MOD 2 L2 Flashcards
1
Q
how many species of tRNA
A
20
2
Q
proteins can be described in four ways
A
▫ Primary
▫ Secondary
▫ Tertiary
▫ Quaternary structure
3
Q
the sequence of the amino acids in the chain and the disulfide links.
A
PRIMARY
4
Q
arrangement of amino acids
A
SEQUENCE
5
Q
peptide bond
A
PRIMARY
6
Q
structure formed by hydrogen bonding. Examples are α-helix and β-pleated sheet.
A
SECONDARY
7
Q
complete 3-D conformation
A
TERTIARY
8
Q
association of two or more peptide chains to form protein.
A
QUATERNARY
9
Q
not all amino acids undergo this structure. only hemoglobins
A
QUATERNARY
10
Q
linear sequence of amino acids
A
PRIMARY
11
Q
units of secondary structure
α-helix β-sheet β-turns loops
A
SECONDARY STRUCTURE
12
Q
associations of secondary structure
α-α, β-α-β, greek key, helix-loop-helix
A
SUPERSECONDARY STRUCURE
13
Q
units of tertiary structure
all alpha, all beta, α/β, αβ
A
DOMAIN STRUCTURE
FOLDS OR MODULES
14
Q
associations of domain structures
multidomain (mosaic) or single domain
A
TERTIARY STRUCTURE
15
Q
association of tertiary structure
two or more polypeptides each polypeptide a subunit
A
QUATERNARY STRUCTURE
16
Q
The primary structure of a protein is its linear sequence of amino acids and the location of any ____
A
DISULFIDE BRIDGE
17
Q
The primary structure of a protein is defined by the
A
sequence of amino acids
18
Q
the sequence of amino acids forms the
A
PROTEIN
19
Q
each component amino
acid
A
“residue” or “moiety”
20
Q
number of amino acids
A
number of residues
21
Q
describes the way that the chain of amino acids folds itself due to intramolecular hydrogen bonding.
A
SECONDARY STRUCTURE
22
Q
Two common secondary structures
A
α-helix
β-sheet
23
Q
how long is the typical α-helix
A
11 amino acids long
24
Q
how many residues/turn in α-helix
A
3.6
25
Amino acids such as **A, D, E, I, L and M (small aminoa acids)** favor the formation of
α-helices
26
favor **disruption** of the helix (producing a **bend**)
G & P
27
The ____ is **important** as it introduces **additional folding** of the polypeptide backbone to **allow the formation of globular proteins**.
DISRUPTION OF THE HELIX
28
1 complete rotation
0.54 nm
3.6 residues
29
Cα-N bond is termed
phi angle
30
phi Φ angle
-57º
31
CO-Cα bond is termed
psi angle
32
psi ψ angle
-47º
33
**fibrous protein** whose structure is nearly entirely α-helical
KERATIN
34
a **globular**, **flexible** molecule whose structure is approximately **80%** α-helical.
HEMOGLOBIN
35
responsible for the formation of H-bonding
BETA PLEATED SHEET
36
* Composed of 2 or more different **regions of stretches** of at least **5-10 amino acids**.
* **Stabilized** by **H-bonding** between amide N’s and carbonyl C’s.
* **H-bonding residues** are present in adjacently opposed stretches of the polypeptide backbone.
BETA PLEATED SHEET
37
same direction
PARALLEL
38
different direction
anti-parallel
39
When the H-bonds are formed **between the polypeptide backbones** of **separate polypeptide chain**, they are termed
INTERCHAIN BONDS
40
The H-bonds of a β-sheet formed by a **single** polypeptide chain **folding back on itself** are termed
INTRACHAIN BONDS
41
Found in both **fibrous** and **globular** proteins
β-sheet protein
42
composed of **twisted** β-pleated sheet fibrils whose **3D structure** is **identical** to that of **silk fibrils**.
AMYLOID PROTEIN
43
are regions that contain **residues beyond the minimum number** necessary to **connect adjacent regions** of secondary structure.
LOOPS
44
refer to **short segments** of amino acids that **join two units** of secondary structure
TURNS & BENDS
45
involves **4 aminoacyl residues**, in which the 1st residue is H-bonded to the 4th, resulting in a **180° turn**.
β turn
46
are often present in β turns
PROLINE & GLYCINE
47
Also known as **Structural motifs**
SUPERSECONDARY STRUCTURES OR FOLDS
48
* maintains the **three dimensional shape** of the protein (give shape to the secondary structure).
* The amino acid chain (in the helical, pleated or random coil form) **links itself** in places to form the **unique twisted** or **folded shape** of the protein.
TERTIARY STRUCTURE
49
# ways to stabilize its tertiary shape
**disulfide bridges formed** when two cysteine molecules combine in which the –SH groups are oxidized
COVALENT BONDING
50
# ways to stabilize its tertiary shape
between **polar groups** on the side chain.
HYDROGEN BONDING
51
# ways to stabilize its tertiary shape
(ionic bonds) formed between –NH3+ and –COO- groups
SALT BRIDGES
52
* **Binding** of a substrate or other ligands.
* **Anchor** a protein to a membrane.
* **Interact** with a regulatory molecule that modulates its function.
FUNCTIONS OF DOMAIN
53
# FUNCTIONS OF DOMAIN
Binding of a ____ or other ____.
substrate, ligands
54
# FUNCTIONS OF DOMAIN
Anchor a ____ to a ___
protein, membrane
55
# FUNCTIONS OF DOMAIN
Interact with a ____ that modulates its function
REGULATORY MOLECULE
56
These tend to form **ball-like structures** where **hydrophobic parts** are **towards the center** and **hydrophilic** are **towards the edges**, which makes them **water soluble**.
GLOBULAR
57
The proteins form **long fibers** and mostly consist of **repeated sequences of amino acids** which are **insoluble in water**.
FIBROUS
58
* **Favor protein folding**
* Between **oppositely charged** R-groups such as K or R and D or E.
CHARGE-CHARGE
59
* Interaction of **ionized R-groups** of amino acids with the **dipole** of the water molecule.
CHARGE-DIPOLE
60
* The **slight dipole** moment that exist in the polar R-groups of amino acid also influences their interaction with water.
* **Majority** of the amino acids found on the **exterior surfaces** of globular proteins contain **charged or polar R-groups**.
DIPOLE-DIPOLE
61
involve the **interactions** among **induced dipoles** that arise from **fluctuations** in the charge densities that occur between adjacent **uncharged non-bonded atoms**.
ATTRACTIVE VAN DER WAALS FORCES
62
involve the **interactions** that occur when **uncharged non-bonded atoms** come **very close together** but **do not induce dipoles**.
REPULSIVE VAN DE WAALS
63
only proteins with **more than one chain** have a
QUATERNARY STRUCTURE
64
Many proteins are **not**
SINGLE STRANDS
65
proteins with **multiple polypeptide chains**; can be composed of multiple **identical** polypeptide chains or multiple **distinct** polypeptide chains.
OLIGOMERIC PROTEINS
66
oligo means
FEW
67
proteins with **identical** subunits
HOMOOLIGOMERS
68
proteins containing several **distinct** polypeptide chains.
HETEROOLIGOMERS
69
* The **oxygen carrying protein** of the blood.
* Contains two α and two β subunits arranged with a **quaternary structure** in the form, α2β2
HEMOGLOBIN
70
hemoglobin is a ____ protein
HETEROOLIGOMERIC
71
Protein fold and unfold in
| time
milliseconds
72
participate the **first time** the protein is folded, but not in subsequent folding
RIBOSOMES
73
**Information needed** for **correct protein folding** is contained in the
PRIMARY STRUCTURE
74
**Native conformation** of a protein is ____ favored
THERMODYNAMICALLY
75
Folding is
MODULAR
76
assist folding
AUXILLARY PROTEINS
77
* **Specialized group** of protein required for the **proper folding** of many species of proteins.
* PCB (Polypeptide chain-binding) protein.
* Acts as **catalysts** by **increasing** the **rates of the final stage** in the folding process.
CHAPERONES
78
* Do not **convey steric information**.
* Do not **form part of the final structure**.
* **Suppress** **non-productive interactions** by binding to transiently exposed portions of the polypeptide chain.
* First identified as **heat shock proteins (Hsp)**.
* Hsp expression is **elevated** when cells are grown at **higher-than-normal temperatures**.
* Use an **ATP-dependent mechanism**.
CHAPERONES
79
chaperones are first identified as
HEAT SHOCK PROTEINS
80
**HSP** expresion is **elevated** when cells are grown at
higher than normal temp
81
# TYPES OF CHAPERONES
* thought to **bind** and **stabilize** the nascent polypeptide chain as it is being **extruded** from the ribosome.
* also involved in "**pulling**" newly synthesized polypeptide into ER lumen.
* bind **short sequences** of
hydrophobic amino acids thus,
**shielding** them from solvent.
HSP70 (cytoplasm, ER,
chloroplasts, mitochondria)
82
# TYPES OF CHAPERONE
forms large **28-subunit
complexes** called **GroEL**
HSP60 (mitochondria,
chloroplasts)
83
provides a **sheltered environment** in which a polypeptide can fold until all hydrophobic regions are **buried** in its interior, thus **eliminating aggregation**.
CHAPERONINS
84
Facilitates formation of disulfide bonds that **stabilize** a protein’s **native conformation**.
PROTEIN DISULFIDE ISOMERASE
85
“**rescue**” unfold proteins
CHAPERONE
86
reduces **inappropriate** disulfide bond
GLUTATHIONE
87
* **Disruption** of the normal structure of a protein, such that it **loses biological activity**.
* Some proteins will **return** to their native structures **under proper conditions**; but **extreme conditions**, such as strong **heating**, usually c**ause irreversible change**.
PROTEIN DENATURATION
88
Changes in temperature & pH can denature ____ a protein so it **no longer works**.
UNFOLD
89
facilitates proper folding
SECONDARY STRUCTURE
90
group of enzyme that can **catalyze interconversion** from **cis** to **trans**
ISOMERASE
91
Cis configuration is commonly found in
β-turns
92
loss of biological activity
DENATURATION
93
regain biological activity
RENATURATION
94
regain biological activity
RENATURATION
95
**unfolding** and **disorganization** of protein structure (not accompanied by hydrolysis of peptide bond)
PROTEIN DENATURATION
96
what is being destroyed by the denaturants?
HYDROGEN BONDS
97
# PD AGENTS
hydrogen bonds are broken by increased **translational** and **vibrational energy**. (**coagulation of egg white albumin on frying**)
HEAT
98
# PD AGENT
Similar to heat
(**sunburn**)
ULTRAVIOLET RADIATION
99
# PD AGENT
**salt** formation; disruption of hydrogen bonds. (skin **blisters** and **burns**, **protein precipitation**.)
STRONG ACIDS OR BASES
100
# PD AGENTS
**competition** for hydrogen bonds.
(**precipitation** of **soluble** proteins.)
UREA
101
# PD AGENT
(e.g. ethanol & acetone) change in **dielectric constant** and **hydration** of **ionic groups**.
(**disinfectant** action and precipitation of protein.)
SOME ORGANIC SOLVENTS
102
# PD AGENT
**shearing** of hydrogen bonds.
(beating egg white albumin into a **meringue**.)
AGITATION
103
Denatured proteins are often ____ and therefore **precipitate** from solution.
INSOLUBLE
104
rare cases
reversible
105
most proteins
PERMANENT
106
* Transmissible **spongiform encephalopathies**.
* **Fatal neurodegenarative diseases** characterized by **spongiform** changes, **Astrocytic gliomas**, and neuronal loss resulting from the deposition of insoluble protein aggregates and neural cell.
* Includes:
a) Creutzfeldt-Jakob disease (Human)
b) Scrapies (sheep)
c) Alzheimer's disease
d) Bovine spongiform encephalopathy (Mad Cow Disease) in cattle
e) **Scurvy**
PRION DISEASES
107
# PRION DISEASES
HUMAN
CREUTZFELDT-JAKOB DISEASE
108
# PRION DISEASE
SHEEP
SCRAPIES
109
# PRION DISEASE
CATTLE / COW
BOVINE SPONGIFORM ENCEPHALOPATHY / MAD COW DISEASE
110
* for **cellular**
* The normal protein has its secondary structure dominated by alpha helices (probably 3 of them)
* is **easily soluble**
* is **easily digested** by proteases
* is **encoded** by a gene designated (in humans) **PRNP** located on our chromosome 20.
PrPc
111
**gene** designated in **humans** that is located in **chromosome 20**
PRNP
112
* for **scrapie**
* The abnormal, **disease-producing protein**
* Primary structures are **identical** but its secondary structure is dominated by beta conformation
* is **insoluble** in all but the **strongest solvents** is **highly resistant** to digestion by proteases
* When this comes in contact with PrPC, it **converts** the PrPC into **more of itself**
* These molecules **bind to each other** forming **aggregates**.
PrPSc
113
PrPc & PrPSc bind to each other and forms
AGGREGATES
114
* **Refolding** or **misfolding** of β - amyloid in human brain tissue.
* **Elevated levels** of β - amyloid undergoes conformational transformation.
ALZHEIMER'S DISEASE
115
**Genetic defects** that **impair** the synthesis of **one polypeptide sub-units (β)** of **hemoglobin**.
BETA - THALASSEMIA
116
absence of one globulin, whether β or α
THALASSEMIA
117
* A **small change** in the sequence of the primary structure **can have a significant impact** on protein structure
* a **glutamic acid** is **replaced** by a **valine** in the amino acid **sequence**
SICKLE CELL ANEMIA
118
**Substitution** of one amino acid for another in hemoglobin causes
SICKLE CELL DISEASE
119
a protein that causes alzheimer's disease
APOLIPOPROTEIN E
120
**Blood sugar level** is controlled by a protein called
INSULIN
121
* Causes the **liver** to **uptake** and **store** **excess sugar as glycogen**.
* The **cell membrane** also contains proteins.
INSULIN
122
# INSULIN
help cells **recognize** other cells
RECEPTOR PROTEINS
123
**tags** aged protein for **degradation**
UBIQUITIN
124
degradation happens through
HYDROLYSIS
125
Ribosome size
30s, 50s
