IMMS revised Flashcards
What is the structure of DNA? (coiling)
double helix
coils around nucleosomes and coils again into supercoils
then into chromosomes
What are the 4 DNA bases and their pairing?
Adenine binds to thymine (2 H bonds)
Guanine binds to cytosine (3 H bonds)
How many chromosomes are there?
46
22 pairs then sex chromosomes
Structure of chromosomes
Long arm (q)
Short arm (p)
Centromere controls movement at division
Telomere seals tip
Each chromosome contains hundreds of genes
What stains can be used to see chromosomes?
Giemsa: G banding
Quinacrine: Q banding
What does mitosis do?
Producing two daughter cells genetically identical to parent cell
Growth
Replace dead cells
What are the stages of the cell cycle?
G1
S phase
G2
Mitosis
Are mitotically inactive cells in the cell cycle?
No
They are in G0
What happens in interphase?
Cell grows
Replication of cytoplasmic organelles and DNA
When in the cell cycle does DNA replication occur?
S phase
What happens in prophase?
Chromatin condenses into chromosomes
Centrosomes nucleate microtubles and move to opposite poles of nucleus
What happens in prometaphase?
Nuclear membrane breaks down
Microtubules invade nuclear space
Chromatids attach to microtubules
What happens in metaphase?
Chromosomes line up along equatorial plane (metaphase plate)
What happens in anaphase?
Sister chromatids separate and are pushed to opposite poles of the cell
What happens in telophase?
Nuclear membranes reform
Chromosomes unfold into chromatin
Cytokinesis begins
Why is mitosis clinically relevant?
Categorising tumours as benign or malignant
Detecting chromosomal abnormalities
Grading malignant tumours
What does meiosis produce?
4 genetically different daughter cells
2 divisions
Where can mitosis and meiosis occur?
Mitosis can occur in all cells
Meiosis can only happen in gametes
How are sperm produced?
Primordial germ cells undergo mitoses to produce spermatogonia
Meiotic divisions commence at puberty
cytoplasm divides evenly
After meiosis II four equal gametes
Millions of mature sperm continuously produced
How long does sperm production take?
60-65 days
How are ova produced?
Primordial germ cell undergoes mitosis in utero to produce oogonia
First meiotic division in utero
Process suspended until ovulation in future
Second meiotic division only at fertilisation
Does the cytoplasm divide equally in ova?
No
1 egg and 3 polar bodies that apoptose
What is non-dysjunction?
Failure of chromosome pairs to separate in Meiosis I or sister chromatids to separate properly in meiosis II
What is trisomy 21?
Downs syndrome
What is gonadal mosaicism?
Occurs when precursor germline cells to ova or spermatozoa are a mixture of two or more genetically different cell lines
One cell line is normal, the other mutated
Increasing risk with advancing paternal age
Parent is healthy, but the fetus may have a genetic disease
What does genotype mean?
genetic constitution of an individual
What does phenotype mean?
Appearance of an individual that results from the interaction of the environment and genotype
What does allele mean?
One of several alternative forms of a gene at a specific locus
What do homozygous and heterozygous mean?
Homo: alleles at locus the same
Hetero: alleles at locus different
What does hemizygous mean?
only one copy of a gene rather than the usual two copies
e.g. men on an X chromosome
What is a rare disease?
Affects 1 in 2000 people
Signs of rare disease
Group of congenital abnormalities
Extreme presentation of common conditions
Neurodevelopmental delay or degeneration early
Extreme pathology
What is the karyotype for a girl with Edwards syndrome?
47, XX, +18
What is the karyotype for a girl with Downs?
47, XX, +21
What is the karyotype for a girl with Patau?
47, XX, +13
What is the karyotype for Turners?
45, X
What is translocation?
A type of chromosome mutation where part of one chromosome is transferred to another part of the same chromosome or a different one
What can deletion of 5p cause?
Cri du chat
What can a deletion of 15q cause?
Prader Willi
Angelman
What is FISH?
Fluorescence in situ hybridisation
Probe labelled with fluorochrome
Separate DNA
Hybridize probes onto DNA
How does microarray work?
Probe DNA
Add to slide
Look under fluorescent microscope at colour ratios
What are constitutional abnormalities?
Occur at gametogenesis and affect most all in body
Heritable
What are acquired abnormalities?
Changes occur during lifetime
Malignant changes in malignant tissue
Not heritable
How can cytogenetics help in acquired abnormalities?
Confirm malignancy
Classification of disease
Prognosis
Monitoring
What is gene deregulation?
Juxtaposition of genes to a regulating gene
Alters regulation
Can result in increased transcription
What are fusion/hybrid genes?
Breakpoints occur within 2 genes
Genes fuse and give rise to a hybrid gene
What are multifactorial conditions?
Diseases that are due to a combination of genetic and environmental factors
What is heritability?
The proportion of the aetiology that can be ascribed to genetic factors as opposed to environmental factors
Characteristics of multifactorial inheritance
incidence of the condition is greatest amongst relatives of the most severely affected patients
risk is greatest for the first degree relatives and decreases rapidly in more distant relatives
If there is more than one affected close relative then the risks for other relatives are increased
What do genome wide association studies do?
compare the frequency of markers in a sample of patients and a sample of healthy controls
Look for markers that is seen more frequently in the disease population
Sequence that area to try to identify the gene and allele associated with the increased likelihood of developing the condition
What environmental agents can affect embryogenesis?
Drugs and Chemicals
Maternal Infections
Physical agents
Maternal Illness
What are some examples of simple molecules?
Sugars
Lipids
Amino acids
What are some examples of macromolecules?
Haemoglobin
DNA
Glycogen
Rhodopsin
Collagen
What are the different types of carbohydrate?
Monosaccharide
Disaccharides
Oligosaccharides
Polysaccharides
What are some sugar derivatives?
Aminosugars e.g. glucosamine
Alcohol-sugars e.g. sorbitol
Phosphorylated e.g. glucose-6-phosphate
Sulphated e.g. heparin
What bond holds amino acids in proteins together?
Peptide
What are the 2 types of glycosidic bonds and where are they found?
OH, O-glycosidic in di-,poly- and oligosaccharides
NH, N-glycosidic in DNA and nucleotides
What are oligosaccharides?
contain 3-12 monosaccharides
Products of digestion of polysaccharides, or part of complex protein/lipids
What is the structure of a disaccharide?
contain 2 monosaccharides joined by an O-glycosidic bond
What are polysaccharides + 2 examples?
Formed by thousands of monosaccharides joined by glycosidic bonds
E.g. starch, glycogen
What are proteoglycans?
long, unbranched polysaccharides radiating from a core protein
What is the structure of lipids?
Straight C chains (mostly 16-20) with a methyl group and a carboxyl group at the ends
Ester bonds
What makes up a nucleotide?
nucleotide
sugar (ribose/deoxyribose)
phosphate group
What is the structure of amino acids?
Building blocks of proteins (20 different)
C with amine group, carboxyl group and side chain (R)
Charge determined by all 3, changes with the pH of the environment
Side chain often determines polarity
What makes up a nucleoside?
Nitrogenous base
Sugar
Joined in N-glycosidic bond
Properties of peptide bonds
Very stable
Cleaved by proteolytic enzymes
Partial double-bond
Flexibility around C atoms not involved in bond, allows multiple conformations.
Usually one preferred native conformation, determined mainly by the type of side chains
What is a protein?
A protein is a large polypeptide, usually from a few 10s to 1000s aminoacids
Huge variety of functions arises from huge number of different 3D shapes
What forces can keep the shape of proteins?
Van der Waals forces
Hydrogen Bonds
Hydrophobic Forces
Ionic bonds
Disulphide bonds
What are van der waals forces?
Weak attractive interactions between atoms due to fluctuating electrical charges
important when two macromolecular surfaces fit closely in shape
What are H bonds?
Interaction between dipoles, involving an hydrogen and an oxygen/nitrogen/fluorine
Allow weak interactions with other chains
What are ionic bonds?
Occur between fully or partially charged groups. Weakened in aqueous systems by shielding by water molecules and other ions in solution
What is the primary structure of proteins?
Linear sequence of aa linked by peptide bonds
What is the β pleated sheet?
Formed by H-bonds between linear regions of polypeptide chains
2 or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds
Can be parallel or antiparallel
What makes up the secondary structure of a protein?
α helix and β pleated sheet
What is the α helix?
The carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain
Pulls the polypeptide chain into a helical structure
R groups free to interact
What is the tertiary structure of a protein?
overall 3D conformation of the protein
Forces involved include electrostatic, hydrophobicity, H-bonds, and covalent bonds
What is the quaternary structure of a protein?
Three dimensional structure of a protein composed of multiple subunits
E.g. haemoglobin and DNA polymerase
What is sickle cell anaemia?
a genetic disorder that is characterized by the formation of hard, sticky, sickle-shaped red blood cells, in contrast to the biconcave-shaped red blood cells
What is the structure of haemoglobin?
Tetramer of 2 identical dimers
Each dimer is 1 alpha and 1 beta chain
four heme groups surrounding a globin group, forming a tetrahedral structure
What is euchromatin?
Actively transcribing cellular DNA
light staining
What is heterochromatin?
Transcripitionally inactive cellular DNA
Dense staining often adjacent to nuclear membrane
Highly condensed
Which bases are purines and pyramidines?
Purine: A & G, 2 rings
Pyramidine: T, C, U, 1 ring
What is the immunoglobulin structure?
2 identical small (light) + 2 identical large (heavy) polypeptide
Chains joined by disulphide bonds
Both light and heavy regions contain variable and constant regions
V regions interact to produce single antigen binding site at each branch
What does antiparallel mean for DNA?
The two strands of DNA run in opposite directions
On one strand the 5 C of the sugar is above the 3 C, so this strand runs in the 5’ to 3’ direction
Other, 3’ above 5’ so runs 3’ to 5’ direction
Process of DNA replication
- DNA helicase disrupts binding to open into replication fork
- Leading strand runs 3’ to 5’, lagging is 5’ to 3’
- RNA primer bonds to leading at 3’ end
- Leading strand replicated by polymerases, continuous
- Lagging strand binds with multiple primers, polymerase adds DNA (okazaki fragments), discontinuous
- When both strands formed, exonuclease removes primers and replace with bases
- DNA Ligase joins lagging strand up
- Telomerase catalyses synthesis of new telomeres at ends
What is the structure of the DNA double helix?
Purine bonded to pyrimidine so equidistant
Stacked bases stabilised by Van der Waals and hydrophobic effects
Phosphate groups on outside, 3rd -OH on phosphate is free and dissociates a H+ at physiological pH, so DNA -ve charge
Contains major and minor grooves where bases can interact with other molecules
Which enzymes and proteins work to open and unwind DNA?
Helicase opens it
Single stranded binding proteins keep it open
Topoisomerase unwinds supercoil
Function of DNA
Template and regulator from transcription and protein synthesis
Structural basis of heredity and genetic disease
What is the P53 protein?
Transcription factor that regulates cell cycle and apoptosis
Halts replication in cells that have suffered DNA damage
Loss of both p53 alleles common in tumours
What does DNA polymerase do?
synthesize DNA only in the 5′ to 3′ direction
needs a primer to initiate synthesis
What is the structure or a eukaryotic ribosome?
80S split into 60S and 40S subunits
60S subunit contains 5S, 28S and 5.8S rRNAs complexed with proteins
4OS contains 18S
What is the structure of a prokaryotic ribosome?
70S split into 50S and 30S subunits
What does DNA helicase do?
hydrolyses ATP to break bonds and unwind DNA double helix
What does DNA primase do?
synthesises a small RNA primer, which acts as a ‘kick-starter’ for DNA polymerase
What does DNA topoisomerase do?
Uncoils DNA
What is the leading strand in DNA replication?
The newly formed strand from DNA polymerase
In a 5’ to 3’ direction
What does DNA ligase do?
Joins okazaki fragments to form lagging strand of DNA
What are the 3 stages of DNA replication?
Initiation
Elongation
Termination
What happens during initiation of DNA replication?
DNA helicase unwinds DNA
Replication begins at replication fork
DNA primase synthesises an RNA primer for DNA polymerase to attach
What happens during elongation in DNA replication?
DNA polymerase adds free nucleotides to the 3’ end of the primer (reads 3-5, synthesises 5-3)
Creates new strand running 5’ to 3’ which becomes leading strand
RNA primers added to other template strand (lagging) and DNA polymerase synthesises in fragments (okazaki)
What happens in termination in DNA replication?
Either when two rep forks meet or no more template to synthesize
RNAase H removes primers from lagging and DNA ligase joins all the fragments to create a strand
New strands are bound and synthesised
What does DNA nuclease do in replication?
catalyze the cleavage of phosphodiester bonds
What is a DNA substitution?
when one or more bases in the sequence is replaced by the same number of bases
What is a DNA deletion?
when a base is deleted from the sequence
What’s the difference between DNA and RNA?
RNA is single stranded (can sometimes helix with itself)
DNA is present in cells at all time, many mRNA species only accumulate following cell stimulation
RNA chains are shorter
RNA contains a ribose sugar
RNA contains uracil not thymine
RNA is more resistant to UV damage
What is insertion in DNA mutations?
when a base is added to the sequence.
What is a point mutation in DNA?
a change in one base in the DNA sequence
What does tRNA do?
tRNA carry amino acids to ribosomes, and check that they are incorporated in the right poistion
What is the structure of mRNA?
long, single-stranded molecule consisting of nucleotides attached by phosphodiester bonds
4 nitrogenous bases: A,U,G,C
What are the stages of DNA transcription?
Initiation
Elongation
Termination
Which enzyme catalyses transcription?
RNA polymerase
What happens in initiation of transcription?
RNA polymerase attaches to and moves along the DNA molecule until it recognises a promoter sequence (may be multiple promoter sequences within a DNA molecule) Transcription factors bind to the promoter sequences with RNA polymerase.
RNA polymerase unwinds a portion of the DNA exposing bases on both sides
What happens in elongation of transcription?
Template strand is read in a 3′ to 5′ direction, other DNA strand is the coding strand.
RNA polymerase uses incoming ribonucleotides to form the new mRNA and catalyses the formation of phosphodiester bonds between adjacent ribonucleotides
Bases can only be added to the 3′ end, so the strand elongates in a 5’ to 3’ direction.
What happens in termination of transcription?
Elongation continues until the RNA polymerase encounters a stop sequence.
RNA polymerase releases the DNA template
Mature mRNA made
Where does translation take place?
In the cytoplasm
What are some features of the genetic code?
- Degenerate but unambiguous: many AA specified by more than one codon, but each codon specifies only one AA
- Universal
- Non-overlapping and without punctuation: codons do not overlap and each nucleotide is only read once
What is translation?
The process by which the genetic code contained within a mRNA molecule is decoded to produce a specific sequence of amino acids in a polypeptide chain.
What are the key components needed for translation?
mRNA, ribosomes, and transfer RNA
Where are the anticodon and AA on the tRNA?
Every tRNA molecule possesses an anticodon that is complementary to the mRNA codon, and at the opposite end lies the attached amino acid
What is the process of translation?
start codon (5’AUG) is recognised
At 5’ cap of mRNA, 40s subunit of the ribosome binds
larger 60s subunit binds to complete the initiation complex
tRNA binds to A site of ribosome, adds AA and leaves
ribosome translocates down mRNA
polypeptide growing at P site
stop codon
What is the purpose of mRNA splicing?
allows the genetic sequence of a single pre-mRNA to code for many different proteins, conserving genetic material
What is changed in mRNA splicing?
Removal of introns (non-coding sequences)
Joining together of exons (coding sequence)
What happens during pre-translational mRNA processing?
5′ Capping
Polyadenylation
Splicing
How is gene expression initiated?
Transcription factors at promoter region. Transcription complex forms at TATA box
Helix opens, DNA strands separate
RNA polymerase II starts building mRNA
What factors turn off gene expression?
Activation of repressors (inhibitors of RNA polymerase binding)
Each step of RNA transcription or processing finds no longer actively produced transcription and processing proteins.
Complexes do not form anymore for lack of phosphorylation.
Enzymes no longer activated
RNA stability
What is Mendel’s law of dominance?
Every gene has 2 alleles that code for a trait.
In heterozygotes, one allele is dominant meaning it will always show, one is recessive and is masked by the dominant allele
What is Mendel’s law of segregation/separation?
Allele pairs separate/segregate randomly from each other during meiosis – each cell has a single allele for each trait
What is Mendel’s law of independent assortment?
Traits are transmitted to offspring independently of one another
What is Mendelian inheritance?
Autosomal and sex-linked
Dominant and recessive
What is non-Mendelian inheritance?
Imprinting
Mitochondrial inheritance
Multifactorial
Mosaicism
What are the categories of genetic disorders?
Chromosome abnormalities
Single gene disorders
Multi-factorial and polygenic disorders
What is an autosome?
Any chromosome, other than the sex chromosomes (X or Y), that occurs in pairs in diploid cells
What is an allele?
One or more alternative forms of a gene at a given location (locus)
What does homozygous mean?
Presence of identical alleles at a given locus
What does heterozygous mean?
Presence of two different alleles at a given locus
What does allelic heterogeneity mean?
different mutations within the same gene result in the same clinical condition e.g. cystic fibrosis
an individual with an autosomal recessive condition may be a compound heterozygote for two different mutations
What does autosomal recessive mean?
Disease manifest in the homozygous state
What are the typical features of an autosomal recessive condition?
Male and females affected in equal proportions
Affected individuals only in a single generation
Parents can be related, i.e. consanguineous
What are some examples of autosomal recessive conditions?
Haemochromatosis
Sickle cell
CF
What is the most common gene for CF mutation?
F508
Approx 80% of cases
What does autosomal dominance mean?
Disease manifest in the heterozygous state
What are some typical features of autosomal dominance?
Male and females affected in equal proportions
Affected individuals in multiple generations
Transmission by individuals of both sexes, to both sexes
What does penetrance mean in genetics?
% of individuals with a specific genotype showing the expected phenotype
What does expressivity mean?
Refers to the range of phenotypes expressed by a specific genotype
What does anticipation mean in genetics?
genetic disorder affects successive generations earlier or more severely, usually due to expansion of unstable triplet repeat sequences
Example – Myotonic Dystrophy
What does somatic mosaicism mean?
Genetic fault present in only some tissues in body
What does gonadal/germline mosaicism mean?
Genetic fault present in gonadal tissue
What does late-onset mean?
Condition not manifest at birth, classically adult-onset
What does sex-linked mean?
Condition inherited in AD pattern that seems to affect one sex more than another
Example – BRCA1/2
What does lyonization mean?
X inactivation
Usually only in one of 2 in women
What is the disorder in prada-willi?
deletion of paternal genes
absence of active paternal genes – maternal uniparental disomy
What is the disorder in angelman?
loss of function of maternal UBE3A due to point mutation or deletion paternal uniparental disomy
What does homoplasmy mean?
a eukaryotic cell whose copies of mitochondrial DNA are all identical
normal healthy tissue
What does heteroplasmy mean?
there are multiple copies of mitochondrial DNA in each cell
level of heteroplasmy can vary between cells in the same tissue or organ, from organ to organ within the same person, and between individuals in the same family
What causes mitochondrial genetic disorders?
mutations in the mitochondrial DNA (15%)
mutations in nuclear genes, whose gene products are imported into the mitochondria
What does an out of frame deletion do?
Clearly disrupts protein
Deletion not a multiple of 3
What does an in frame deletion do?
Whole codon deleted
AA missing
What happens with a non-sense DNA mutation?
Change codon to stop
Out of frame deletion produces a stop codon either at deletion site or further along
RNA detaches from the ribosome and is eliminated
What’s a mis-sense varient?
Single base substitution
Changes the type of amino acid in the protein
May or may not be pathogenic
What does locus heterogeneity mean?
Variants in different genes give the same clinical condition
What does allele heterogeneity mean?
Lots of different variants in one gene e.g. cystic fibrosis
What happens with a gain of function disorder?
Increased gene dosage
Increased protein activity
What is a loss of function disorder in genetics?
Only one allele functioning
What are dominant negative variants in genetic mutation?
Where the protein from the variant allele interferes with the protein from the normal allele
What is predictive testing?
Testing healthy at-risk family members for a previously identified familial variant – often dominant
What is pre-natal testing?
Genetic test performed in pregnancy where there is a increased risk of a specific condition affecting the fetus
Chorionic villous sample or amniocentesis
What are the roles of genetic testing?
To confirm a clinical diagnosis
To give information about prognosis
To inform management
Allow pre-symptomatic/predictive testing in close relatives
Carrier testing
To give accurate recurrence risks
Prenatal diagnosis
What does Sanger sequencing do?
Uses PCR to amplify regions of interest followed by sequencing of products
Useful for single gene testing
Downsides of Sanger sequencing?
Slow
Expensive
Positives of Sanger sequencing?
Very accurate
The gold standard
What does next gen sequencing allow?
allows rapid sequencing of targeted gene panels
generates millions of short DNA fragments
fast
low cost per gene
What does anabolic mean?
synthesise larger molecules from smaller components
What does catabolic mean?
break down larger into smaller molecules
provides energy
What are the 4 pathways for metabolism?
Biosynthesis
Fuel storage
Oxidative
Waste disposal
Are biosyntheis and fuel storage anabolic or catabolic?
Anabolic
Are oxidation and waste disposal anabolic or catabolic?
Catabolic
What are the 3 main dietary energy sources?
Carbohydrates
Lipids
Proteins
What happens to excess energy intake?
Store as triglycerides in adipose (approx 15kg)
Store as glycogen (up to 200g in liver & 150g in muscle), 80g in the liver after overnight fast
Store as protein in muscle (approx 6kg).
How much energy per gram of carb and protein?
4kcal
How much energy per gram of lipid?
9kcal
How much energy per gram of alcohol?
7kcal
What is basal metabolic rate?
A measure of the energy required to maintain non-exercise bodily functions
What are some functions included in BMR?
respiration,
contraction of the heart muscle,
biosynthetic processes,
repairing & regenerating tissues,
ion gradients across cell membranes
What are the conditions for measuring BMR?
Post-absorptive (12 hour fast)
Lying still at physical and mental rest
Thermo-neutral environment (27 – 29oC)
No tea/coffee/nicotine/alcohol in previous 12 hours
No heavy physical activity previous day
Establish steady-state (~ 30 minutes)
What factors can decrease BMR?
Age (old)
Gender (female)
Dieting/Starvation
Hypothyroidism
Decreased muscle mass
What factors increase BMR?
Body weight (BMI) (higher)
Hyperthyroidism
Low ambient temp.
Fever/infection/chronic disease
What intake does the NHS recommend for BMR?
25-35 kCal/kg/day for patients who are not severely ill or injured, nor at risk of re-feeding syndrome
How much glucose does the brain require?
150g of glucose a day
After an overnight fast, how much glycogen does the liver have?
80g glycogen
What happens during an overnight fast?
Insulin decrease
Glycogenolysis
What happens after a few days of starvation?
Insulin low
Cortisol increases
Gluconeogenesis: from glycerol, AA and lactate
What happens after 4 days of starvation?
Liver makes ketones from fatty acids
Brain adapts
BMR decreases
What is the recommended alcohol intake?
not to regularly drink more than 14 units of alcohol a week
What is the recommended protein intake?
0.8g/kg/day protein
What is recommended saturated fat intake?
Men: 30g
Women: 20g a day
What is homeostasis?
maintenance of a constant internal environment
What is autocrine communication?
Cells talking to themselves
messenger molecules bind with receptors in the cell where they are produced
What is paracrine communication?
Cells talking to neighbour cells
Signal diffuses across gap between cells
Inactivated locally, so doesn’t enter the blood stream
What is endocrine communication?
Cells talking to cells elsewhere in the body
Hormones
Examples of paracrine communication
Interleukins
Platelet derived growth factor
What is a hormone?
Molecule that act as a chemical messenger
Structure of peptide hormones
Made of amino acids
Vary in size from few amino acids to small proteins
Some have carbohydrate side chains (glycoproteins)
Hydrophillic (like water)
How fast are peptide and steroid hormone responses produced?
Peptides fast
Steroids slow
What do ribosomes do?
Translate mRNA into protein
What does the golgi apparatus do?
Mediates protein sorting to specific sites
What happens in the mitochondria?
TCA cycle
Oxidative phosphorylation
What happens at the sER?
No ribosomes
Site of lipid synthesis
Some drug metabolism
What happens at the rER?
Studded with ribosomes
Site of protein synthesis
What do the cell microtubules do?
Give structure to cell
What makes up the phospholipid bilayer?
Phospholipids (hydrophillic head, hydrophobic tail inwards)
Cholesterol
Proteins (extrinsic and intrinsic)
Glycoproteins
What is the structure of phospholipids?
Phosphate head: charged, hydrophillic
Fatty acid tail: non-polar, hydrophobic
What can freely move through the phospholipid bilayer?
Water (aquaporins)
Gases (CO2, N2, O2)
Small uncharged polar molecules
What is the phospholipid bilayer impermeable to?
Ions (Na+, K+, Cl-, Ca2+ etc.)
Charged Polar molecules (ATP, Glucose-6-phosphate)
Large uncharged polar molecules (Glucose)
What uses simple diffusion to get across membranes?
Blood gases, water
Urea, free fatty acids
Ketone bodies
What uses facilitated diffusion to get across membranes?
Glucose (hexose sugars)
GLUT family
What uses primary active transport to get across membranes?
Ions (Na+, K+, Ca2+, H+, HCO3-)
Water-soluble vitamins
What uses secondary active transport to get across membranes?
Glucose (hexose sugars)
Symporters (Na+ + X)
What does the membrane potential mean?
Potential difference across the cell membrane generated by differential ion concentrations of key ions
K+ major determinant
What plays a major role in K+ homeostasis?
Kidneys and aldosterone
Why is temperature important for the cell membrane?
Too cold – proteins slow down; membrane less fluid
Too hot – proteins denature; increased membrane fluidity
Why is pH regulation important for cell membranes?
Both extremes damage protein
Inhibits cell function
Why is the cell membrane selectively permeable?
Maintains the internal environment
What are some features of the channel proteins in the cell membrane?
Narrow aqueous pore
Selective: size and charge dependent
Passive
May be gated (voltage or ligand)
Usually ions (e.g. Na+, K+) or water (aquaporins) going through
What are some features of the carrier proteins in the cell membrane?
Specific binding site
Carrier undergoes a conformational change
Different types:
Uniport – single substance
Symport – two substances in the same direction
Antiport – two substances in the opposite direction
Active (pumps) or passive
What are the 3 main forces driving things across the membrane?
Chemical
Electrical
Electrochemical
How does the chemical driving force work?
Based on concentration differences across the membrane
Force directly proportional to the concentration gradient
How does the electrical driving force across the membrane work?
Membrane potential
Based on the distribution of charges across the membrane
Only charged substances e.g. Na+, K+
Force depends on size of membrane potential and charge of the ion
How does the electrochemical driving force work?
Combines the chemical and electrical forces
Net direction is equal to the sum of chemical and electrical forces
Only charged substances e.g. Na+, K+
What are the 2 types of passive transport?
Simple diffusion
Facilitated diffusion (mediated by proteins)
What happens in passive transport?
Does not require an input of energy
Substance moves down its gradient (high to low)
E.g. glucose via GLUT4
How does active transport work?
Requires an input of energy
Substance moves against its gradient (low to high)
Primary and secondary
What happens in primary active transport?
Directly uses a source of energy, commonly ATP
E.g. sodium potassium atpase
What does the sodium potassium pump do?
Pumps 3 Na+ out of the cell, 2 K+ into the cell
What happens in secondary active transport?
Transport of a substance against its gradient coupled to the transport of an ion (usually Na+ or H+), which moves down its gradient
Uses energy from the
- generation of the ions
- electrochemical gradient (usually by primary active transport)
E.g. Na+/Glucose SLGT
What is cAMP?
A secondary messenger
What is a coenzyme?
cannot in themselves catalyze a reaction but can help enzymes to do so
Bind with the enzyme protein molecules to form active enzymes
What is a splice site mutation?
affects the accurate removal of an intron
What is ATP?
a high-energy molecule composed of adenine (purine base), ribose, and three phosphate groups
Steps of glycolysis
Glucose
Glucose-6-phosphate
Fructose-6-phosphate
Fructose-1,6-bisphosphate
DHP and Glyceraldehyde-3-phosphate
1,3-bisphosphoglycerate
3-phosphoglycerate
2-phosphoglycerate
Phosphoenolpyruvate
Pyruvate
What is the rate-limiting step of glycolysis?
Fructose-6-phosphate to fructose-1,6,bisphosphate
ATP to ADP
Catalysed by phosphofructokinase 1
Irreversible
What are the 3 irreversible steps of glycolysis?
Glucose to glucose-6-phosphate (hexokinase)
Fructose-6-phosphate to fructose-1,6-bisphosphate (PFK1)
Phosphoenolpyruvate to pyruvate (pyruvate kinase)
What steps form ATP in glycolysis?
1,3-bisphosphoglycerate to 3-phosphoglycerate forms 2 ATP
Phosphoenolpyruvate to pyruvate forms 2 ATP
Which steps of glycolysis require ATP?
Glucose to glucose-6-phosphate
Fructose-6-phosphate to fructose-1,6-bisphosphate
Which step of glycolysis produces water?
2-phosphoglycerate to phosphoenolpyruvate
Which step of glycolysis produces NADH?
G3P to 1,3-bisphosphoglycerate
Where does glycolysis occur?
Cytoplasm of all cells
What is the ATP exchange in glycolysis?
2 ATP used
4 ATP made
What happens in glycolysis if there isn’t enough oxygen?
Lactate dehydrogenase removes H from NADH to make pyruvate
Also makes lactate and NAD+
NAD+ keeps glycolysis going
What enzyme gets Acetyl CoA from pyruvate?
Pyruvate dehydrogenase
What enzymes regulate glycolysis?
Kinases
PFK1 main regulator
What enzymes regulate the krebs cycle?
4 Dehydrogenases
Where does Krebs take place?
Occurs in mitochondrial matrix
Aerobic conditions
What does Krebs do?
Generates 30-36 ATP
Provides final common pathway for oxidation of carbohydrates, fat & protein via acetyl CoA
Produces intermediates for other metabolic pathways
Stages of Krebs cycle
Acetyly CoA combines with oxaloacetate
Citrate
Isocitrate
alpha-ketoglutarate
succinyl-CoA
succinate
fumarate
malate
back to oxaloacetate
What regulates pyruvate dehydrogenase?
ATP and NADH, acetyl coa inhibit
ADP and pyruvate activate
What regulates citrate synthase?
ATP, NADH, Citrate, Succinyl CoA inhibit
ADP stimulates
What is the rate limiting step in Krebs?
Isocitrate to alpha-ketoglutarate
Enzyme: isocitrate dehydrogenase
NADH and CO2 out
Which steps in Krebs produce NADH?
Isocitrate to alpha-ketoglutarate
alpha-kg to succinyl-CoA
malate to oxaloacetate
Which step in Krebs produces FADH2?
Succinate to fumarate
Which steps in Krebs produce CoA?
Acetyl and oxaloacetate to citrate
Succinyl-CoA to succinate
Which steps in Krebs send out CO2?
Isocitrate to alpha-ketoglutarate
alpha-kg to succinyl-CoA
What inhibits and stimulates isocitrate dehydrogenase?
ATP and NADH inhibit
ADP stimulates
Where does oxidative phsophorylation occur?
Occurs in the inner mitochondrial membranes
aerobic conditions
How does oxidative phosphorylation work?
NADH and FADH2 donate their electrons
Electrons passed down chain
Energy generated and used to pump H+ into intermembrane space
Electrochemical gradient between intermembrane space and matrix
Protons reenter matrix via ATP synthase
Energy from this makes ATP from ADP
