Biology Exam 1 Lecture 3

Question 1

_____ is an excellent “example” protein

Answer 1

Hemoglobin

Question 2

hemoglobin is a ____ in which each subunit binds a ___ group which then binds an _____

Answer 2

heterotetramer, heme, oxygen

Question 3

Proteins fold into conformations that represent ___

Answer 3

energy minima

Question 4

Unfolded proteins are said to be ____

Answer 4

denatured

Question 5

____ in the cell help proteins fold into their correct conformations

Answer 5

Molecular chaperones

Question 6

What are the 4 levels of structural organization in proteins?

Answer 6

Primary- linear amino acid sequence
Secondary- folding patterns
Tertiary- 3D organization of secondary structures, Protein domains
Quaternary- organization of protein complexes

Question 7

A protein’s structure will be determined by its ____.

Answer 7

primary sequence.

Question 8

Relevant parts of the protein will be the ____ and the side chains or ___ of each specific amino acid.

Answer 8

polypeptide backbone, R-groups

Question 9

Which of the four types of amino acids is represented by the most members?

Answer 9

Non-polar

Question 10

Proteins can fold into many possible ____,
however energetics drives them to ___ ____ _____
for each protein. Folding starts _____

Answer 10

conformations, one stable one, co-translationally

Question 11

_____ bonds serve to generate structure
in proteins. These can occur between R groups or parts of the polypeptide backbone

Answer 11

Weaker, non-covalent

Question 12

In cells different _____
help to fold and refold proteins

Answer 12

chaperones

Question 13

_____ interactions will often help to drive interactions placing non-polar groups
near the ____ of the protein’s structure.

Answer 13

water, center

Question 14

Modifications like N- and
O-linked ____ can
influence structure

Answer 14

glycosylation

Question 15

In the cytosol, which sequence of amino acid side chains would most likely be found in the interior structure of a globular protein?

uncharged polar – hydrophobic – basic
basic – basic – hydrophobic
nonpolar – nonpolar – nonpolar
acidic – acidic – uncharged polar
They are all equally likely to be on the protein’s outside

Answer 15

nonpolar – nonpolar – nonpolar

Question 16

____in proteins are part of _____
They are often arrangements of linked regions of alpha helices and beta sheets.

Answer 16

Domains, tertiary structure

Question 17

______ between domains can
provide a variety of functions

Answer 17

Unstructured regions

Question 18

what is the favored conformation when all of the R groups locally
are hydrophobic?

Answer 18

alpha helices

Question 19

A protein’s primary structure is dependent upon _____ bonds that _____.

Answer 19

peptide; link adjacent amino acids

Question 20

Z-Mapp is a drug treatment used for Ebola – what is it?

Answer 20

A “cocktail” of inhibitory antibodies

Question 21

____ can form _____ ____ ______, which can
help stabilize protein structures in harsh environments.

Answer 21

Cysteines, covalent disulfide bridges

Question 22

Antibodies contain many intra- and inter-polypeptide _____ that help maintain their conformations

Answer 22

disulfide bridges

Question 23

Two other extracellular proteins containing many disulfide
bridges

Answer 23

collagen and elastin

Question 24

Non-protein components of proteins -

Answer 24

retinal (rhodopsin), heme (hemoglobin)

Question 25

A common theme in cells is ___ ____of subunits
into a ____ - this is particularly true with regard to
cytoskeletal proteins

Answer 25

dynamic assembly, filament

Question 26

Weaker, non-covalent bonds also are key to specific _____ binding of proteins. This occurs through the formation
of _____.

Answer 26

ligand, binding sites

Question 27

Specific membrane compartments such as lysosomes and peroxisomes can be isolated from cell lysates by differential centrifugation? T or F

Answer 27

True

Question 28

Gel filtration chromatography:

Answer 28

Can separate proteins based on size/shape

Question 29

Different _____ ______ ______
have different separation properties that will cause proteins to interact with them in distinct ways. This allows using different columns to either bind and concentrate a protein or exclude it while binding other contaminating proteins.

Answer 29

column chromatography matrices

Question 30

True/False: Two ways that antibodies can be used for immunodetection of cellular proteins are:

1. By decorating them with gold particles to enable their visualization in EM when bound to cell proteins
2. By labeling them for use in detecting proteins extracted from cells and separated on gels then blotted to membranes (so called immunoblot)

Answer 30

True

Question 31

The structure or conformation of a protein can be predicted by certain methods and also empirically determined by biochemical methods such as ____ and _____ as well as enzymatic methods.

Answer 31

NMR, X-Ray crystallography

Question 32

Antibodies are highly useful for…

Answer 32

detection and purification of specific proteins

Question 33

______ is now a very commonly used method of determining protein identity
and modification ______

Answer 33

Mass spectrometry, proteomics

Question 34

Proteins can be studied by mass spectrometry – in this method:

Answer 34

Proteins are fragmented and sized to identify them

Question 35

Ribozymes are…

Answer 35

Catalytic RNA molecules thatact as enzymes

Question 36

Prions:

Answer 36

Proteinaceous Infectious Particles

Question 37

Prion Diseases:

Answer 37

Spongiform Encephalopathies, Bovine spongiform encephalopathy

Question 38

Prion Properties:

Answer 38

Transmissible
No nucleic acid component
Species barriers
Protein present in normal cells

Question 39

Protein conformation changes underlie prion formationand formation of ____

Answer 39

amyloid fibers

Question 40

Prions, commonly denoted PrPSc,
can ____ their conformation to
cellular PrP

Answer 40

template

Question 41

Spongiform encephalie

Answer 41

Formation of protein aggregates
or plaques in brain cells,
these lead to lysosomal lysis
and the formation of holes
in tissues where now dead cells
once resided.

Question 42

_____and _____ carry out the reversible modification of many substrate proteins

Answer 42

Protein kinases, phosphatases

Question 43

T/F : Phosphorylation of some substrates by protein kinases can serve to inactivate protein functions.

Answer 43

True

Question 44

For proteins regulated by GTP/GDP binding, it is the case that:

Answer 44

GTP is bound to the protein and converted to GDP + Pi as it acts on another protein.

The protein with GDP bound releases GDP and then binds a new molecule of GTP to do another cycle of regulation

Question 45

The ____ level or _____ of any individual species of protein in the cell will be a unique function of the factors controlling both its ____ (production) and _____ (destruction).

Answer 45

steady state, concentration

synthesis, degradation

Question 46

The half-life of a protein is half the average number of minutes (or hours) the protein spends in the cell. This can be determined by a ____

Answer 46

pulse-chase experiment.

Question 47

Proteins originate on ____ or on ____

Answer 47

free ribosomes, ribosomes directed to the ER

Question 48

Misfolded proteins in the cell can be degraded by what structures?

Answer 48

Proteasomes

Question 49

The posttranslational modification that targets proteins to the proteasome is?

Answer 49

Ubquitylation

Question 50

what are Proteasomes?

Answer 50

Proteasomes are multi-protein complexes found in the cytosol and nucleus

Question 51

what do proteasomes do?

Answer 51

They function to receive and degrade cellular proteins that are damaged or that have been specifically targeted for degradation by modification with ubiquitin.

Question 52

What are Lysosomes?

Answer 52

Lysosomes are a membrane bound cellular compartment containing proteases and dedicated to the degradation of proteins found in membranes or soluble proteins imported into the cell

Question 53

what is actin?

Answer 53

Actin - An example of sequestering proteins
regulating protein assembly and function

Question 54

Sequestration – The activities of proteins can be controlled by _____that _______. Another type of sequestration involves _____ – for example some transcription factors are held in the cytosol until signals cause modifications that allow their entry into the nucleus where they can function

Answer 54

sequestering proteins, bind and prevent assembly.

localization

Question 55

Many enzymatic reactions or pathways are
self-regulated by ___ mediated
by the end products

Answer 55

feedback inhibition

Question 56

True or False:Feedback inhibition typically occurs by enzymes sensing too much product for their reaction building up via a special regulatory site on the enzyme

Answer 56

True

Question 57

When a protein binds a ligand or another protein and this induces a conformational change that opens another binding site in the molecule this is known as:

Answer 57

allosterism

Question 58

An ____ change due to binding of a ligand that promotes the binding of a second ligand

Answer 58

allosteric

Question 59

Kinases _____ phosphate groups, which ____ substrate proteins.

Answer 59

add; activate or deactivate

Question 60

4 key mechanisms plus many others control protein activities:

Answer 60

1. Modification by attachment of ubiquitin to lysine residues
2. Modification by protein phosphorylation/dephosphorylation
   Occurs on polar non-charged residues – ser, thr, tyr
3. Nucleotide binding and hydrolysis
4. Modification by lipid anchor addition to C terminal Cys
5. Other modifications include proteolytic processing, methylation, acetylation and glycosylation of specific amino acids in proteins, among many others.

Question 61

By modifying proteins, cells create_____

Answer 61

at least two potential states of activity for any modified protein.

Question 62

if the modification or ligand binding is
_____, as many are, the protein can run through many cycles of function

Answer 62

reversible

Question 63

Dynamics of the _____ are regulated by ____ and_____ through the cell cycle

Answer 63

nuclear lamins, phosphorylation and dephosphorylation

Question 64

Phosphatases _____ phosphate groups, which ____ substrate proteins

Answer 64

remove; activate or deactivate

Question 65

GTP hydrolysis inactivates

Answer 65

GTP-binding proteins

Question 66

Binding GTP activates

Answer 66

GTP-binding proteins

Question 67

“histone code”

Answer 67

methylation
phosphorylation
acetylation

Question 68

____ and _____ occur as
covalent modifications of _____

Answer 68

methylation, acetylation

basic amino acids

Question 69

***T/F : Phosphorylation of some substrates by protein phosphatases is typically reversible

Answer 69

False***