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Chapter 1 Flashcards

1
Q

What are the four main types of macromolecules?

A

Lipids, Carbs, Proteins, nucleic acids

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2
Q

Two types of carbs and their energy usage

A

Monosaccharide: quick energy source
Polysaccharide: energy storage

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3
Q

Function of lipids

A

energy storage and structure

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4
Q

Function of nucleic acids

A

storage and transfer of genetic info

DNA and RNA

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5
Q

Function of proteins

A 
Structure
Regulation 
Signaling 
Transport 
Enzymes 
Motor proteins
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6
Q

Structures of proteins

A

Primary: linear sequence of amino acids
Secondary: beta sheets or alpha helices
Tertiary: three dimensional shapes
quaternary : polypeptides into multi chain complexes

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7
Q

Organelles of a cell and their functions

A

Nucleus:
Mitochondria: powerhouse of the clel
Golgi Apparatus: package and secretion
Ribosome: creation of proteins
Lysosome: getting rid of waste
smooth ER: lipid production and metabolism
Rough ER: helping with creationg of proteins

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8
Q

What help to keep cells together and to communicate

A

Junctions: tight junctions, gap junctions

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9
Q

Two components of cell metabolism

A

anabolic: building, uses ATP
catabolic: breaking down creates ATP

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10
Q

Polypeptide structure details

A

held together by peptide bonds
Amino acid end (Nterminus)
carboxyl end (c terminus)

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11
Q

What are chaperones

A

class of proteins that help to promote protein folding
found in all organisms
located everywhere in cell

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12
Q

Two types of chaperones

A

molecular: stabilizing polypeps and prevent degradation
Chaperonins: directly help fold polypeptides

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13
Q

What dictates the proper folding

A

primary amino acid sequence

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14
Q

Types of modifications

A 
acetylation
fatty acid
phosphorylation:
gylcosylation
methylation
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15
Q

Acetylation

A

adding acetyl group (Ch3CO) to N terminus

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16
Q

Fatty acid modification

A

adding long chain hydrocarbon to ends

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17
Q

Phosphorylation

A

adding phosphate (PO4) to serine, threonine, tyrosine, or histidine residue

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18
Q

Glycosylation

A

addition of carbohydrate to serine, threonine or asparagine

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19
Q

Methylation

A

addition of methyl group

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20
Q

why do cells degrade proteins

A

misfolded
foreign
amino acids from food
need to decrease cytoplasmic concentration of protein

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21
Q

How do cells degrade extracellular pathways

A

Digestive proteases- break down proteins we eat
endopeptidases- cut polypeptides at specific sites
exopeptidases- sequentially remove amino acids from each end of a polypeptide

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22
Q

How do cell degrade intracellular pathways

A

lysosomes: degrades anything ingested by cells

Ubiquitin pathways: specific targeting and degradation of cytosolic proteins

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23
Q

Ubiquitin Pathway

A

specific proteins tagged with ubiquitin and degraded by large proteolytic complex called proteasome

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24
Q

Steps of ubiquitin pathway

A

1: 3 enzymes add single ubiquitin molecule to lysine on protein destines to be degraded
2: repeats at same site- end up with chain of UB on single lysine residue
3: UB chains recognized by proteasome which degrade the tagged protein into peptides and UB chain into individual molecules

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25
Are all lysines tagged with UB
No, only certain ones
26
Ligands
almost all proteins bind to other molecules called ligands in order to function properly
27
2 major characteristics of protein ligand binding
Specificity | Affinity - how strong the interaction if between protein and ligand
28
Protein ligand ex
antibody- antigen | enzyme-substrate
29
in what ways can an enzyme alter a biochemical rxn
changing gibbs free energy of substrate
30
Ways a protein function is regulated
allostery phosphorylation/dephosphorylation protein cleavage changes in protein location/ concnetration
31
Allostery
3D shape of protein is altered as result of binding to ligand can inhibit or activate protein function
32
Phosphorylation/ dephosphorylation
addition or removal of phosphate groups from a Ser. Thr, Tyr, or His residues alters the charge and shape of proteins
33
what adds phosphate groups in phosphorylation
kinase
34
what removes phosphate group
phosphatase
35
Protein Cleavage
some proteins are produced as inactive precursors so when the time is right they are cleaved which activates them this is irreversible
36
Changes in protein location/ concentration
proteins sequestered on whatever cellular compartment they normally function cell can alter function by moving them selective produce or degrade proteins
37
How do we separate and purify proteins
By their differences 1. size/mass- how many aa in a chain 2. 3D shape - difficult 3. density- most are pretty similar 4. charge- how many acidic and basic AA 5. ability to bind to specific ligands- (enzymes, receptors)
38
Centrifugation
first step in purifying/ isolating protein from a mixture spinning will cause them to move to bottom of tube at different rates depending on their mass and density
39
Two types of centrifugation
differential | rate zonal
40
differential Centrifugation
separates proteins based on density (note many proteins have the same density) all or nothing clump into a pellet
41
Rate zonal centrifugation
separates proteins based on mass/shape (proteins differ greatly in mass proteins separate into discrete bands (big-> bottom faster)
42
Gel electrophoresis
separating molecules in a mixture by adding the mixture to a semi solid gel and applying electric current through the gel
43
what are molecules separated by in electrophoresis
charge, mass and 3D shape small molecules move faster though gels than large more negative a molecule is faster it will move
44
SDS
type of electrophoresis that uses negatively charged detergent SDS and heat to denature proteins and break up complexes prior to adding them to the gel SDS will coat neg proteins SDS will remove all 2nd ,3, and 4 structures proteins will primarily separate based on size ALONE
45
Liquid Chromatography
mixture with protein placed on top of column of beads , proteins move through beads and will separate from each other based on mass charge or binding affinity collect fractions of liquid flow through (different proteins would be dif fractions)
46
types of liquid chromatography
Gel filtration ion exchange affinity
47
Gel filtration Chromatography
based on SIZE beads have depression over their entire surface larger will exit column first
48
Ion Exchange chromatography
based on CHARGE beads that are + or - charge + beads will bind and hold onto neg charge proteins, - would just go through the column beads washed with NaCl to remove bound proteins stronger the attraction the more NaCl needed
49
Affinity Chromatography
Based on their attraction to a specific ligand molecule ligand molecules that bind to the protein that you are trying to purify will be chemically attached to the beads (EX. purify actin- attach antibody that is specific to actin to the beads) only protein with affinity will attach all others will just move through column Most specific of the techniques
50
How to actually count or detect a specific protein
antibodies
51
Three antibody dependent protein detection assays
Western blot ELISA IF
52
Western Blot
- separate protein via SDS - add protein bands to nitrocellulose membrane - add antibody specific for protein of interest - add second antibody specific to first and contains special enzyme attached to it - add colorless substrate enzyme will convert it to a colored product
53
Radioactivity with proteins
- easy to detect/quantify proteins | - pulse chase experiments: used for tracking movement and degradation of protein over time
54
bases in nucleic acids react via what bond
Hydrogen bond
55
Where is RNA transcribed
nucleus
56
Where is RNA processed
nucleus
57
RNA Processing
5' phosphate cap 3' hydroxy tail introns spliced
58
Transcription
- DNA transcribed into RNA chain by RNA polymerase | - ribonucleotides added to 3' end of RNA
59
Organization of genes in prokaryote v eukaryote
prokaryote: several protein coding genes commonly clustered into an operon which is transcribed from a single promoter into one mRNA Eukaryote: each protein coding gene is transcribed from its own promoter
60
RNA is synthesized
5'-> 3'
61
What helps promote tRNAs decoding function
its folded structure
62
when are amino acids activated
when covalently linked to tRNAs
63
Three roles of RNA is protein synthesis
mRNA carries codon, tRNA carries anti codon with amino acid, rRNA unit
64
New strands of DNA are formed in what direction
5' to 3 '
65
What initiates DNA replication
DNA polymerases require a primer
66
DNA replication
DNA unwound, daughter strand formed at the replication fork, one strand elongated continuously (leading) other in Okazaki fragments (lagging)
67
what proofreads when DNA is replicating
DNA polymerase
68
viruses
small parasites that replicate only in host cells could be DNA or RNA viruses and either single or double stranded
69
Viral Capsids
regular arrays of one or a few types of proteins
70
Outer envelope
on viruses similar to plasma membrane but contains viral transmembrane proteins
71
what leads to the death of host cells
lytic viral growth cycles
72
lytic viral infection
absorption, penetration, synthesis of viral proteins and progeny genomes, assembly of progeny virions and release of thousands of virions leading to death of host cell
73
lytic replication cycle
1. free virion absorped and injected 2. expression of viral early proteins 3. replication of viral DNA, expression of viral late proteins 4. assembly 5. lysis and release

Cell Molec (5 decks)

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