point (pI)
Electrophoresis
The movement in an electric field
Two dimensional gel electrophoresis
Separates proteins on the basis of isoelectric point (pl) and molecular weight (a) + (b)
Protein Shape:
Fibrous Proteins
- Linear, serve structural roles
Protein Shape:
Globular Proteins (aq environment)
- Hydrophobic on amino acids on inside
- Hydrophilic amino acids on outside
Protein Shape:
Membrane Proteins (hydrophobic environment)
- Interact with membrane lipids
- Hydrophobic amino acids on *outside
- in entirely different environment than globular proteins
Collagen is an example of what protein shape?
Fibrous protein
Myoglobin is an example of what protein shape?
Globular protein
Bacteriorhodopsin is an example of what protein shape?
Membrane protein
What is primary structure?
Amino acid sequence of a protein
What is secondary structure?
- Short range 3D structure in a protein
- Localized conformation of the polypeptide backbone
What are the two types of secondary structure?
- a-helix
- b-strand
What causes a secondary structure?
Due to H-bonding of backbone atoms (-CO-NH-)
What is tertiary structure?
Folding of a polypeptide into its 3D shape
What causes a tertiary structure?
Due to R-side chain interactions
What are the 4 properties of tertiary structures?
1.Hydrophobic
2. H-bonding
3. Charge
4. Disulfide bonds
lots of weak interactions make strong interaction
What are quaternary structures?
- Numbers and kinds of polypeptide subunits in a protein
- Polypeptide chains in a protein with multiple subunits
What are the levels of protein structure?
Primary, secondary, tertiary, quaternary
What does the sequence of amino acids that go from the amino terminal end to the carboxyl terminal end tell you?
- What type of protein
- Function of protein
- Everything you need to know about proteins
What causes the a-helix in secondary structure?
H-bonding along one strand
What causes the b-strand in secondary structure?
H-bonding between two or more strands
In secondary structure, each C=O is _____ _____ to the N-H group ____ ____ _____ along the chain
hydrogen bonded, four amino acids
What are the two types of the B-strand in secondary structures?
- Parallel
- Antiparallel
- Can both exist in the same protein
- Can form extensive B-pleated sheet structures
This type of secondary structure is formed by hydrogen bonding of C=O and N-H groups along the backbone of a single polypeptide chain
a-helix
How many amino acid residues per turn of the helix?
3.6 amino acids per turn of the helix
Is the a-helix left or right handed?
Right handed
What is the pitch of the a-helix?
5.4A
What is the diameter of the a-helix?
6A
What stabilizes the a-helix structure?
Hydrogen bonds
Are the B-strands hydrogen bonding between or within strands?
The hydrogen bonding is between strands
What is the arrangment of B-strands in the secondary structure?
Parallel and antiparallel
Are parallel B-strands linear or bent?
Bent
Are antiparallel B-strands linear or bent?
Linear
The ______ B-strand is the most common
Antiparallel
The ____ B-strand is the strongest
Antiparallel
The four horizontal ______ form an antiparallel B-Plated sheet with _____ strands in _____ directions
B-strands, adjacent, opposite
B-pleated sheets follow the __ and ____
peaks and valleys
Antiparallel B-plated sheets are very ____
stable
B-turn is a ____ _____ in the ______ _____ that allows the strand to _____ its direction
sharp bend
polypeptide chain
reverse
The B-turn ____ the direction of the strand
reverses
Tertiary structure is the _______ of a ____ _____ ___ in 3D
folding, single polypeptide chain
Globular proteins contain segments of both ____ and ____, while fibrous proteins have _____ ____ ____
a-helix, b-strand, specialized tertiary structure
What three things make up fibrous proteins?
- Collagen
- a-keratin
- Fibroin and B-keratin
The special collagen helix consists of three interwined polypeptide chains
Collagen
Formed by the coiling of a-helices
a-keratin
Consists primarily of B-sheet
B-keratin
What is tropocollagen?
A triple helix
What is the main protein of connective tissue?
Collagen
Makes up 25-35% of the whole body
Collagen
How many common types of collagen are there?
28 types
Type l collagen -
Most abundant, found in tendons, ligaments, skin, blood vessels, bone
Type ll collagen -
Cartilage, found in joints between bones, rib cage, nose, ears
What is the sequence of formation of tropocollagen and collagen?
- Procollagen
- Tropocollagen
- Cross-linked fiber
Amino & carboxyl terminal ends - peptides DO NOT twist together
Procollagen
Protein component of skin, hair, fingernails are made up of _____
a-keratin
Cute amino & carboxyl terminal ends of procollagen
Peptidases
2 coiled coils (4 a-helices)
protofilament
4 protofibrils (32 a-helices)
intermediate filament
2 protofilaments (8 a-helices)
protofibril
Two a-helices
coiled coil
Pair of coiled coils
protofilament
Four right hand twisted protofibrils
filament
Disulfide bond formation creates ____ in hair
curls
Main silk protein
Fibroin
B-sheet of _____
Fibroin
Component of bird feathers, beaks, claws
B-Keratin
Antiparallel arrangement of B-sheet
Strands in opposite directions
Parallel arrangement of B-sheet
Strands in same direction
Antiparallel or parallel arrangment most stable?
Antiparallel
Globular proteins can be classified according to the type and arrangement of secondary structure:
- All a-helix proteins
- All b-strand proteins
- a/B proteins
- Proteins with little secondary structure
What are the four classes of globular protein structures? (ABBA LSS)
- All a-helix proteins
- All b-strand proteins
- a/B proteins
- Proteins with little secondary structure
A typical globular protein is _____
ribonuclease
Example of a-helix
growth hormone
Example of a b-strand
yB-crystallin (lens cornea of eye)
Example of a/B proteins
Flavodoxin (bacteria)
Example of protein with little secondary structure
Tachystatin (antimicrobial peptide)
What type of globular protein is ribonuclease?
a/B protein
Protein domains are also known as ____
modules
Protein domains or modules are ___ ____ ____ that are used repeatedly in the same protein or that are found in different proteins
amino acid sequences
How main amino acids does a protein domain typically contain?
40-100
Produced by the duplication of DNA segments within a gene or by the insertion of a copy of DNA segment into another gene
Protein domains
Protein domains are produced by the _____ of DNA segments within a gene
protein domains
Protein domains can be produced by the ____ of a copy of a DNA segments into another gene
insertion
Protein domains are produced by _____ or _____ of DNA segments
duplication or insertation
___ ____ are amino acid sequences used repeatedly in a single protein or that are found in different proteins
Protein domains/modules
What type of protein domain is unusual and less common?
different proteins
Domains in the ____ occur from faulty DNA replication
same protein
Domains in ____ occur after the insertion of a copy of a DNA segment into another gene
different proteins
Some domains are ___ and their function is unknown
neutral
Domains ___ over time and become unrecognizable to the original
mutate
Protein folding is the process of folding a _____ ___ into a ___ ___ with a precise 3D structure
polypeptide chain, globular protein
Step 1 of protein folding
- newly synthesized polypeptide first forms segments of secondary structure (a-helix & B-sheet)
Step 2 of protein folding
- These coalesce into a globular structure, primarily through hydrophobic interactions
Step 3 of protein folding
- The final stable tertiary structure is generated by small adjustments to the folded structure
Step 4 of protein folding
- In the cell, protein folding may require the assistance of molecular chaperones
In general the #D of folding of extended protein chain is dependent upon the ___ ___ ___ of that protein chain
amino acid sequence
(1) protein folding: A newly synthesized protein first forms segments of ___ ___
secondary structure
(2) protein folding: secondary structure of polypeptides arrange into a ____ shape by _____ interactions
globular, hydrophobic
(3) protein folding: final stable tertiary structure is generated by ____ _____ to the folded structure
small adjustments
Secondary structure of polypeptide arrange into a globular shape by _____ ____
hydrophobic interactions
(4) protein folding: Protein folding may need the assistance of ___ ___
molecular chaperones
Amyloid deposits
misfolded, insoluble, and aggregated proteins in brain cells
Two examples of amyloid deposits
Alzheimer’s disease
Parkinson’s disease
What protein is misfolded in Alzheimers disease?
amyloid-B
What protein is misfolded in Parkinson’s disease?
a-synuclein
(1) step globular protein folding
rapid and reversible formation of local secondary structure (a-helix, B-strand)
(2) step globular protein folding
establishment of partially folded intermediates
(3) step globular protein folding
final tertiary structure
The association of protein subunits to form multi-subunit complexes is ____
quaternary structure
Do all proteins have quaternary structure?
NO
Proteins with quaternary structure are composed of ____ subunits or ____ types of ____ ____
identical , different, protein chains
The ____ producing quaternary structure are the same as those responsible for tertiary structure
forces
What four forces are involved in tertiary and quaternary structures?
- hydrophobic int
- hydrogen bonding
- ionic int
- disulfide bons
Quaternary structure allows for ___ ____ between protein subunits
cooperative behavior
In hemoglobin, there are ___ subunits
4
How does hemoglobin exhibit cooperative behavior?
The binding of the first O2 molecule makes it easier for three other O2 molecules to each bind to a subunit
Hemoglobin aides in what physiological function?
rapid release of O2 into the lungs
What are the two types of quaternary structure?
- fixed number of subunits
- open structure of microtubules
What are microtubules?
long, hollow tubes
Where are microtubules found?
cytoskeletion (cell structure)
mitotic spindles (cell division process)
Tubulin dimers ___ to form microbtubules
polymerize
Microtubules are dynamic and can easily ___
increase or decrease in length
Microtubules have ___ quaternary structure
open
