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Cell Molec > Chapter 1 > Flashcards

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
Q

Are all lysines tagged with UB

A

No, only certain ones

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26
Q

Ligands

A

almost all proteins bind to other molecules called ligands in order to function properly

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27
Q

2 major characteristics of protein ligand binding

A

Specificity

Affinity - how strong the interaction if between protein and ligand

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28
Q

Protein ligand ex

A

antibody- antigen

enzyme-substrate

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29
Q

in what ways can an enzyme alter a biochemical rxn

A

changing gibbs free energy of substrate

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30
Q

Ways a protein function is regulated

A

allostery
phosphorylation/dephosphorylation
protein cleavage
changes in protein location/ concnetration

31
Q

Allostery

A

3D shape of protein is altered as result of binding to ligand
can inhibit or activate protein function

32
Q

Phosphorylation/ dephosphorylation

A

addition or removal of phosphate groups from a Ser. Thr, Tyr, or His residues

alters the charge and shape of proteins

33
Q

what adds phosphate groups in phosphorylation

A

kinase

34
Q

what removes phosphate group

A

phosphatase

35
Q

Protein Cleavage

A

some proteins are produced as inactive precursors so when the time is right they are cleaved which activates them

this is irreversible

36
Q

Changes in protein location/ concentration

A

proteins sequestered on whatever cellular compartment they normally function
cell can alter function by moving them

selective produce or degrade proteins

37
Q

How do we separate and purify proteins

A

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
Q

Centrifugation

A

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
Q

Two types of centrifugation

A

differential

rate zonal

40
Q

differential Centrifugation

A

separates proteins based on density (note many proteins have the same density)

all or nothing
clump into a pellet

41
Q

Rate zonal centrifugation

A

separates proteins based on mass/shape (proteins differ greatly in mass

proteins separate into discrete bands (big-> bottom faster)

42
Q

Gel electrophoresis

A

separating molecules in a mixture by adding the mixture to a semi solid gel and applying electric current through the gel

43
Q

what are molecules separated by in electrophoresis

A

charge, mass and 3D shape

small molecules move faster though gels than large
more negative a molecule is faster it will move

44
Q

SDS

A

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
Q

Liquid Chromatography

A

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
Q

types of liquid chromatography

A

Gel filtration
ion exchange
affinity

47
Q

Gel filtration Chromatography

A

based on SIZE

beads have depression over their entire surface

larger will exit column first

48
Q

Ion Exchange chromatography

A

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
Q

Affinity Chromatography

A

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
Q

How to actually count or detect a specific protein

A

antibodies

51
Q

Three antibody dependent protein detection assays

A

Western blot
ELISA
IF

52
Q

Western Blot

A
  • 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
Q

Radioactivity with proteins

A
  • easy to detect/quantify proteins

- pulse chase experiments: used for tracking movement and degradation of protein over time

54
Q

bases in nucleic acids react via what bond

A

Hydrogen bond

55
Q

Where is RNA transcribed

A

nucleus

56
Q

Where is RNA processed

A

nucleus

57
Q

RNA Processing

A

5’ phosphate cap
3’ hydroxy tail

introns spliced

58
Q

Transcription

A
  • DNA transcribed into RNA chain by RNA polymerase

- ribonucleotides added to 3’ end of RNA

59
Q

Organization of genes in prokaryote v eukaryote

A

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
Q

RNA is synthesized

A

5’-> 3’

61
Q

What helps promote tRNAs decoding function

A

its folded structure

62
Q

when are amino acids activated

A

when covalently linked to tRNAs

63
Q

Three roles of RNA is protein synthesis

A

mRNA carries codon, tRNA carries anti codon with amino acid, rRNA unit

64
Q

New strands of DNA are formed in what direction

A

5’ to 3 ‘

65
Q

What initiates DNA replication

A

DNA polymerases require a primer

66
Q

DNA replication

A

DNA unwound, daughter strand formed at the replication fork, one strand elongated continuously (leading) other in Okazaki fragments (lagging)

67
Q

what proofreads when DNA is replicating

A

DNA polymerase

68
Q

viruses

A

small parasites that replicate only in host cells

could be DNA or RNA viruses and either single or double stranded

69
Q

Viral Capsids

A

regular arrays of one or a few types of proteins

70
Q

Outer envelope

A

on viruses similar to plasma membrane but contains viral transmembrane proteins

71
Q

what leads to the death of host cells

A

lytic viral growth cycles

72
Q

lytic viral infection

A

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
Q

lytic replication cycle

A
  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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