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3 - Molecular and medical genetics > 3.1 > Flashcards

3.1 Flashcards

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USMLE® Step 1 flashcards Biology 101 flashcards
1
Q

what is a gene

A

inherited unit of information that on the gross level determines phenotype (morphological characteristics) and on the molecular level determines amino acid sequence of a polypeptide / RNA

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1
Q

types of mutations

A

substitution
deletion - frameshift
insertion - frameshift
duplication - frameshift

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2
Q

types of substitution

A

missense - change in amino acid

nonsense - premature stop codon

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3
Q

types of swaps of amino acids

A

transitions - pyrimidine to pyrimidine or purine to purine

transversions - pyrimidine to purine + vice versa

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4
Q

what is a silent mutation

A

when the point mutation in a base causes the same amino acid to still be coded for = does not effect polypeptide

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5
Q

how do mutations occur

A

spontaneous or induced via mutagens

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6
Q

w - hwo do mutations occur…

A
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7
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14
Q

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15
Q

what is the molecular structure of DNA

A

double helix
two antiparallel strands
made up of nucleotides - deoxyribose sugar + phosphate + nitrogenous base
AT - 2 - H bonds
CG - 3 - H bonds
Sugar phosphate back bone - phosphodiester bonds
major + minor grooves
5’ - 3’ directionality

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16
Q

what are major + minor grooves

A

allows specific protein-DNA interactions, particularly in transcription

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17
Q

hierarchal organisation of DNA

A

3d structure
nucleosomes
chromatin
chromatin loops
topologically associated domains
compartments
chromosome terrorties

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18
Q

what is a nucleosome

A

made up of eight
histone proteins 2X( H2A, H2B, H3, H4) on
which 146 nucleotides are wound up
twice.

Linker DNA connects nucleosomes
into a “beads” structure compacting about 5 fold

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19
Q

what is chromatin

A

complex of DNA and proteins (mainly histones) found in the nucleus

basic unit is nucleosome

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20
Q

Chromatin Loops

A

Structures where 30 nm chromatin fibers form loops of 40-100 kb anchored to the nuclear matrix or scaffold. These loops bring distant regulatory elements like enhancers into proximity with promoters, facilitating gene regulation.

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21
Q

Topologically Associated Domains (TADs)

A

: Self-interacting chromatin regions where DNA sequences within the domain interact more frequently with each other than with sequences in other domains.

TAD boundaries are marked by CTCF and cohesin and help organize gene regulation.

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22
Q

A/B Compartments

A

Large-scale functional segregation of the genome into two compartments: A compartments (gene-rich, transcriptionally active, euchromatin) and B compartments (gene-poor, transcriptionally inactive, heterochromatin).

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23
Q

Chromosome Territories

A

Distinct, non-overlapping regions occupied by individual chromosomes within the nucleus during interphase. Active regions are located toward the nuclear interior, while inactive regions are positioned near the nuclear periphery.

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24
Q

Nucleoside

A

consisting of a nitrogenous base (purine or pyrimidine) covalently bonded to a pentose sugar (ribose in RNA or deoxyribose in DNA).

Example: Adenine + Ribose = Adenosine

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25
Q

Difference Between Nucleoside and Nucleotide

A

Nucleoside: Base + Sugar (no phosphate).

Nucleotide: Base + Sugar + Phosphate group(s).

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26
Q

3 steps of semi conservative DNA replication

A

Initiation
elongation
termination

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27
Q

describe initiation

A
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28
Q

describe elongation + termination

A
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29
Q

what direction is semi conservative replication

A

bidirectional

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30
Q

what is in the replisome

A

DNA helicase

SSBs (RPA)

topoisomerase

Pol alpha (DNA polymerase alpha / DNA primase)

DNA polymerase

PCNA

RFC

FEN1 / RNase

DNA ligase

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31
Q

what are SSB’s

A

single-stranded specific binding protein - prevents 2 strands from re-annealing

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32
Q

what is topoisomerase

A

reduces torsional strain on DNA caused by unwinding

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33
Q

what is PCNA and RFC

A

PCNA - DNA clamp that tethers DNA polymerase to DNA
RFC - auxillary factors that loads PCNA onto DNA

34
Q

what are telomeres

A

non coding regions at the end of the chromosomes that prevent shortening of chromosomes during proliferation + differentiate the ends of chromosomes from DNA double strand breaks preventing end to end fusion of chromosomes

35
Q

how does telomerase work

A
36
Q

telomerase in cancer

A

cancer cells can keep it active

allows cancer cells to replicate infinitely without reaching replicative senescence

37
Q

accuracy of replication

A

polymerases have proof reading ability that require 3’ to 5’ exoribonuclease activity

expand on this in detail - on spec

38
Q

DNA repair enzymes + their importance + cancer

A
39
Q

Control of Gene Expression at the Level of Transcription

A

promoters
transcription factors
silencers
enhancers
insulators

40
Q

Eukaryotic Promoter Structure

A

Promoters are DNA sequences that initiate transcription.

Include core promoter elements, proximal promoter elements and are surrounded by distal regulatory elements

41
Q

Core Promoter Elements

A

Key elements include:

TATA Box

Initiator Element (Inr)

BRE (TFIIB Recognition Element)

These elements help in RNA polymerase II recruitment and transcription initiation.

42
Q

TATA Box

A

A DNA sequence (TATAAA) found approximately 25-30 bp upstream of the TSS.

It binds the TATA-binding protein (TBP), a subunit of Transcription Factor IID (TFIID).

Facilitates the assembly of the transcription initiation complex.

43
Q

Initiator Element (Inr)

A

A DNA sequence centered around the transcription start site (TSS).

It helps position RNA polymerase II at the correct site for transcription initiation.

Often works together with the TATA box but can function independently as well.

44
Q

BRE (TFIIB Recognition Element)

A

Located upstream of the TATA box.

Recognized by Transcription Factor IIB (TFIIB).

Helps stabilize the binding of RNA polymerase II and general transcription factors.

45
Q

Proximal Promoter Elements

A

DNA sequences ~50-200 bp upstream of the TSS.

Include elements such as the CAAT box and GC box.

Bind transcription factors that recruit RNA polymerase II and other transcription machinery components.

46
Q

Enhancer Binding Sites

A

DNA sequences located far upstream, downstream, or even within introns.

Bind activator proteins, increasing transcription efficiency by interacting with the promoter via chromatin looping.

47
Q

Silencer Binding Sites

A

DNA regions where repressor proteins bind, inhibiting transcription.

Prevent RNA polymerase II recruitment or disrupt enhancer-promoter interactions.

48
Q

insulator

A

regulate expression between neighborung genes

49
Q

locus control region

A

regulates expression of a cluster of genes to ensuring correct sequence of expression

50
Q

General Features of Eukaryotic Transcription Factors

A

Proteins that regulate gene expression by binding to DNA sequences near promoters, enhancers, or silencers.

Composed of DNA-binding domains and activation/repression domains.

Activator TFs: Enhance transcription by interacting with RNA Polymerase II and general transcription factors.

Repressor TFs: Inhibit transcription by blocking RNA Polymerase II recruitment or altering chromatin structure.

51
Q

DNA-Binding Domains

A

Specialized regions of TFs that bind specific DNA sequences.

Examples:

Helix-Turn-Helix: Found in homeodomain proteins.

Zinc Finger: Binds DNA through zinc ions.

Leucine Zipper: Facilitates dimerization and DNA binding.

52
Q

Categories of Transcription Factors

A

General Transcription Factors (GTFs): Essential for RNA Polymerase II initiation, e.g., TFIID, TFIIB.

Specific Transcription Factors: Bind to enhancers and silencers, regulate gene-specific transcription.

53
Q

Coactivators and Corepressors

A

Coactivators: Proteins that interact with activator TFs and RNA Polymerase II to enhance transcription.

Corepressors: Proteins that bind to repressor TFs, preventing RNA Polymerase recruitment and altering chromatin.

54
Q

Epigenetic Modifications

A

Epigenetic changes alter gene activity without changing the DNA sequence.

Include DNA methylation and histone modifications

55
Q

DNA Methylation

A

Involves the addition of a methyl group (CH₃) to the 5th carbon of cytosine residues.

Typically occurs in CpG dinucleotides, often near gene promoters.

Methylation represses transcription by:

Preventing transcription factor binding

Recruiting methyl-CpG-binding proteins and histone deacetylases.

56
Q

Effects of DNA Methylation on Gene Expression

A

Hypermethylation: Often leads to gene silencing (e.g., tumor suppressor genes).

Hypomethylation: Can result in gene activation or genomic instability.

Affects cell differentiation, development, and disease states like cancer.

57
Q

Histone Tail Modifications

A

Histone proteins have amino acid tails on the N - terminals that can be chemically modified.

acetylation, methylation, phosphorylation, and ubiquitination.

58
Q

Histone Acetylation

A

The addition of an acetyl group (CH₃CO) to lysine residues on histone tails.

Carried out by histone acetyltransferases (HATs).

Acetylation neutralizes lysine charge, resulting in a looser chromatin structure, which enhances transcription by increasing accessibility.

59
Q

Histone Deacetylation

A

The removal of an acetyl group by histone deacetylases (HDACs).

Leads to tighter chromatin packing, making DNA less accessible for transcription.

Suppresses gene expression by preventing transcription factor binding.

60
Q

Histone Methylation

A

addition of methyl groups (CH₃) to lysine or arginine residues on histone tails.

Can be activating or repressive, depending on which lysine residue is methylated.

H3K4 methylation: Often activates transcription.

H3K27 methylation: Typically represses transcription.

61
Q

Chromatin Organization and Gene Activity

A

Euchromatin: Loosely packed chromatin, associated with active transcription.

Heterochromatin: Tightly packed chromatin, associated with gene silencing.

62
Q

Facultative vs. Constitutive Chromatin

A

Facultative Chromatin: Condensed in some cell types but loosely packed in others, gene expression is cell-type specific.

Constitutive Chromatin: Always tightly packed, often gene-silent, found in areas with highly repetitive DNA (e.g., centromeres).

63
Q

3 eukaryotic RNA polymerases and their products

A

RNA polymerase I -> transcribes rRNAs

RNA polymerase II -> transcribes mRNA, snRNA, snoRNA, miRNA

RNA polymerase III -> tRNA, some snRNAs

64
Q
  • mRNA
A

messenger, contains codons that are complementary to the anticodons on tRNA- transfers genetic information outside the nucleus

65
Q
  • rRNA
A

ribozyme – constituent of ribosomes, carries out protein synthesis. 28s, 18s, 5.8s made by RNA polymerase I (in nucleolus) – 5s and 7s made by RNA polymerase III (in nucleoplasm)

66
Q
  • tRNA
A

each RNA is specific for a particular group of amino acids – contains an anticodon complementary to a codon on mRNA, so that amino acids are sequenced in the correct positions – also has an amino acid binding site so carries the amino acid to the ribosome

67
Q
  • snRNA
A

small nuclear RNA – synthesised mainly by RNA polymerase II – codes for proteins of spliceosome and telomerase enzyme

68
Q
  • miRNA
A

micro-RNA, functions in RNA silencing and post-translational regulation of gene expression, function via base pairing with complementary sequences within mRNA molecules

69
Q
  • snoRNA
A

small nucleolar RNAs, guide chemical modifications of other RNAs (mainly rRNA, tRNA and snRNA)

70
Q

RNA bases

A
  • A, U, C, G -> uracil has replaced thymine
  • Uracil is energetically less expensive to produce than thymine so it’s used in RNA
71
Q

What is the structure of RNA Polymerase II in eukaryotes?

A

RNA Polymerase II is composed of 12 subunits (Rpb1–Rpb12).

Rpb1 contains the Carboxy-Terminal Domain (CTD), crucial for mRNA processing and transcription regulation.

Other subunits (Rpb2, Rpb3, Rpb5) contribute to enzyme stability and transcriptional function.

72
Q

What is the role of the CTD (Carboxy-Terminal Domain) of Rpb1 in RNA Polymerase II?

A

contains repeated heptapeptide sequences (YSPTSPS).

acts as a dynamic scaffold for RNA processing factors during transcription.

CTD coordinates mRNA capping, splicing, and polyadenylation by recruiting specific proteins at different stages of transcription.

integrates transcription with RNA maturation processes, ensuring that the RNA transcript is correctly processed, modified, and stabilized before leaving the nucleus.

CTD also facilitates transition from transcription initiation to elongation, making it crucial for gene expression regulation.

73
Q
  • WHY CONVERT TO RNA
A

If you use DNA you are restricted to only producing 1 protein at a time

Use mRNA -> can make multiple copies which can all be translated at the same time

74
Q

RNA structure differs from DNA structure

A

Single stranded

Uracil instead of thymine

Sugar backbone is deoxyribose instead of ribose

OH group on second carbon – makes RNA more reactive (emphasis in splicing)

75
Q

RNA polymerase vs DNA polymerase

A

Don’t require function of a primer to synthesise a new strand = just need a DNA template and free nucleotides

Like DNA pol, they polymerise nucleotides in a 5’ – 3’ direction (this is common to all polymerases)

Orientation of gene makes a difference as to what is used as the template strand

An RNA polymerase that moves from left –> right makes RNA by using bottom strand as a template and vice versa

Non-coding strand used as a template

76
Q

transcription - initation

A
77
Q

draw out diagram for assembly of the initiation complex and describe

A
78
Q

transciption - elongation

A
79
Q

why does RNA have lower fidelity then DNA and does it matter

A

RNA polymerases do not have any proof-reading mechanisms

less important as RNA isn’t inherited

Many copies of RNA are made when a gene is expressed so a few mistakes are unlikely to affect overall levels of protein synthesis

80
Q

transciption -Promoter proximal pause

A

After around 40 nucleotides have been transcribed, polymerase stops -> promoter proximal pause

From the pause state, RNA polymerase has to be released again by specific enzyme action -> addition of an additional kinase CDK9; resides in transcription elongation factor called pTEFb

Can now phosphorylate serine-2 of heptad repeat -> changes RNA polymerase so it can elongate and transcribe the rest of the gene until it reaches the terminator region

81
Q

function of promoter proximal pause

A

pause allows for fine-tuned gene expression control, ensuring transcriptional accuracy and coordination

82
Q

termination - transcription

A
  • SIGNAL FOR TERMINATION LIES IN NEWLY FORMED RNA NOT IN DNA TEMPLATE
83
Q
  • Proteins that assist termination transcription
A

Rho protein -> binds to newly made RNA at C-rich G-poor regions -> scans along the RNA toward RNA polymerase in an ATP-dependant manner

When it catches up with RNA polymerase, it breaks the DNA/ RNA association and terminates transcription

3 - Molecular and medical genetics (1 decks)

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