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Step1 > Molecules and cells > Flashcards

Molecules and cells Flashcards

0
Q

Heterochromatin

A

Condensed transcriptionally inactive, sterically inaccessible chromatin

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1
Q

Chromatin structure

A

Negatively charged DNA loops twice around positively charged histone octamer to form nucleosome beads

Nucleosome core is composed of histones H2A, H2B, H3, and H4, 2 of each

Histones are rich in amino acids lysine and arginine

Histone H1 binds to nucleosome and stabilizes chromatin fiber

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2
Q

Euchromatin

A

Less condensed, transcriptionally active, sterically accessible

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3
Q

DNA methylation

A

CpG (cytosine-phosphate-guanosine) methylation makes DNA mute

In prokaryotes, template strand cytosine and adenine are methylated in DNA replication to help mismatch enzymes to distinguish between old and new strands

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4
Q

Histone methylation

A

Usually reversibly represses DNA transcription, but can activate it in some cases

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5
Q

Histone acetylation

A

RElaxes DNA coiling allowing for transcription

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6
Q

Purines

A

Adenosine, guanosine, 2 rings

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7
Q

Pyrimidines

A

Cytosine, thymine, uracil, 1 ring

GC bonds (3 H bonds) stronger than AT bonds (2 H bonds)

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8
Q

De novo purine synthesis

A

Start w sugar and phosphate (PRPP)

Add base

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9
Q

De novo pyramiding synthesis

A

Make temporary base
Add sugar and phosphate
Modify base

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10
Q

Adenosine deaminase deficiency

A

Excess ATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase, preventing DNA synthesis

Leads to decreased lymphocyte count

One of the major causes of autosomal recessive SCID

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11
Q

Lesch-Nyhan syndrome

A

Defective purine salvage due to absent HGPRT

Results in excess guanine and subsequently uric acid production and de novo purine synthesis

X link recessive

Features: hyperurecemia, gout, aggression, retardation, dystony

Treatment: allopurinol, elimination of excess uric acid

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12
Q

Features of genetic codes

A

Unambiguous: each codon only specifies 1 amino acid

Redundancy: most AA are coded by multiple codons

Non overlapping: read from a fixed starting point as a continuous sequence of bases

Universal: genetic code is conserved throughout evolution

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13
Q

Origin of replication

A

Particular sequence in DNA where replication begins

Single in prokaryotes and multiple in eukaryotes

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14
Q

Replication fork

A

Y shaped region along DNA template where leading and lagging strands are synthesized

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15
Q

Helicase

A

Unwinds DNA template at replication fork

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16
Q

Single stranded binding protein

A

Prevents strand from reannealing

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17
Q

DNA topoisomerases

A

Create a single or double stranded break in helix to break supercoils to relieve strain (gyrase in prokaryotes)

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18
Q

Primase

A

Makes RNA primer on which DNA polymerase III can initiate replication (usually on lagging strand)

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19
Q

DNA polymerase III

A

Prokaryotes only

Elongates leading strand by adding nucleotides to the 3’ end

Elongates lagging strand until it reaches primer of preceding fragment (Okazaki fragment)

Proofread 3’-> 5’ w exonuclease activity with each added nucleotide

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20
Q

DNA polymerase I

A

Prokaryotes only

Degrade RNA primer with RNA 5’ to 3’ exonuclease and replaces with DNA

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21
Q

DNA ligase

A

Catalyzes the formation of a phosphodiester bond within a strand of double stranded DNA ie joining Okazaki fragments

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22
Q

Telomerase

A

An RNA dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material with every duplication

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23
Q

Silent mutation

A

Nucleotide substitution but codes for same AA, often base change in the third position of codon

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24
Q

Missense mutation

A

Nucleotide substitution resulting in changed AA
Called conservative if new AA is similar in structure to old
Ex: sickle cell disease

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25
Q

Nonsense mutation

A

nucleotide substitution results in early stop codon

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26
Q

Frameshift mutation

A

Deletion or insertion of a number of nucleotides not divisible by 3, resulting in misreading of all nucleotides downstream, usually resulting in a truncated nonfunctional protein

Ex: duchenne muscular dystrophy

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27
Q

Mismatch repair

A

Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed

Ex: defective in HNPCC

28
Q

Nucleotide excision repair

A

Endonuclease release the oligonucleotide containing damaged bases

Defective in xeroderma pigmentosum, which prevents repair of pyrimidine dimers because of ultraviolet light exposure

29
Q

Non homologous end joining

A

Bring together 2 ends of double stranded DNA fragments to repair breaks

Mutated in ataxia telangiectasia

30
Q

DNA RNA synthesis

A

DNA and RNA both synthesized 5’ to 3’ with the 5’ end of incoming nucleotide bearing the triphosphate

mRNA is read 5’ to 3’

Start codons: AUG codes for methionine, which maybe removed before translation is completed

Stop codons: UGA, UAA, UAG

31
Q

Promoter region

A

Site where RNA polymerase and multiple other transcription factors binds to upstream from gene locus

Usually rich in AT, known as TATA or CAAT boxes

Mutation commonly results in decreased level of gene transcription

32
Q

Enhancer and silencer region

A

Stretch of DNA that alters gene expression by binding transcription factors

Site where negative regulators or repressors bind

Both maybe located close to or far from or even within (in an intron) the gene whose expression it regulates

33
Q

RNA polymerase

A

Eukaryotes
RNA Polymerase I makes rRNA, most numerous
RNA polymerase II makes mRNA, largest RNA
RNA polymerase III makes tRNA, smallest RNA

Prokaryotes
1 RNA polymerase makes all 3 kinds of RNA

34
Q

RNA processing (eukaryotes)

A

Initial transcript is called heterogenous nuclear RNA or hnRNA

In nucleus: capping of 5’ end w 7-methyl guanosine cap, polyadenylation of 3’ end (poly A tail), splicing out of introns, result is mRNA

mRNA is transported out into cytosol where it is translated

35
Q

Splicing of pre-mRNA

A
  1. Primary transcript combines w small nuclear ribonucleoproteins (snRNP) and other proteins to form sliceosome
  2. Lariat shaped (loop) intermediate is generated
  3. Lariat is released to precisely remove intron and join exons

Antibodies to spliceosomal snRNP are highly specific for SLE

36
Q

tRNA

A

Structure
3’ end with CCA, or the AA acceptor stem
T-arm: containing the sequence necessary for ribosome binding
D-arm: contains residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase
Anti-codon loop: matches mRNA, opposite of AA Receptor stem

Charging:
Aminoacyl tRNA synthetase (1 per AA, uses ATP) scrutinizes AA before and after it binds to tRNA

37
Q

Protein synthesis

A

Initiation
Initiated by GTP hydrolysis, initiation factors help assemble the 40s ribosomal subunit with the initiator tRNA and are released when the mRNA and the 60s ribosomal subunit assemble w complex (prokaryote subunits 30s and 50s)

Elongation

  1. Aminoacyl tRNA binds to A site
  2. rRNA Catalyzes peptide bond formation, transfers growing polypeptide to AA in A site
  3. Ribosome advances 3 nucleotides toward 3’ end of mRNA and moves peptidyl tRNA to P site

Termination
Stop codon is recognized by release factor and completed polypeptide is released from ribosome

38
Q

Chaperone protein

A

Intracellular protein involved in facilitating and maintaining protein folding

39
Q

Cell cycle phases

A

G0 G1

G1 -> S -> G2 -> mitosis -> G1

40
Q

Cell dependent kinases

A

Constitute and inactive, regulate cell cycle w activation by cyclins

41
Q

Cyclin

A

Regulatory protein that control cell cycle events, phase specific, activates CDK

42
Q

Cyclin CDK complexes

A

Must be both activated or inactivated for cell cycle to progress

43
Q

Tumor suppressors

A

P53 and retinoblastoma protein normally inhibit G1 to S progression
Mutations in these genes result in unrestrained cell division, ie Li-Fraumeni syndrome

44
Q

Permanent cells

A

Remain in G0
Regenerate from stem cells
Neurons, skeletal and cardiac muscle, RBC

45
Q

Stable (quiescent) cells

A

Enter G1 from G0 when stimulated

Hepatocytes, lymphocytes

46
Q

Labile cells

A

Never in G0, divide rapidly, most affected by chemotherapy

Bone marrow, gut epithelium, hair follicle, skin, germ cells

47
Q

Rough endoplasmic reticulum

A

Site of synthesis of secretory proteins

Mucus secreting goblet cells in the small intestine and antibody secreting plasma cells are rich in RER

48
Q

Smooth endoplasmic reticulum

A

Site of steroid and detoxification of drugs and poisons
Lack surface ribosome
Liver hepatocytes and steroid hormone producing cells of the adrenal cortex and gonads are rich in SER

49
Q

Golgi apparatus

A

Distribution center for proteins and lipids from ER to vesicles and plasma membrane
Location of N-oligosaccharide and O-oligosaccharide addition
Location of mannose-6-phosphate to proteins for trafficking to lysosomes

50
Q

I cell disease

A

Inherited lysosomal storage disorder
Defect in Golgi to add phosphate to mannose
Proteins are secreted extracellularly rather than sent to lysosomes
Results in coarse facial features, clouded corneas, restricted joint movement, and high plasma level of lysosomal enzymes
Fatal in childhood

51
Q

Signal recognition particle

A

Abundant cytosolic ribonucleoprotein that traffics proteins from ribosomes to the RER
Absent or dysfunctional SRP results in protein accumulation in cytosol

52
Q

Vesicular trafficking proteins

A

COPI: Golgi retrograde, Golgi to ER

COPII: Golgi ante grade, ER to Golgi

Clathrin: trans Golgi to lysosomes plasma membrane to endosomes

53
Q

Peroxisome

A

Membrane enclosed organelle involved in catabolism of very long chain fatty acids, branched chain fatty acids, and amino acids

54
Q

Proteosome

A

Barrel shaped protein complex that degrades damaged or ubiquitin tagged proteins.
Defects in the ubiquitin proteosome system have been associated w Parkinson’s disease

55
Q

Microtubules

A

Cylindrical structure composed of helical array of polymerized heterodimers of alpha and beta Tubulin

Incorporated into flagella, cilia, mitotic spindles

Grows slowly, collapses quickly

Involved in axoplasmic transport in neurons

56
Q

Dynein

A

Molecular motor protein

Transport cellular cargo retrograde to microtubule

57
Q

Kinesin

A

Molecular motor protein

Transports cargo ante grade to microtubules

58
Q

Cilia

A

9+2 arrangement of microtubules
Axonemal dynein: ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets

59
Q

Kartagener syndrome

A

Primary ciliary dyskinesia

Immobile cilia due to dynein arm defect

Results in male and female infertility due to infertile sperm and dysfunctional Fallopian tube cilia

Increased risk of pregnancy

Can cause bronchiectaisis, recurrent sinusitis, and situs inversus

60
Q

Actin and myosin

A

Actins are long structural polymers
Myosins are dimeric, ATP driven motor proteins that move along Actins
Involved in muscle contractions

61
Q

Intermediate filaments

A 
Vimentin: connective tissue
Desmin: muscle
Cytokeran: epithelial cells
Glial fibrillary acid proteins: neuroglia
Neurofilaments: neurons
62
Q

Collagen types

A

Be so totally cool read books

Type 1: most common, 90%, bone, skin, tendon
Type2: cartilage,vitreous body
Type3: reticulin, blood vessels, granulation tissue, fetal tissue
Type4: basement membrane, basal lamina

63
Q

Collagen synthesis

A

Inside fibroblast
Translation of collagen alpha chains
Hydroxylation of specific AA residues, requires vitamin C, deficiency leads to scurvy
Glycosylation of pro-alpha-chain and formation of pro collagen via hydrogen and disulfide bonds (triple helix of 3 alpha chains)

Outside fibroblasts
Cleavage of disulfide bonds forming insoluble tropocollagen
Reinforcement of staggered tropocollagen by covalent lysine-hydroxylysine cross linkage

64
Q

Osteogenesis imperfecta

A

Problem w forming triple helix
Brittle bone disease
Manifestations include multiple fractures with minimal trauma, blue sclera, hearing loss, and dental imperfections

65
Q

Ehlers Danlos syndrome

A

Faulty collage synthesis causing hyper extensible skin, tendency to bleed, and hypermobile joints
Autosomal dominant or recessive, associated w joint dislocation, berry and aortic aneurysms, organ rupture

66
Q

Menkes disease

A

Connective tissue disease caused by impaired copper absorption and transport
Leads to decreased activity of lysyl oxidase and results in brittle hair, growth retardation, and hypotonia

67
Q

Elastin

A

Stretchy protein within skin, lung, arteries

Broken down by elastase, which is normally inhibited by A1AT

68
Q

Marfan syndrome

A

Caused by defect in fibrillin, a glycoproteins that forms a sheath around elastin

Features include unusual tallness and various cardiac complications such as aortic aneurysm

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