flash2.py

import streamlit as st
import random
import base64
import os

# Page config
st.set_page_config(page_title="MSI/MSII Flashcards", page_icon="🧬", layout="wide")

# # Initialize session state
# if 'current_card' not in st.session_state:
#     st.session_state.current_card = 0
# if 'is_flipped' not in st.session_state:
#     st.session_state.is_flipped = False
# if 'shuffled' not in st.session_state:
#     st.session_state.shuffled = False
# if 'filter_category' not in st.session_state:
#     st.session_state.filter_category = "All"

# """
# How to add images:
# Add "question_image": "filename.png" or "answer_image": "filename.png" to flashcard data
# Images should be placed in the 'images' folder
# Example:
# {
#     "category": "MSI - Enzyme Kinetics",
#     "question": "Interpret this Michaelis-Menten graph",
#     "question_image": "mm_graph.png",
#     "answer": "The graph shows...",
#     "answer_image": "mm_explained.png"
# }
# """

flashcards = [
    {
        "category": "MSI - Protein Structure",
        "question": "Classify the 20 amino acids by their charge/polarity.",
        "answer_image": "amino_acids.png",
        "answer": "Nonpolar/Hydrophobic: Gly, Ala, Val, Leu, Ile, Met, Pro, Phe, Trp\nPolar/Uncharged: Ser, Thr, Cys, Tyr, Asn, Gln\nPositively Charged (Basic): Lys, Arg, His\nNegatively Charged (Acidic): Asp, Glu"
    },
    {
        "category": "MSI - Protein Structure",
        "question": "Describe the primary structure of proteins including interactions that maintain the structure.",
        "answer_image": "aa_struct.png",
        "answer": "Primary structure is the linear sequence of amino acids connected by peptide bonds (covalent bonds between the carboxyl group of one amino acid and the amino group of the next). The peptide bond is the main interaction maintaining primary structure."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "Describe the secondary structure of proteins including interactions that maintain that structure.",
        "answer": "Secondary structure includes α-helices and β-sheets formed by hydrogen bonds between backbone carbonyl oxygen and amide hydrogen atoms. α-helices form spiral structures, while β-sheets form extended strands that can be parallel or antiparallel."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "Describe the tertiary structure of proteins including interactions that maintain that structure.",
        "answer": "Tertiary structure is the 3D folding of a single polypeptide chain. Maintained by: hydrogen bonds, ionic interactions (salt bridges), disulfide bonds (Cys-Cys), hydrophobic interactions, and van der Waals forces between R groups."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "What amino acids would be found lining the K+ channel and why?",
        "answer": "Polar and negatively charged amino acids (Asp, Glu, Ser, Thr) to stabilize the positive charge of K+ ions passing through the aqueous channel."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "What amino acids would be in the cytosolic domain of a transmembrane protein like K+ channel?",
        "answer": "Polar and charged amino acids (both positive: Lys, Arg, His and negative: Asp, Glu) as well as polar uncharged (Ser, Thr, Asn, Gln) to interact with the aqueous cytosolic environment."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "What amino acids would be in the extracellular domain of a transmembrane protein like K+ channel?",
        "answer": "Polar and charged amino acids (Lys, Arg, His, Asp, Glu) and polar uncharged (Ser, Thr, Asn, Gln) to interact with the aqueous extracellular environment. May also have glycosylation sites (Asn, Ser, Thr)."
    },
    {
        "category": "MSI - Protein Structure",
        "question": "What amino acids would be in contact with membrane lipids in a transmembrane protein?",
        "answer": "Hydrophobic amino acids (Val, Leu, Ile, Phe, Trp, Met) to interact favorably with the lipid bilayer's hydrophobic core."
    },
    {
        "category": "MSI - Protein Separation",
        "question": "Describe the principle of gel filtration chromatography.",
        "answer_image": "gel_fil.png",
        "answer": "Separates proteins by size. Small proteins enter pores in beads and travel slower; large proteins cannot enter pores and travel faster through the column. Also called size-exclusion chromatography."
    },
    {
        "category": "MSI - Protein Separation",
        "question": "Describe the principle of ion exchange chromatography.",
        "answer_image": "ixc.png",
        "answer": "Separates proteins by charge. Cation exchangers have negative charges (bind positive proteins); anion exchangers have positive charges (bind negative proteins). Proteins eluted by increasing salt concentration or changing pH."
    },
    {
        "category": "MSI - Protein Separation",
        "question": "Describe Reverse Phase Chromotography",
        "answer_image": "rpc.png",
        "answer": "Separates proteins by hydrophobicity. Column has hydrophobic stationary phase; hydrophobic proteins bind strongly and elute later with increasing organic solvent concentration. Hydrophilic proteins elute first."
    },
    {
        "category": "MSI - Protein Separation",
        "question": "Describe the principle of affinity chromatography.",
        "answer_image": "afc.png",
        "answer": "Separates proteins based on specific binding interactions. Column contains ligand that specifically binds target protein. Target protein retained while others wash through. Eluted by changing conditions or adding competing ligand."
    },
    {
        "category": "MSI - Protein Modifications",
        "question": "Which amino acids are acetylated and what are the results?",
        "answer": "Lysine residues (and N-terminus). Results: histone acetylation loosens chromatin structure, promotes transcription; N-terminal acetylation affects protein stability and localization."
    },
    {
        "category": "MSI - Protein Modifications",
        "question": "What amino acids are phosphorylated and what are the results?",
        "answer": "Serine, threonine, and tyrosine (also histidine in prokaryotes). Results: alters protein activity, creates binding sites for other proteins, changes protein localization, can activate/inactivate enzymes in signaling cascades."
    },
    {
        "category": "MSI - Protein Modifications",
        "question": "Identify as many protein modifications as you can, and indicate what makes each modification, and what amino acids are modified. (phosphorylation, proteolysis, etc.)\na. Provide specific examples of protein modifications and an ultimate function (eg. Phosphorylated tyrosines in RTK signaling)",
        "answer_image": "ptms.png",       
        "answer": """  - Phosphorylation: Ser, Thr, Tyr; alters activity, signaling (e.g., RTK signaling)
                       - Acetylation: Acetyltransferases: Lys; regulates chromatin structure (activates genes by loosening DNA around histones) H3K9ac
                       - Ubiquitination: E1 (ATP activating), E2 (conjugating), E3(ligating) enzymes: Lys; poly targets for degradation via proteasome, mono targets for histone, multi targets to endosome
                       - Methylation: Methyltransferases: Lys, Arg; regulates chromatin, protein interactions (Histidine in prokaryotes) H3K9me3, H3K27me3 (represses genes)
                       - Glycosylation: glycosyl transferases: Asn (N-linked), Ser/Thr (O-linked); protein folding, stability, cell-cell recognition. N-linked glycosylation in ER oligosaccharyltransferase
                       - Sumoylation: Lys; alters localization, activity
                       - Lipidation: Cys (palmitoylation, prenylation), Gly (myristoylation); membrane targeting
                       - Proteolysis: Proteases: various; activates/inactivates proteins (e.g., proenzymes to enzymes)Protease K
                       - Hydroxylation: Hydroxylase: Pro, Lys; collagen stability
                       - Nitrosylation: nitrosylases: Cys; regulates activity, signaling
                       - ADP-ribosylation: Arg, Glu; DNA repair, signaling
                       - Disulfide bond formation: Cys; stabilizes extracellular protein structure
                       - Carbonylation: various; oxidative damage marker
                       - Deamidation: Asn, Gln; alters charge, function
                       - Citrullination: Arg; affects protein function, immune response
                       - Oxidation/reduction: Oxidases, Peroxidases, Dehydrogenase/Reductases: Met, Cys 
                    """
    },
    {
        "category": "MSI - Enzyme Kinetics",
        "question": "Define Vmax and Km in Michaelis-Menten kinetics.",
        "answer": "Vmax: Maximum reaction velocity when enzyme is saturated with substrate.\nKm: Substrate concentration at which reaction velocity is half of Vmax; indicates enzyme's affinity for substrate (lower Km = higher affinity)."
    },
    {
        "category": "MSI - Enzyme Kinetics",
        "question": """How would Michaelis-Menten data change?\n
                        a.	Define Vmax and Km.\n
                        b.	Using your graph, identify Vmax and Km\n
                        c.	How would the data change if your enzyme had higher affinity for substrate?\n
                        d.	How would the data change if you added a competitive inhibitor?\n
                        e.	How would the data change if you added a non-competitive inhibitor?\n
                    """,
        "answer": "Km would decrease (curve shifts left) - less substrate needed to reach half Vmax. Vmax remains unchanged."
    },
    {
        "category": "MSI - Enzyme Kinetics",
        "question": "How does a competitive inhibitor affect Michaelis-Menten kinetics?",
        "answer_image": "mm_kin.png",
        "answer": "Increases Km (appears to decrease affinity) but Vmax remains unchanged. Inhibitor competes with substrate for active site; can be overcome with high substrate concentration."
    },
    {
        "category": "MSI - Enzyme Kinetics",
        "question": "List all the enzymes",
        "answer": "See Below",
        "answer_image": "all_enzymes.png"
    },
     {
        "category": "MSI - Enzyme Kinetics",
        "question": "How do enzymes bind their substrate?",
        "answer": "See Below",
        "answer_image": "enz_cat.png"
    },
    {
        "category": "MSI - Enzyme Kinetics",
        "question": "How does a non-competitive inhibitor affect Michaelis-Menten kinetics?",
        "answer": "Decreases Vmax but Km remains unchanged. Inhibitor binds to different site than substrate, reducing effective enzyme concentration. Cannot be overcome by adding more substrate."
    },
    {
        "category": "MSI - DNA Structure",
        "question": "What difference between RNA and DNA helps explain DNA's greater stability?",
        "answer": "DNA has deoxyribose (dNTPs) (lacks 2'-OH group) while RNA has ribose (rNPs) (has 2'-OH). The 2'-OH in RNA makes it susceptible to base-catalyzed hydrolysis, making RNA less stable than DNA."
    },
    {
        "category": "MSI - DNA Structure",
        "question": "How does the structure of DNA support its function?",
        "answer": "Double helix with complementary base pairing allows replication and repair; antiparallel strands provide template for synthesis; stable structure protects genetic information; bases inside protect from damage; hydrogen bonds allow strand separation for replication/transcription."
    },
    {
        "category": "MSI - Chromatin",
        "question": "What is a nucleosome and what role do histones play?",
        "answer": "Nucleosome is the basic unit of chromatin: ~147 bp of DNA wrapped 1.65 turns around an octamer of histone proteins (2 copies each of H2A, H2B, H3, H4). H1 histone links nucleosomes. Histones compact DNA and regulate access."
    },
    {
        "category": "MSI - Chromatin",
        "question": "What does the chromatin remodeling complex do?",
        "answer_image": "crc.png",
        "answer": """ Nucleosome removal and histone exchange catalyzed by ATP-dependent chromatin-remodeling complexes.
                      Nucleosome sliding - moves nucleosome along DNA.
                      """
    },
    {
        "category": "MSI - Chromatin",
        "question": "Briefly describe the 'histone code'.",
        "answer": "Post-translational modifications on histone tails (acetylation, methylation, phosphorylation, ubiquitination) that regulate chromatin structure and gene expression. Different combinations of modifications recruit specific proteins and determine transcriptional state."
    },
    {
        "category": "MSI - Chromatin",
        "question": "What are the main components of a histone?",
        "answer_image": "hisstruct.png",
        "answer": """H2A, H2B, H3, H4 (core histones) form octamer. H1 (linker histone) binds DNA between nucleosomes. Histones have positively charged residues (Lys, Arg) that interact with negatively charged DNA backbone.
                     Histone tails are sites of post-translational modifications.
                     DNA wraps around histone octamer ~1.65 turns (~147 bp). 
                     """
    },
    {
        "category": "MSI - Chromatin",
        "question": "What histone modifications are associated with transcribed vs repressed genes?",
        "answer": "Transcribed: H3K4me3, H3K9ac, H3K27ac (acetylation generally activates)\nRepressed: H3K9me3, H3K27me3 (certain methylations repress)"
    },
    {
        "category": "MSI - DNA Replication",
        "question": "Compare/contrast DNA replication on leading vs lagging strand.",
        "answer": "Leading strand: synthesized continuously 5'→3' in same direction as replication fork movement.\nLagging strand: synthesized discontinuously 5'→3' as Okazaki fragments in opposite direction of fork movement. Requires multiple RNA primers; fragments joined by ligase."
    },
    {
        "category": "MSI - DNA Replication",
        "question": "What are the players at the replication fork?",
        "answer_image": "repfork.png",
        "answer": """ - DNA Pol alpha/primase
                      - DNA Pol epsilon - leading strand (exonuclease activity)
                      - DNA Pol delta - lagging strand (exonuclease activity)
                      - CMG - helicase complex
                      - single strand DNA binding proteins on the lagging strand (RPA)
                      - PCNA - sliding clamp and clamp loader
                      - Okazaki fragments
                      - ligase
        """
    },
    {
        "category": "MSI - DNA Replication",
        "question": "Describe directionality of Replication",
        "answer": """As helicase unwinds, DNA polymerase is reading from 3'-5', but synthesizing in the 5'-3' direction
        """
    },
    {
        "category": "MSI - DNA Replication",
        "question": "DNA Pol Active Site",
        "answer_image": "dnapolactive.png",
        "answer": """Mg2+ and Aspartic residues pull on 3'OH and make the O nucleophilic
                    Why buffers need magnesium"""
    },
    {
        "category": "MSI - DNA Replication",
        "question": "How does the lagging strand get synthesized",
        "answer_image": "laggstrand.png",
        "answer": """See below"""
    },
    {
        "category": "MSI - DNA Replication",
        "question": "Formation of nucleosomes behind a replication fork",
        "answer_image": "nucleosome.png",
        "answer": """ - NAP1 loads H2A, H2B dimers
                      - CAF1 loadsH3, H4
                      - FACT loads H3, H4 onto newly synthesized DNA strand
                      - """
    },
    {
        "category": "MSI - DNA Replication",
        "question": "origin licensing and activation at S",
        "answer_image": "originrep.png",
        "answer": """Loading of replication machinery during S phase. Cdt1, Cdc6, Geminin, loads the CMG helicase, """
    },
    {
        "category": "MSI - DNA Replication",
        "question": "How are telomeres replicated and why is this different?",
        "answer_image": "telorep.png",
        "answer": """
                    First RNAse H degrades RNA Primer on leading strand. Telomeres replicated by telomerase, a reverse transcriptase with RNA template. 
                    Different because DNA polymerase delta cannot fully replicate 5' ends of linear chromosomes (end-replication problem).
                    Not encoded in the genome 
                    Telomerase adds TTAGGG repeats to 3' end to prevent shortening. Binds leading strand. Makes primer, DNA pol alpha comes and finishes it. 
                    ligase at the very end.
                    Lengthens chromosome to protect it from decay during division. Form t loops because still gap and protects DNA."""
    },
    {
        "category": "MSI - DNA Repair",
        "question": "Compare/contrast homologous recombination and non-homologous end joining.",
        "answer": """Homologous recombination: uses sister chromatid as template; accurate repair; occurs in S/G2 phase. Highly accurate. Theres a strand invasion causing a holiday junction. DNA synthesis starts her and continues, eventually ligase connects newly repaired strands\n
                    NHEJ: directly ligates broken ends without template; error-prone (may lose/gain nucleotides); occurs throughout cell cycle; faster but less accurate."""
    },
    {
        "category": "MSI - DNA Repair",
        "question": "Name the players and mechanism in HRR",
        "answer_image": "hrr.png",
        "answer": """RAD50, MRE11, XRS2 recognize double strand break. RAD52 binds single strand and stabalizes it as 
                     RAD51 (BRCA1|2) causes strand invasion\n
                     DNA Pol I extends the base pairs on invaded strand and repairs, ligase comes in and puts 
                     DNA back together"""
    },
    {
        "category": "MSI - DNA Repair",
        "question": "Name the players and mechanism in NHEJ",
        "answer_image": "nhej.png",
        "answer": """Ku70/80 binds to ends of broken DNA (non clean break). Recruits DNA-PKcs which phosphorylate and 
                     activate other machinery. Nuclease, polymerase, XRCC4 and ligase finish repair. Error prone, INDELS.
                     """
    },
    {
        "category": "MSI - DNA Repair",
        "question": "Describe MMR (mismatch repair) and give an example.",
        "answer_image": "mmrrepair.png",
        "answer": """MMR corrects base-base mismatches and insertion/deletion loops after replication. Recognizes distortion in DNA helix, removes error from newly synthesized strand (identified by lack of methylation), "
                    and resynthesizes. Example: G-T mismatch from replication error. Helicase unwinds, exonuclease takes it out and DNA pol delta finishes the job"""
    },
    {
        "category": "MSI - DNA Repair",
        "question": "Describe two potential outcomes of irreparable DNA damage.",
        "answer": "1. Apoptosis: programmed cell death to prevent propagation of damaged DNA\n2. Senescence: permanent cell cycle arrest (cells remain alive but don't divide)\n3. Cancer."
    },
    {
        "category": "MSI - Transposons",
        "question": "What are transposable elements and describe their transposition process.",
        "answer_image":"transposonmech.png",
        "answer": """Mobile DNA sequences that can move within genome. Two types:\n1. DNA transposons: cut-and-paste mechanism using transposase, have DNA intmd\n2. Retrotransposons: copy-and-paste via RNA intermediate using reverse transcriptase (includes LINEs and SINEs)
                        First, endonuclease nicks DNA next to T-sits
                        3'OH of transposase will be nucelophile and covalently attach into target DNA. Fairly non-specefic."""
    },
    {
        "category": "MSI - Transposons",
        "question": "What are the differen transposable elements?",
        "answer_image":"transposons.png",
        "answer": """See below"""
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe the process of transcription initiation.",
        "answer": """1. Transcription factors bind promoter elements\n2. RNA Pol II recruited to form preinitiation complex\n3. Mediator complex facilitates enhancer-promoter interactions\n4. DNA unwinds at transcription start site\n5. RNA Pol II begins synthesis, escapes promoter after phosphorylation of CTD
                        TATA box is where RNA pol reads from 5' to 3'\n
                        Splicing and capping happen at the same time.
                        7-methylguanosine cap signifies the 5′ cap
                        
                        """,
        "answer_image": "trans_init.png"
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe the process of transcription elongation.",
        "answer": """rNTPs added by RNA Pol II at 3' OH, forming phosphodiester bonds. RNA Pol II has exonuclease activity and can check base pairs.
                        There is also 5' capping going on, splicing and polyadenylation."""
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe splicing.",
        "answer_image": "splicing.png",
        "answer": """Creation of the splicesome where snRNPs recognize intronic regions
                    you have a lariat structure that ends up being spliced out.
                    Exon Junction Complexes come and bind to splice sites."""
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe the process of poly adenylation.",
        "answer": """CF proteins recognize AAUAAA signal. PAP and PABP are recruited and start the process of polymerizing As."""
    },
    {
        "category": "MSI - Transcription",
        "question": "What is needed for mature RNA to be exported from nucleus?",
        "answer": """CBP, Poly A tail with PABPs, REF, NXF1, NXT1 - Nuclear export factors"""
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe the players in transcription .",
        "answer": """RNA Polymerase(s)
                - General transcription factors (sigma factors for prokaryotes)
                - TFIID (and TBP)
                - TFIIB
                - TFIIH
                - SWI/SNF family members
                - Histone acetyltransferases (HATs)
                - Histone deacetylases (HDACs)
                - Histone methyltransferases (HMTs)
                - Mediator, enhancer
                - cap binding protein
                - poly A tail
                """
    },
    {
        "category": "MSI - Transcription",
        "question": "Describe the process of transcription termination.",
        "answer": "In eukaryotes: polyadenylation signals (AAUAAA) recognized by cleavage factors; RNA cleaved downstream; polymerase continues briefly then terminates. Exonuclease degrades remaining transcript, helping release polymerase."
    },
    {
        "category": "MSI - Transcription",
        "question": "What do the different RNA Pols do?.",
        "answer": "RNA pol I = rRNA\nRNA pol II = mRNA\nRNA pol III tRNA"
    },
    {
        "category": "MSI - RNA Regulation",
        "question": "Describe mechanisms of post-transcriptional gene regulation/RNA stability.",
        "answer": "5' cap and 3' poly(A) tail protect from degradation; RNA-binding proteins stabilize/destabilize; miRNAs target for degradation; AU-rich elements (AREs) in 3' UTR decrease stability; nonsense-mediated decay removes aberrant transcripts."
    },
    {
        "category": "MSI - RNA Processing",
        "question": "How can you achieve transcript heterogeneity in a single gene?",
        "answer": "Alternative splicing: different combinations of exons included/excluded; alternative promoters; alternative polyadenylation sites; RNA editing (A-to-I, C-to-U). Results in multiple protein isoforms from one gene."
    },
      {
        "category": "MSI - Translation",
        "question": "Describe the players in transcription .",
        "answer": """RNA Polymerase(s)
                    - Ribosomal subunits - 40S, 60S
                    - rRNAs
                    - tRNAs
                    - Eukaryotic initiation factors (eIFs) - several of these (eIF2, eIF4 complex, )
                        * eIF2 recruits 40S subunit first and situate Met-tRNA, it starts scanning mRNA
                        * Once AUG found then 60S subunit comes in and starts forming peptide bonds with activated tRNA
                    - Elongation factors
                    - Release factors
                """
    },
    {
        "category": "MSI - Translation",
        "question": "Enumerate Translation Elongation.",
        "answer": """tRNA-GTP comes into A site of full ribosome. GTP is hydrolized to get free energy to create peptide bond with current protein in the P site.
                    The tRNA from the P site gets pushed to the E site where it leaves as the ribosome moves down along the RNA.
                """
    },
    {
        "category": "MSI - Translation",
        "question": "Explain two distinct mechanisms of translation initiation.",
        "answer": "1. Cap-dependent: ribosome binds 5' cap, scans for AUG start codon (Kozak sequence)\n2. IRES-mediated: Internal Ribosome Entry Site allows cap-independent binding in 5' UTR; used during stress or by some viruses"
    },
    {
        "category": "MSI - Translation",
        "question": "Explain the concept of NMD (Nonsense-Mediated Decay).",
        "answer": "Quality control mechanism that degrades mRNAs with premature termination codons (PTCs). Triggered when stop codon is >50-55 nucleotides upstream of exon-exon junction. Prevents production of truncated, potentially harmful proteins."
    },
    {
        "category": "MSI - Translation",
        "question": "Translation termination process",
        "answer": """UAA, UGA, UAG are the stop codons. Once they are read, the ribosomes attract an inert tRNA that causing it to pause as release factors come in to break the complex"""
    },
    {
        "category": "MSI - Translation",
        "question": "What can happen with a ribosome at the beginning of translation",
        "answer": """It can start at an AUG, it can stop and be held up, or it can skip the first AUG or entire exon."""
    },
    {
        "category": "MSI - Translation",
        "question": "How does Nonsense Mediated Decay Work and how can it arrise??",
        "answer": """EJCs found on transcript that don't get knocked off by ribosome during translation intiate this process.
                    This can happen due to an improper splice event that introduces an early stop codon leaving EJCs on mRNA.
                    UPFs serveile and recognize EJCs. Recruit enzymes to rapidly decay mRNA becaue EJC signal of damage.
                    """
    },
    {
        "category": "MSI - Translation",
        "question": "What are the forms of Non-Nonsense Mediated Decay?",
        "answer": """AU-rich elements trigger degradation of mRNA, miRNAs/RISC complex trigger mRNA degradation"""
    },
    {
        "category": "MSI - Translation",
        "question": "How can you increase or decrease translation of a gene of interest?",
        "answer": """ 
                    Increase:
                      - put stronger Kozak sequences in front of gene, increases promoter strength
                      - Increase number of copies of mRNA
                      - add IRES sites in front of gene
                      - weaken promoter elements of uORF or take uORF out alltogether 

                    Decrease:
                      - put weaker Kozak sequences in front of gene to decrease translation
                      - add uORFs in front of gene
                      - weaken the promoter region
                      - add miRNA binding sites in 3' UTR
        """
    },
    {
        "category": "MSI - Translation",
        "question": "How would the presence of a uORF impact translation?",
        "answer": "Upstream Open Reading Frame (uORF) generally reduces translation of main ORF. Ribosome may translate uORF and dissociate, or reinitiate at main start codon. Can regulate protein expression in response to cellular conditions."
    },
    {
        "category": "MSI - RNA Processing",
        "question": "What are exon-junction complexes?",
        "answer": "Protein complexes deposited 20-24 nucleotides upstream of exon-exon junctions during splicing. Mark properly spliced mRNAs; play roles in mRNA export, localization, translation enhancement, and NMD. Removed by translating ribosomes."
    },
    {
        "category": "MSI - Non-coding RNA",
        "question": "What are non-coding RNAs and how are they involved in regulation?",
        "answer": "RNAs that don't code for proteins but have regulatory functions: miRNAs (post-transcriptional silencing), lncRNAs (chromatin regulation, transcription), siRNAs (silencing), snRNAs (splicing), snoRNAs (rRNA modification). Regulate gene expression at multiple levels."
    },
    {
        "category": "MSI - Non-coding RNA",
        "question": "Describe the process of miRNA-dependent regulation.",
        "answer": "1. Pri-miRNA processed to pre-miRNA by Drosha\n2. Exported from nucleus\n3. Dicer cleaves to mature miRNA duplex\n4. One strand loaded into RISC complex\n5. miRNA guides RISC to complementary mRNA sequences (usually 3' UTR)\n6. Results in translational repression or mRNA degradation"
    },
    {
        "category": "MSI - Mutations",
        "question": "Define and provide an example of a point mutation.",
        "answer": "Single nucleotide change in DNA sequence. Example: sickle cell anemia - A→T substitution in β-globin gene (GAG→GTG, Glu→Val)"
    },
    {
        "category": "MSI - Mutations",
        "question": "Define and provide an example of a frameshift mutation.",
        "answer": "Insertion or deletion of nucleotides not divisible by 3, shifting reading frame. Example: Tay-Sachs disease - 4 bp insertion in HEXA gene causing frameshift and premature stop"
    },
    {
        "category": "MSI - Mutations",
        "question": "Define and provide an example of an insertion/deletion mutation.",
        "answer": "Insertion: addition of nucleotides into DNA sequence. Deletion: removal of nucleotides from DNA sequence. If not divisible by 3, causes frameshift. If divisible by 3, may just add/remove amino acids without frameshift. Example: Cystic fibrosis - deletion of 3 bp (ΔF508) removes single Phe residue without frameshift."
    },
    {
        "category": "MSI - Mutations",
        "question": "Differentiate between nonsense, missense, and silent mutations.",
        "answer": "Nonsense: creates stop codon, truncates protein (e.g., UAC→UAG)\nMissense: changes amino acid (e.g., sickle cell Glu→Val)\nSilent: changes nucleotide but same amino acid due to codon degeneracy (e.g., UCU→UCC, both Ser)"
    },
    {
        "category": "MSI - Mutations",
        "question": "How might effects of promoter mutation differ from coding region mutation?",
        "answer": "Promoter mutation: affects expression level (how much protein made), timing, or tissue specificity. Protein sequence unchanged.\nCoding region: affects protein structure/function but expression level may be normal. Can cause loss of function, gain of function, or dominant negative effects."
    },
    {
        "category": "MSI - Gene Regulation",
        "question": "Briefly describe how cell differentiation is transcriptionally regulated.",
        "answer": "Master transcription factors activate cell-type-specific genes; chromatin remodeling makes genes accessible/inaccessible; DNA methylation silences pluripotency genes; positive feedback loops maintain differentiated state; lineage-specific enhancers activated; epigenetic marks inherited through cell division."
    },
    {
        "category": "MSI - Gene Regulation",
        "question": "Describe mechanisms allowing sequence-specific transcription factors to interact with DNA.",
        "answer": "Recognition through: helix-turn-helix, zinc fingers, leucine zippers, helix-loop-helix domains. Read DNA sequence via major groove contacts; recognize specific base sequences; use hydrogen bonds and van der Waals interactions; cooperative binding increases specificity."
    },
    {
        "category": "MSI - Gene Regulation",
        "question": "How do sequence-specific transcription factors influence chromatin at gene-regulatory elements?",
        "answer": "Recruit chromatin remodeling complexes (move/eject nucleosomes); recruit histone-modifying enzymes (HATs, HDACs, methyltransferases); create accessible regions for other factors; stabilize nucleosome-depleted regions; facilitate enhancer-promoter looping."
    },
    {
        "category": "MSI - Gene Regulation",
        "question": "Compare/contrast cis and trans regulatory elements.",
        "answer": "Cis: DNA sequences on same chromosome as gene they regulate (promoters, enhancers, silencers); act locally.\nTrans: factors that regulate genes (transcription factors, regulatory RNAs); produced elsewhere, can diffuse; act on multiple genes."
    },
    {
        "category": "MSI - Model Organisms",
        "question": "How would you generate a mouse model lacking a gene of interest?",
        "answer": "CRISPR/Cas9 or homologous recombination to knockout gene in ES cells; inject into blastocysts; generate chimeric mice; breed for germline transmission. If embryonic lethal: use conditional knockout (Cre-lox system) with tissue-specific or inducible Cre."
    },
    {
        "category": "MSI - Membrane Structure",
        "question": "Describe the make-up of a eukaryotic cell membrane.",
        "answer": "Lipid bilayer with:\n- Phospholipids: phosphatidylcholine, phosphatidylserine (inner leaflet), phosphatidylethanolamine\n- Sphingolipids: sphingomyelin, glycolipids (outer leaflet)\n- Cholesterol: both leaflets, modulates fluidity\nAsymmetric distribution; fluid mosaic model with embedded proteins"
    },
    {
        "category": "MSI - Membrane Structure",
        "question": "Compare/contrast phospholipids, sphingolipids, and sterols.",
        "answer": "Phospholipids: glycerol backbone, 2 fatty acid tails, phosphate head\nSphingolipids: sphingosine backbone, 1 fatty acid, variable head group; includes ceramide, sphingomyelin\nSterols: rigid 4-ring structure (cholesterol); modulates membrane fluidity and permeability"
    },
    {
        "category": "MSI - Membrane Proteins",
        "question": "Discuss how proteins are anchored to the membrane.",
        "answer": "1. Transmembrane domains: α-helices or β-barrels spanning bilayer\n2. Lipid anchors: GPI anchor, palmitoylation, myristoylation, prenylation\n3. Protein-protein interactions: binding to transmembrane proteins\n4. Electrostatic interactions: with charged lipid head groups"
    },
    {
        "category": "MSI - Methodology",
        "question": "How could you experimentally determine if a protein domain is intracellular/extracellular?",
        "answer": "Protease protection assay: treat intact cells with protease (cannot cross membrane); if domain digested, it's extracellular; if protected, intracellular. Or use antibodies against domain in non-permeabilized cells (only bind if extracellular). Glycosylation also indicates extracellular."
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "",
        "answer": """"""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "Give an example of two membranes from different organelles and how their composition differs",
        "answer": """Liver hepatoycte vs Pancreatic exocrine cell
                     - liver hepatocyte has less rough ER membrane and more smooth ER membrane. 
                     - Pancreatic exocrine cell has more rough ER membrane and less smooth ER membrane. It needs to 
                       secrete more proteins."""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "What are the different compartments and their compositions in a cell and why important",
        "answer_image": "memstruct.png",
        "answer": """BARRIER FUNCTION AND COMPARTMENTATLIZATION
                        mitchondrial matrix similar to extracellular matrix
                        so is endosome/golgi/nuclear envelop membrane space"""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "What are the three main classes of membrane lipids (compare/contrast) and what are their characteristics?",
        "answer_image": "memlipids.png",
        "answer": """Phospholipids - two fatty acid mocules to glycerol backbone, 
                    and different kinds of head groups attached, huge diversity because of head groups and fatty 
                    acids attached with different carbons and double bonds
                      - glycerophospholipids
                      - sphingomyelin - they look similar to glycerol, but they have sphingosine, 
                        have a fatty acid similar to fatty acid - and can have different head groups

                    Glycosphingolipids - Branched sugars instead of phosphate head groups
                    Sterols - 
                    
                    * all amphipathic molecules with polar head groups, insoluble in water, """
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "What are the types of glycerophospholipids and what makes them diff from sphingophospholipids?",
        "answer_image": "glycerophospholipids.png",
        "answer": """Phosphotidylinositol, phosphotidylserine, phosphotidylethanolamine, phosphotidylchloine, phosphotidic acid
                    Sphingophospholipids - sphingomyelin, both fatty acid tails are saturated with no double bonds"""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "What characterises the different levels of organism's membrane composition and structure?",
        "answer": """bacteria simple, no vesicle trafficking, mostly PE, PG and CL with membrane proteins
                    Yeast - SP, GPs and sterols, more complex, vesicle trafficking and budding, all same cells
                    Higher order organisms - more complex, different cell types with different specific functions, 
                    tissue specific SP. Complex cellular architecture."""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "Which is more thick a membrane of phospholipids or sphingolipids and why?",
        "answer_image": "memthick.png",
        "answer": """SPhingolipids would be thicker due to being saturated and not having double bonds
                whereas phospholipids have double bonds and kinks in them making them less thick"""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "",
        "answer": """"""
    },
    {
        "category": "MSII - Membrane Dynamics",
        "question": "How could you experimentally determine lateral mobility of a membrane protein?",
        "answer": "FRAP (Fluorescence Recovery After Photobleaching): tag protein with fluorophore, bleach region, measure fluorescence recovery rate. Faster recovery = higher mobility. Or single-particle tracking to follow individual molecules."
    },
    {
        "category": "MSII - Membrane Structure",
        "question": "Discuss the structure and function of lipid rafts.",
        "answer": "Membrane microdomains enriched in cholesterol, sphingolipids, and specific proteins (GPI-anchored, src-family kinases). More ordered/rigid than surrounding membrane. Function: concentrate signaling molecules, organize receptors, facilitate endocytosis, compartmentalize cellular processes."
    },
    {
        "category": "MSII - Cell Organization",
        "question": "Explain the concept of cellular compartmentalization.",
        "answer": "Separation of biochemical processes into membrane-bound organelles. Allows: concentration of specific enzymes/substrates, optimization of local conditions (pH, ions), protection from incompatible reactions, regulated transport between compartments, increased efficiency."
    },
    {
        "category": "MSII - Organelles",
        "question": "Explain the primary role(s) of each cellular organelle.",
        "answer": "Nucleus: DNA storage, transcription\nER: protein/lipid synthesis, Ca2+ storage\nGolgi: protein modification, sorting\nMitochondria: ATP production\nLysosomes: degradation\nPeroxisomes: fatty acid oxidation, H2O2 breakdown\nEndosomes: sorting endocytosed material"
    },
    {
        "category": "MSII - Cytoskeleton",
        "question": "Describe a function of each cytoskeletal structure.",
        "answer": "Actin (microfilaments): cell shape, motility, muscle contraction, cytokinesis\nMicrotubules: intracellular transport, chromosome segregation, cell polarity, cilia/flagella\nIntermediate filaments: mechanical strength, nuclear structure, tissue integrity"
    },
    {
        "category": "MSII - Cytoskeleton",
        "question": "Describe the roles of cytoskeletal structures in mitosis.",
        "answer": "Microtubules: form mitotic spindle, attach to kinetochores, separate chromosomes\nActin: forms contractile ring for cytokinesis, generates force for cleavage furrow\nIntermediate filaments: disassemble nuclear lamina at prophase, reassemble at telophase"
    },
    {
        "category": "MSII - Cytoskeleton",
        "question": "Compare/contrast structure and processing of microfilaments and microtubules.",
        "answer": "Actin: 7nm diameter, helical polymer of actin monomers, plus end grows faster, ATPase activity, treadmilling\nMicrotubules: 25nm diameter, hollow tube of αβ-tubulin dimers (13 protofilaments), plus end grows faster, GTPase activity, dynamic instability (rapid growth/shrinkage)"
    },
    {
        "category": "MSII - Cytoskeleton",
        "question": "Describe the process of cargo movement along microtubules.",
        "answer": "Motor proteins (kinesins, dyneins) bind cargo via adaptor proteins. Kinesins move toward plus end (periphery); dyneins toward minus end (center). Use ATP hydrolysis for conformational changes that generate movement. Step processively along microtubule surface."
    },
    {
        "category": "MSII - Cell Motility",
        "question": "How does actin aid in cellular locomotion?",
        "answer": "Actin polymerization at leading edge pushes membrane forward (lamellipodia/filopodia formation); myosin II contraction at rear generates pulling force; focal adhesions provide traction; coordinated assembly/disassembly creates net forward movement; Rho GTPases regulate dynamics."
    },
    {
        "category": "MSII - ECM",
        "question": "Describe the major components of the extracellular matrix.",
        "answer": "Fibrous proteins: collagen (tensile strength), elastin (elasticity), fibronectin (cell adhesion)\nProteoglycans: core protein with GAG chains; resist compression; bind water\nGlycoproteins: laminin (basement membrane)\nProvide structural support, regulate cell behavior, reservoir for growth factors"
    },
    {
        "category": "MSII - Membrane Transport",
        "question": "Differentiate between various membrane transporters.",
        "answer": "Channels: passive, always open or gated (voltage/ligand)\nCarriers: bind substrate, undergo conformational change\nPumps: active transport using ATP\nPores: large opening for multiple molecules\nUniporters: one molecule one direction\nSymporters/antiporters: coupled transport"
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "Describe what an action potential is and the contributing ion movement.",
        "answer": "Rapid depolarization then repolarization of membrane potential.\n1. Depolarization: voltage-gated Na+ channels open, Na+ influx\n2. Repolarization: Na+ channels inactivate, K+ channels open, K+ efflux\n3. Hyperpolarization: excess K+ efflux\n4. Return to resting via Na+/K+ ATPase"
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "How are action potentials propagated?",
        "answer": "Local depolarization spreads to adjacent membrane, triggering voltage-gated Na+ channels there. In myelinated axons: saltatory conduction jumps between nodes of Ranvier (faster, more efficient). Refractory period prevents backward propagation."
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "Describe the process of synaptic transmission.",
        "answer": "1. Action potential reaches presynaptic terminal\n2. Voltage-gated Ca2+ channels open\n3. Ca2+ influx triggers vesicle fusion (SNARE proteins)\n4. Neurotransmitter released into cleft\n5. Binds postsynaptic receptors\n6. Triggers postsynaptic response\n7. Neurotransmitter cleared by reuptake/degradation"
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "Compare/contrast excitatory and inhibitory postsynaptic currents.",
        "answer": "EPSC (glutamate): opens Na+/K+ channels, depolarization, increases firing probability\nIPSC (GABA): opens Cl- or K+ channels, hyperpolarization, decreases firing probability\nIntegration of EPSCs and IPSCs determines whether postsynaptic neuron fires"
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "Describe synaptic plasticity.",
        "answer": "Activity-dependent changes in synaptic strength. Includes short-term (facilitation/depression lasting seconds-minutes) and long-term changes (LTP/LTD lasting hours-years). Basis for learning and memory. Involves changes in receptor number, neurotransmitter release, or synapse structure."
    },
    {
        "category": "MSII - Neurophysiology",
        "question": "What is long term potentiation and what is its mechanism?",
        "answer": "Persistent strengthening of synapses after high-frequency stimulation. Mechanism: glutamate binds AMPA receptors (depolarization); removes Mg2+ block from NMDA receptors; Ca2+ influx through NMDA; activates CaMKII and other kinases; increases AMPA receptors at synapse; structural changes. Requires coincident pre/postsynaptic activity."
    },
    {
        "category": "MSII - Protein Trafficking",
        "question": "Describe the production of a secreted protein starting with mRNA.",
        "answer": "1. Translation begins in cytosol\n2. Signal sequence recognized by SRP\n3. SRP-ribosome complex binds ER\n4. Ribosome docks, translation continues into ER lumen\n5. Signal sequence cleaved\n6. N-glycosylation in ER\n7. Folding with chaperones\n8. Quality control\n9. Transport through Golgi (further modifications)\n10. Packaged in vesicles, secreted"
    },
    {
        "category": "MSII - Protein Trafficking",
        "question": "Describe inserting a multi-pass transmembrane protein into the ER.",
        "answer": "SRP recognizes first signal-anchor sequence; ribosome docks at translocon; start-transfer sequence opens lateral gate, inserts into membrane; stop-transfer sequence follows, closes gate; alternating start/stop sequences create multiple passes; hydrophobic segments remain in lipid bilayer; topology determined by charge distribution (positive inside rule)."
    },
    {
        "category": "MSII - ER Stress",
        "question": "Describe the three components of the unfolded protein response.",
        "answer": "1. PERK: phosphorylates eIF2α, reduces translation, activates ATF4 (increases chaperones)\n2. IRE1: splices XBP1 mRNA, XBP1 TF increases ER capacity\n3. ATF6: cleaved in Golgi, TF activates chaperone genes\nCollectively: reduce protein load, increase folding capacity, activate ERAD, or trigger apoptosis if unresolved"
    },
    {
        "category": "MSII - Endocytosis",
        "question": "What are the major functions of endocytosis?",
        "answer": """Regulation of cell surface expression of proteins (and uptake of bound ligands) to terminate, sustain, or diversify cell signaling
                    Internalization of nutrients
                    Uptake & digestion of extracellular debris
                    Recovery of membrane inserted into the plasma membrane during exocytosis
                    """
    },
    {
        "category": "MSII - Endocytosis",
        "question": "What are the major types of endocytosis?",
        "answer": """Clatherin - medium coated invaginations - 3 heavy and light chains basketlike - 
                                PIP2 recruits AP2 (adapter protein)
                                AP2 open binds clatherin and cargo receptors which add attract cargo, 
                                BAR domain proteins bend membrane, GTPase-dynamin pinches it off. 
                     Caveolin - caveolin coated small invaginations - in lipid rafts (sphingolipids and cholesterol) - BBB transcytosis
                     Macropinocytosis - clatherin independent, surface receptor causes actin filament structure- ruffled surface - similar to phagocytosis, but only liquid is taken up. Large vesicle of solutes 
                     Phagocytosis - No invagination clatherin independent. Cell surface receptor instigated. Macrophages, neutrophils -  actin filament catalyzation to form large vesicle pseudopod around macromolecules outside of cell and uptake into phagosome - fuse with lysosome.
                    """
    },
    {
        "category": "MSII - Endocytosis",
        "question": "What are the different Phosphotidylinositols (PI) and PI-phosphates (PIP) Role in endocytosis",
        "answer": """Phosphatases & kinases localized to different organelles, catalyze the production of different PIPs
                    TRANSDUCTION. They provide binding site for recruitiment of signalling molecules. 
                    Important for cellular trafficking. Recruit different proteins. 
                    ---
                    PIP2 mainly on cell surface
                    PI3P mainly on endosomes
                    PI4P on golgi
                    PI 3, 4, 5, P3 – phagocytosis – enclosure of phagosome
                    PI 3 KINASE VERY IMPORTANT 
                    """
    },
    {
        "category": "MSII - Endocytosis",
        "question": "What are the different kinds of endosomes?",
        "answer": """Recycling endosome (pH ~6.5)- Intermediate stage in the passage of recycled receptors back to cell membrane. Can store proteins until later needed
                    Lysosome (pH as low as 4.5). Contains hydrolytic enzymes. Degrades endocytosed material
                    Early endosome (pH ~6.0) Receiving & sorting compartment Fuse with endocytic vesicles Internalized cargo sorted: 
                    return to plasma membrane send to late endosome for degradation
                    Late endosomes (pH 5-5.5)Formed from bulbous, vacuolar portion of early endosome via “endosome maturation” Fuse with lysosomes to form endolysosomes 
                    and degrade contents
                    pH decreases as endosomes develope: Recycling 6.5 (dont want to destroy proteins) > Early endosome (6) > Late endosome (5) > lysosome (4.5 - degradation)
                    """
    },
    {
        "category": "MSII - Endocytosis",
        "question": "Explain the process of receptor-mediated endocytosis.",
        "answer": "1. Ligand binds cell surface receptor\n2. Receptors cluster in clathrin-coated pits\n3. Adaptor proteins (AP2) link receptors to clathrin\n4. Pit invaginates\n5. Dynamin pinches off vesicle\n6. Clathrin coat removed\n7. Vesicle fuses with early endosome\n8. Receptors sorted: recycling vs degradation (late endosome/lysosome)"
    },
    {
        "category": "MSII - Phagocytosis",
        "question": "Explain the process of phagocytosis.",
        "answer": "1. Recognition of particle (opsonins, pattern recognition receptors)\n2. Actin-driven pseudopod extension engulfs particle\n3. Forms phagosome\n4. Phagosome matures: acidification, fusion with lysosomes\n5. Forms phagolysosome\n6. Degradation by hydrolases and ROS\n7. Antigen presentation (in immune cells)"
    },
    {
        "category": "MSII - Exocytosis",
        "question": "Describe vesicle formation/coating in exocytosis.",
        "answer": """ """
    },
    {
        "category": "MSII - Exocytosis",
        "question": "Describe Vesicle Trafficking Pathway for Exocytosis",
        "answer": """Can go directly to extracellular space.
                     Can be sent to early endosome - and then out to extracellular space
                     Can be sent right late endosome then lysosome.
                     Can be recycled after release.
                     Rab GTPases are critical regulators of vesicle targeting to specific membrane compartments. Rab GTP recognizes tethering protein

                    """
    },
    {
        "category": "MSII - Exocytosis",
        "question": "Describe Regulated Exocytosis",
        "answer": """Very dense vesicles - requires signal. Docking, priming, fusion. 
                     STX1 - syntaxin - t-SNARE- associated with target membrane; SNAP25-also target membrane; 
                     VAMP2 - synaptobrevin - v-SNARE - associated with vesicle membrane;
                     Synaptotagmin - Ca2+ sensor.
                     Munc13, 18 - allow for trans orientation
                     IE: GLUT vesicles responding to insulin, neurotransmitter release in response to calcium. 
                     Vesicle docked. With Complexin preventing membrane fusion. AP - Ca2+-triggered. Ca2+ binds synaptotagmin displacing Complexin
                     Pore open and release vesicle contents. Dissasembly by NSF-ATPase for recycling.
                    """
    },
    {
        "category": "MSII - Exocytosis",
        "question": "Where does mannos 6 phosphate direct vesicles? and what to GTPases do in exocytosis?",
        "answer": """Lysosome. N-linked Mannose 6 Phosphate from GlcNac\nRab GTPases and motor proteins direct vesicles along cytoskeleton; tethering factors capture vesicles\nFusion: v-SNARE on vesicle pairs with t-SNARE on target membrane; 
                    """
    },
    {
        "category": "MSII - Exocytosis",
        "question": "Describe Constitutive Exocystosis",
        "answer": """No signal needed. Content is more soluble and less dense than regulated vesicles. Used for upkeep of plamsa membrane. 
                    
                    """
    },
    {
        "category": "MSII - Protein Trafficking",
        "question": "How are proteins trafficked to mitochondria?",
        "answer": """Matrix - Proteins synthesized in cytosol with N-terminal mitochondrial targeting sequence (amphipathic α-helix, positively charged). Chaperones keep unfolded. TOM(20-40)/TIM23/PAM-ATP complex (outer membrane) and TIM complex (inner membrane) import protein. Requires membrane potential and ATP. 
                     Signal sequence cleaved by matrix peptidase (MPP).
                     Inner Membrane Space - cystein rich residues, imported through TOM40 directly.
                     Outer Membrane - Beta Barrel stucture - TOM then TIM 9/10 chaperones and into the SAM complex to be put into membrane
                     Inner Membrane Carrier Proteins (metabolite) - in through TOM40, shuttled by TIM 9/10 and into TIM 22 carrier translocase
                     Outer membrane alpha helices - Mitochondrial import complex, no TOM
                    """
    },
    {
        "category": "MSII - Protein Trafficking",
        "question": "How are proteins trafficked to the nucleus?",
        "answer": "Nuclear localization signal (NLS, rich in basic amino acids Lys/Arg) recognized by importins. Importin-cargo complex docks at nuclear pore complex. Ran-GTP gradient drives translocation. In nucleus, Ran-GTP causes cargo release. Can occur on folded proteins (unlike other organelles)."
    },
    {
        "category": "MSII - Ubiquitination",
        "question": "How do proteins become ubiquitinated?",
        "answer": "Three-enzyme cascade:\n1. E1 (ubiquitin-activating): activates ubiquitin using ATP\n2. E2 (ubiquitin-conjugating): transfers ubiquitin from E1\n3. E3 (ubiquitin ligase): provides substrate specificity, catalyzes transfer to lysine on target\nCan form chains (polyubiquitination) via different lysine linkages"
    },
    {
        "category": "MSII - Ubiquitination",
        "question": "What are the functions of ubiquitination?",
        "answer_image": "ubiqk.png",
        "answer": "Poly - K48-linked chains: proteasomal degradation, K63-linked chains: DNA repair\nMono-ubiquitination: histone regulation, Multi - ubiquitination: endocytosis"
    },
    {
        "category": "MSI - Methodology",
        "question": "Design an experiment to identify a binding partner of your favorite protein.",
        "answer": "Co-immunoprecipitation (Co-IP): lyse cells, immunoprecipitate protein of interest with specific antibody, identify bound proteins by mass spectrometry. Or yeast two-hybrid screening. Or proximity labeling (BioID, APEX) followed by mass spec. Validate interactions by co-IP, pull-downs, or in vitro binding assays."
    },
    {
        "category": "MSI - Methodology",
        "question": "Design an experiment to determine if a protein binds DNA and identify the sequence.",
        "answer": "ChIP-seq: crosslink protein to DNA, fragment chromatin, immunoprecipitate protein, sequence bound DNA fragments, map to genome. Or EMSA (gel shift) to test binding. Or DNA affinity purification. Use motif analysis to identify consensus binding sequence. Validate with EMSA using specific sequences."
    },
    {
        "category": "MSI - Methodology",
        "question": "Describe methods to map transcription factor binding across a genome.",
        "answer": """ChIP-seq: gold standard, requires specific antibody, shows in vivo binding.
                        Strengths: physiological conditions, direct binding
                        Weaknesses: requires antibody, crosslinking artifacts
                     DNase-seq/ATAC-seq: maps open chromatin (indirect)
                        Strengths: no antibody needed\n
                        Weaknesses: doesn't identify specific TF
                     CUT&RUN: Mn5 mnase bound to ab for protein of interest. Cleaves around bound ab. 
                        Stregnths: newer, less input material, high signal-to-noise. Can be done at physiological conditions so better for TFs.
                        Weaknesses: Still have to do ligation and PCR amplification
                     CUT&Tag: Tn5 Transposase, newer, less input material, high signal-to-noise.
                        Strengths: less processing steps since Tn5 does tagmentation
                        Weaknesses: Has to be done at high salt, only good for histone DNA binding.
                    """
    },
    {
        "category": "MSI - Protein Modifications",
        "question": "Identify protein modifications, what makes them, and what amino acids are modified.",
        "answer": "Phosphorylation: kinases, Ser/Thr/Tyr\nAcetylation: acetyltransferases (HATs), Lys\nMethylation: methyltransferases, Lys/Arg\nUbiquitination: E1/E2/E3 enzymes, Lys\nSUMOylation: E1/E2/E3 enzymes, Lys\nGlycosylation: glycosyltransferases, Asn/Ser/Thr\nProteolysis: proteases, various\nPalmitoylation: palmitoyltransferases, Cys\nMyristoylation: NMT, Gly"
    },
    {
        "category": "MSI - Protein Modifications",
        "question": "Provide specific examples of protein modifications and their functions.",
        "answer_image": "protmod.png",
        "answer": """
                - Acetyl on Lys Helps to activate genes in chromatin by modifying histones.
                - Palmityl group on Cys This fatty acid addition drives protein association with membranes. 
                - Phosphate on Ser, Thr, or Tyr Drives the assembly of a protein into larger complexes.
                - Methyl on Lys Helps to create distinct regions in chromatin by forming either monomethyl, dimethyl, or
                    trimethyl lysine in histones.
                - Glycosylation on Asparagine - Critical for protein folding, stability, cellular targeting, and protein-protein interactions. 
                - Hydroxylation of proline - protein stability.
                - N-Acetylglucosamine on Ser or Thr Controls enzyme activity and gene expression in glucose homeostasis
                - Ubiquitin on Lys Monoubiquitin/Multiubuquitin addition regulates the transport of membrane proteins in vesicles, polyubiquitin chain targets a protein for degradation.
                """
    },
    {
        "category": "MSI - Enzyme Mechanisms",
        "question": "Describe the ways an enzyme can catalyze reactions at the molecular level.",
        "answer": "1. Stabilize transition state (lower activation energy)\n2. Provide acid-base catalysis (proton donors/acceptors)\n3. Induce strain in substrate bonds\n4. Orient substrates properly for reaction\n5. Provide nucleophilic/electrophilic groups\n6. Stabilize intermediates\n7. Shield reaction from water (if needed)\n8. Use cofactors/prosthetic groups"
    },
    {
        "category": "MSI - Gene Structure",
        "question": "Describe the structure of a typical gene.",
        "answer": "5' to 3': Promoter (TATA box, CAAT box, GC box), 5' UTR, start codon (ATG), exons and introns, stop codon, 3' UTR, polyadenylation signal (AATAAA). Also: enhancers (upstream/downstream/intronic), silencers, insulators. Core promoter spans ~40 bp around TSS."
    }
]


# Gather unique categories
categories = ["All"] + sorted(set(card["category"] for card in flashcards if "category" in card))

# --- Session State Initialization and Core Functions ---

# Initialize session state (Added 'deck' to store the active, filtered list)
if 'current_card' not in st.session_state:
    st.session_state.current_card = 0
if 'is_flipped' not in st.session_state:
    st.session_state.is_flipped = False
if 'shuffled' not in st.session_state:
    st.session_state.shuffled = False
if 'filter_category' not in st.session_state:
    st.session_state.filter_category = "All"
if 'deck' not in st.session_state: # NEW: Holds the cards currently being used/shuffled
    st.session_state.deck = []


def update_deck(category):
    """Filters cards based on category and resets state."""
    st.session_state.filter_category = category
    if category == "All":
        st.session_state.deck = list(flashcards)
    else:
        st.session_state.deck = [card for card in flashcards if card["category"] == category]
    
    # Reset state
    st.session_state.current_card = 0
    st.session_state.is_flipped = False
    st.session_state.shuffled = False

def shuffle_cards():
    """Shuffles the currently active deck in session state."""
    # **THIS IS THE CRITICAL CHANGE:** Shuffle the session state 'deck'
    random.shuffle(st.session_state.deck)
    st.session_state.shuffled = True
    st.session_state.current_card = 0
    st.session_state.is_flipped = False

def reset_cards():
    """Resets to All category and initial order."""
    update_deck("All")
    st.session_state.shuffled = False
    st.session_state.current_card = 0
    st.session_state.is_flipped = False

# Ensure the deck is loaded on initial run
if not st.session_state.deck and 'category_select' not in st.session_state:
    update_deck(st.session_state.filter_category)

# Get the current active deck
filtered_cards = st.session_state.deck

# Adjust current card if out of range (due to filtering)
if st.session_state.current_card >= len(filtered_cards) and len(filtered_cards) > 0:
    st.session_state.current_card = 0
elif len(filtered_cards) == 0:
    st.session_state.current_card = 0

# Helper function to get image data as base64 (Retained)
def get_image_base64(image_filename):
    path = os.path.join("images", image_filename)
    if os.path.exists(path):
        # NOTE: This function isn't used in your final display logic, 
        # but is kept for completeness.
        return base64.b64encode(open(path, "rb").read()).decode()
    else:
        return None

# Custom CSS for nicer style, including images (Retained)
st.markdown("""
<style>
.main {
    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
}
.stButton>button {
    width: 100%;
}
.flashcard {
    background: white;
    border-radius: 15px;
    padding: 40px;
    box-shadow: 0 10px 30px rgba(0,0,0,0.3);
    min-height: 400px;
    display: flex;
    flex-direction: column;
    align-items: center;
}
.category-badge {
    display: inline-block;
    background: #667eea;
    color: white;
    padding: 8px 16px;
    border-radius: 20px;
    font-size: 14px;
    margin-bottom: 20px;
}
.answer-badge {
    display: inline-block;
    background: #48bb78;
    color: white;
    padding: 8px 16px;
    border-radius: 20px;
    font-size: 14px;
    margin-bottom: 20px;
}
img {
    max-width: 100%;
    height: auto;
    margin: 15px 0;
    border-radius: 10px;
    box-shadow: 0 4px 8px rgba(0,0,0,0.1);
}
</style>
""", unsafe_allow_html=True)

# Title
st.title("🧬 MSI/MSII Flashcards")
st.markdown(f"**{len(filtered_cards)} cards** • Study smarter, not harder!")

# Controls
col1, col2, col3, col4 = st.columns([2, 1, 1, 1])

with col1:
    # Use on_change callback to trigger update_deck and re-render
    st.selectbox(
        "Filter by Category",
        categories,
        index=categories.index(st.session_state.filter_category),
        key="category_select",
        on_change=lambda: update_deck(st.session_state.category_select)
    )

with col2:
    # Changed button action to call the fixed function
    if st.button("🔀 Shuffle", use_container_width=True):
        shuffle_cards()
        st.rerun()

with col3:
    # Changed button action to call the fixed function
    if st.button("↻ Reset", use_container_width=True):
        reset_cards()
        st.rerun()

with col4:
    if st.button("🔄 Flip Card", use_container_width=True):
        st.session_state.is_flipped = not st.session_state.is_flipped
        st.rerun()

st.markdown("---")

# Flashcard display
if len(filtered_cards) > 0:
    current_card_data = filtered_cards[st.session_state.current_card]
    
    if not st.session_state.is_flipped:
        # Question side (Retained)
        flashcard_html = f"""
        <div class="flashcard">
            <div class="category-badge">{current_card_data["category"]}</div>
            <h2 style="color: #2d3748; line-height: 1.6;">{current_card_data['question']}</h2>
            <br><br>
            <p style="text-align: center; color: #a0aec0; font-size: 14px;">👆 Click 'Flip Card' button to reveal the answer</p>
        </div>
        """
        st.markdown(flashcard_html, unsafe_allow_html=True)

        # Display Question Image (Retained)
        if "question_image" in current_card_data:
            img_file = current_card_data["question_image"]
            img_path = os.path.join("images", img_file)
            if os.path.exists(img_path):
                st.image(img_path, caption=current_card_data["question"])
            else:
                st.error(f"Question image not found: {img_file}")

    else:
        # Answer side (Retained)
        answer_text = current_card_data["answer"].replace("\n", "<br>")
        
        flashcard_html = f"""
        <div class="flashcard">
            <div class="answer-badge">Answer</div>
            <div style="color: #2d3748; font-size: 18px; line-height: 1.8; white-space: pre-wrap;">
                {answer_text}
            </div>
        </div>
        """
        st.markdown(flashcard_html, unsafe_allow_html=True)
        
        # Display Answer Image (Retained)
        if "answer_image" in current_card_data:
            img_col1, img_col2, img_col3 = st.columns([1, 4, 1])
            img_file = current_card_data["answer_image"]
            img_path = os.path.join("images", img_file)
            if os.path.exists(img_path):
                with img_col2:
                    st.image(img_path, caption="Answer Illustration")
            else:
                st.error(f"Answer image not found: {img_file}")
    
    st.markdown("---")
    
    # Navigation (Retained)
    col1, col2, col3 = st.columns([1, 2, 1])
    
    with col1:
        if st.button("⬅️ Previous", use_container_width=True):
            st.session_state.current_card = (st.session_state.current_card - 1) % len(filtered_cards)
            st.session_state.is_flipped = False
            st.rerun()
    
    with col2:
        st.markdown(f"<h3 style='text-align: center;'>Card {st.session_state.current_card + 1} of {len(filtered_cards)}</h3>", unsafe_allow_html=True)
        progress = (st.session_state.current_card + 1) / len(filtered_cards)
        st.progress(progress)
    
    with col3:
        if st.button("Next ➡️", use_container_width=True):
            st.session_state.current_card = (st.session_state.current_card + 1) % len(filtered_cards)
            st.session_state.is_flipped = False
            st.rerun()
else:
    st.warning("No cards available for the selected category.")

# Footer (Retained)
st.markdown("---")
st.markdown("💡 **Study Tips:** Try to answer each question before flipping. Use the shuffle feature to test your recall without position cues!")