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BIO130—sec 1 MR > week 2 > Flashcards

week 2 Flashcards

1
Q

what is the primary sequence of a protein?

A

The a.a. sequence, most simple

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2
Q

what is the secondary structure of a protein?

A

local folding i.e. alpha helix, beta sheet

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3
Q

what is the tertiary structure of a protein?

A

long-range folding, 3D structure, overall shape

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4
Q

what is the quaternary structure of a protein?

A

multi-metric organization

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5
Q

what proteins have a quaternary structure?

A

proteins that have more than one polypeptide chain

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6
Q

what part of the amino acid structure is variable and determines the type of amino acid?

A

The R group (side chain)

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7
Q

what are the four major categories of amino acids?

A

acidic, basic, (both important to overall structure) uncharged polar (H-bond in water), nonpolar (often found in interior of protein and lipid bilayer)

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8
Q

why is cysteine a unique amino acid?

A

due to -SH grp, it can form disulphide bonds (disulphide bridges)

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9
Q

To form a peptide bond, what groups react?

A

The carboxyl group on one a.a. and the amino group on another a.a

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10
Q

What type of reaction forms a peptide bond

A

condensation reaction (releases water)

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11
Q

what does ‘residue’ refer to?

A

a.a. w/n peptide chain (what is left over after loss of H2O)

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12
Q

How many H-bonds are there in a alpha helix for each residue?

A

n+4

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13
Q

where are some common places that alpha helices are found?

A

skin, hair, cell membranes (lipid bilayer)

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14
Q

approximately how many residues long is an alpha helix?

A

10

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15
Q

what kind of bonding is associated with an alpha helix?

A

local H-bonding

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16
Q

Where does H-bonding occur in a beta sheet?

A

between the carbonyl oxygen of one a.a. and the amide hydrogen of an a.a. in a NEIGHBOURING strand

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17
Q

Are R groups involved in structure of beta sheet

A

no

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18
Q

how many beta strands does a beta sheet usually contain

A

4-5 (can contain up to 10)

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19
Q

why can alpha helices and beta sheets form from many types of a.a. sequences?

A

R-grps are not involved

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20
Q

what is the difference in bonding between an alpha helix and a beta sheet

A

alpha helix forms bonds between a.a. four residues away, beta sheet forms bonds b/w neighbouring strands

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21
Q

What are the two types of beta sheet?

A

parallel and anti-parallel

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22
Q

In beta sheet diagrams, where do the arrows point

A

towards the carboxyl end of protein/strand

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23
Q

which type of beta sheet needs more a.a. between strands?

A

parallel

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24
Q

which atoms are hydrogen bonded in secondary structures?

A

carbonyl oxygen & amide hydrogen—in peptide backbone, not R grp

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25
What kind of secondary structure is a coiled coil?
amphipathic alpha helix
26
amphipathic
has both hydrophobic and hydrophilic parts
27
why are coiled coils amphipathic?
non-polar a.a. forma stripe down the helix
28
where are coiled coils found?
alpha-keratin of skin, hair and also myosin motor proteins
29
where does the hydrophilic end of a coiled coil face?
aqueous environment
30
what level of protein structure are alpha helix, beta sheet, and coiled coil?
secondary structure
31
what holds together the tertiary structure of a protein?
hydrophobic interactions, non-covalent bonds, covalent disulphide bonds
32
what conformation do proteins generally fold into?
The most energetically favourable conformation
33
what do chaperone proteins do?
help make the protein folding process more efficient and reliable.
34
are electrostatic interactions involved in tert. structure?
yes
35
Protein domains are a portion of a protein that has its own ________________
tertiary structure
36
protein domains function in a __________________ manner
semi-independent
37
how many protein domains do eukaryotic proteins often have
2 or more
38
how are protein domains connected
intrinsically disordered sequences (allow flexibility, conformation can change)
39
what are protein domains specialized for?
different functions
40
What are protein domains important for?
the evolution of proteins
41
what do kinases do?
they phosphorylate proteins (add on a phosphate grp)
42
How many protein domains does Src protein kinase have? List them
Three: kinase domain, SH3, SH2 (regulates)
43
what similarities to members of the same protein family share?
similar aa sequences and tertiary structures
44
what have members of the same protein family evolved to have differently?
different functions (but related)
45
most proteins belong to families with similar structural _____________
domains
46
protein families are groups of proteins with common
evolutionary origin
47
domains are added if useful through
natural selection
48
how many subunits does hemoglobin have? Name them.
4: 2 alpha, 2 beta
49
each subunit of hemoglobin is a separate ____________
polypeptide
50
sickle cell anemia is caused by ______________ in hemoglobin
mutation in the beta subunit
51
hemoglobin is an example of a protein with ____________ structure
quaternary (it has more than one pp chain)
52
multi protein complexes can be:
many identical subunits, mixtures of different proteins and DNA/RNA, dynamic assemblies of proteins to form molecular machines
53
what is an example of a multiprotein complex with identical subunits
actin filaments
54
what is an example of a multiprotein complex with different proteins and DNA/RNA
viruses and ribosomes
55
what is an example of a molecular machine
machines for DNA replication initiation or for transcription
56
what is scaffold?
an entity (usually protein but can be RNA) that binds proteins and gets them in close enough proximity that they can interact
57
pros and cons of AI being used to predict protein structure
very powerful, speeding up the study of proteins, not perfect
58
what is proteomics
large scale study of proteins (looking at interactome): identity and structure of proteins, protein-protein interactions, abundance and turnover, location in cell or tissue
59
what stabilizes the positive charge in some side chains?
resonance: causes greater basicity (basic side chains have a positive charge)
60
when are both amino and carboxyl grps ionized
at a neutral pH (7)
61
what is the result of the alpha carbon being asymmetric?
Allows for L and D isomers
62
what atoms are involved in a peptide bond
C, N (bond is b/w them), carbonyl O, amine H
63
is there rotation around the C-N bond
no, the four atoms in a peptide bond form a rigid planar unit
64
why are long chains of aa flexible
single bonds b/w Cs allow for rotation
65
what charge do acidic side chains have?
negative
66
what groups do uncharged polar side chains have on their end
either -NH2 or -OH
67
nonpolar side chain primary consist of __________
hydrocarbons
68
every molecule of a protein has the exact same _________
amino acid sequence
69
The polypeptide backbone is formed from a repeating sequence of what core atoms?
N-C-C
70
what gives each aa its unique properties
side chains
71
why is the folding process energetically favourable?
it releases heat
72
how can a protein be denatured/unfolded?
with solvents that disrupt the noncovalent interactions holding the chain together
73
renaturation
when a protein refolds spontaneously (will often happen under right conditions)
74
can proteins fold into their correct conformation w/o the help of chaperone proteins?
yes
75
isolation chambers
formed by chaperone proteins, where a single polypeptide chain can fold w/o the risk of forming aggregates in the crowded conditions of the cytoplasm
76
amyloid structures
beta sheets stacked together in long rows with their aa side chains interdigitated (like the teeth of a zipper), sometimes formed from misfolded proteins
77
what disorders are amyloid structures thought to contribute to?
neurodegenerative disorders e.g. Alzheimer's and Huntington's disease
78
what can misfolded prions do?
convert properly folded version of a protein to the abnormal conformation
79
why are prions considered infectious
they can spread from an affected individual to a normal individual
80
the modular unit from which many larger proteins are constructed is called
protein domain
81
Binding site
any region on a protein's surface that interacts with another molecules through sets of noncovalent bonds
82
what happens when a binding site recognizes the surface of a second protein?
the tight binding of the two folded pp chains (subunits) at this site will create a larger protein
83
Dimer
a symmetrical complex of two protein subunits formed from the folding of two identical pp chains
84
what holds dimers together?
interactions b/w two identical binding sites
85
pp chain folded up into a compact shape like a ball with an irregular surface is called
globular protein
86
fibrous proteins
span a large distance, relatively simple elongated 3-D structure
87
gel-like, formed from fibrous proteins, helps bind cells together to form tissues
extracellular matrix
88
how are extracellular proteins stabilized?
covalent cross linkages
89
what happens inside the nucleolus
ribosomal RNAs are transcribed and ribosomal subunits are assembled

BIO130—sec 1 MR (5 decks)

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