Biochem - Exam 1 and 2 Flashcards
(176 cards)
1
Q
What are the main types of chemical bonding?
A
Covalent
Non-Covalent:
- Ionic
- Hydrogen
- Van der Waals attractions
- Hydrophobic Interactions, i.e. protein folding
2
Q
What are the four main molecule types in living things (list both monomers and the polymers they form)?
A
Sugars = polysaccharides AAs = protein FAs = fats, lipids, membranes Nucleotides = nucleic acidss
3
Q
What is the structure of a….
- Hydroxyl
- Carboxyl
- Ketone
- Methyl
- Amino
- Aldehyde
- Sulfhydryl
- Disulfide
- Phosphate
A
- Hydroxyl = -OH
- Carboxyl = -COOH
- Ketone = =O
- Methyl = -CH3
- Amino = -NH2
- Aldehyde = =O + H
- Sulfhydryl = -SH
- Disulfide = -S-S-
- Phosphate = PO4 (one =)
4
Q
How many cells do we have and how big are they?
A
Humans have around 10^14 cells with varying sizes.
Most cells in an organism have a diameter less than 30μm.
White blood cells =±3μm long and nerve cells up to 1m.
5
Q
Why does the number of cells in an organism increase as the organism gets larger, but not the size of individual cells?
A
Maintenance of SA:V
To allow adequate exchange of nutrients, ions, waste, gases etc
6
Q
What are the defining features of Prokaryotes?
A
- No nucleus
- No membrane bound organelles
- cell division by fission (not mitosis) – rapid growth and reproduction
- Size range: 1-10μm
7
Q
What are the defining features of Eukaryotes?
A
- Nucleus and nucleolus
- Membrane-bound organelles
- Cell division by mitosis or meiosis
- Bigger than prokaryotes
- Many are multicellular (i.e. animals and plants)
8
Q
What are the defining features of viruses?
A
- These are not cells.
- The nucleocapsid is comprised of an outer protein coat (capsid) and an inner core of nucleic acids
- Tail
- End Plate
- Tail Fibers
9
Q
What type of reaction often forms polymers?
A
condensation reactions (opposite of hydrolysis where water is added).
10
Q
What are the main chemical features of carbs?
A
Monomer – monosaccharides
Basic unit – CnH2nOn, where n is between 3-8.
Polority – Polar, therefore water soluble
Main Functional Groups – Aldehyde, Ketone
Bonds - glycosdic
11
Q
What are Glycosidic bonds and in what macromolecule are they relevant?
A
Glycosidic bonds are covalent bonds forms between monosaccharides from a condensation reaction. I.e. glucose. An O atom bonds to carbons on each monosaccharide.
12
Q
What molecules are used for storage?
A
Starch – plant cell and seed storage
Cellulose – structural sugar in plants
Glycogen – animal cell storage – 1000s of glucose monomers
13
Q
What causes lactose intolerance?
A
Lack of lactase – the enzyme that breaks down lactose into glucose and galactose. Bacteria multiply in the undigested milk sugar in the gut which results in gas, cramps, bloating.
Can be seen in children after one month if they pull legs up in pain after 1-2 hours after feeding screaming.
Primary Lactose Intolerance – remove lactose from diet
Secondary lactose intolerance – following bad GI infection, can last months.
14
Q
What are the chemical properties of lipids?
A
Monomer – fatty acids
Polority – non-polar, therefore not water soluble
Bonds – ester bonds
15
Q
What are the main types of lipids?
A
3 main types: Fats & oils & waxes, phospholipids, steroids.
16
Q
What is a triaglyceride?
A
Triaglyceroles = glycerol + 3xfatty acids
Saturated has higher mpt.
Formed when three fatty acids join to a glycerol linked by ester bonds.
17
Q
What is a phospholipid?
A
Contain N and P as well as C,H,O.
One fatty acid is replaced by phosphate, which is polar and therefore water soluble. Phospholipids are therefore amphipathic.
Often the phosphate group is attached to another functional N-containing group.
18
Q
What are steroids?
A
Regulatory molecules composed of interconnected rings.
Non-polar, therefore hydrophobic
Examples – vitamins, hormones, cholesterol
19
Q
What is rickets?
A
Disorder involving lipids (cholesterol and Vitamin D (cholecalciferol). At age one year, will be underweight with soft, pliable bones (inadequate calcification). Receive vitamin D treatment.
In adults – osteomalacia.
20
Q
What are the chemical properties of proteins?
A
Bonds – peptide bonds
Formation - condensation
20 Amino acids
Central carbon attached to an H, amino group, carbocylic acid
They are chiral with L and D forms. Our proteins are L.
Always write from amino terminal to carboxyl.
21
Q
What are the ionic forms of proteins?
A
- In acidic pH: Cation (NH3+)
- In neutral pH: Zwitterion (NH3+ and COO-)
- In Basic pH: Anion (COO-)
22
Q
What is a peptide bond?
A
- C(=O) - N(H) -
23
Q
What are the structures of gly, ala, phe and tyr?
A
Glycine - R = H
Alanine - R = CH3
Phenylalanine - R = CH2-@
Tyrosine - R = CH2-@-OH
24
Q
What are the structure levels of protein?
A
Primary - AA sequence
Secondary - repeating patterns - helixes, pleated sheets and random coil.
Tertiary - Overall confirmation - Driven by hydrophobic forces and disulfide bonds.
Quaternary - Interaction of subunits
25
What are the effects of a change in AA sequence on protein?
A change in it’s primary structure can have: -
- no effect (genetic variation within species),
- little effect (interspecies variation), or
- enormous effect (i.e. disease causing mutation such as sickle cell anaemia which only has a single amino acid change).
26
What is a simple protein?
A protein containing only AA’s and no other chemical groups
27
What is a conjugated protein?
A protein containing AA’s AND other chemical components. The non-AA part is called a prosthetic group.
Examples of prosthetic groups:
Lipoproteins (contain lipids)
Metalloproteins (contain a specific metal, such as myoglobin which contains iron).
Glycoproteins (contain sugar groups)
28
What is a denatured protein?
“Native” proteins are stabilized in 3D by secondary, tertiary and quaternary structures. If it’s conformation is altered/destroyed, the protein is denatured and won’t function normally. Denaturing does not alter the primary structure, and can sometimes be reversible.
29
What are some of the main functional proteins?
- Transport protein
- Nutrient and Storage Proteins
- Movement (motile) proteins
- Defense proteins
- Regulatory Proteins
- Structural Proteins – support cell and organ shape
- Enzymes
- Others – i.e. anti freeze proteins.
30
What are the main components/features of a cell membrane?
- Phospholipid bilayer with peripheral proteins (attached loosely) and integral proteins (tansmembrane proteins).
- ‘Fluid mosaic’ – lipid (and some protein) molecules can move laterally.
- Selectively Permeable. H20, O2 and CO2 cross freely, while ions and other polar molecules must move through selective pores.
31
What effects do saturated or unsaturated fatty acids have on the cell membrane?
Unsaturated fats kink at the double bond, and have greater fluidity. Whereas Saturday fatty acids give close packing.
Cholesterol enhances order and rigidity, and stabilizes the straight chain arrangement of saturated fatty acids.
32
What is the nucleus and it’s main characteristics?
Location of main genome, site of most DNA/RNA synthesis. It is surrounded by a double membrane – the nuclear envelope, which is continuous with the ER and is perforated by nuclear pores.
- Also selectively permeable
- Usually contains nucleoli – which is the site of rRNA synthesis and assembly of ribosomal subunits.
33
What is the cytoskeleton and it’s main characteristics?
It gives and maintains structure and shape of the cell, and governs its internal organization. It is essential in cell division.
It’s comprised of:
a) microtubules
b) microfilaments.
34
What are ribosomes and their main characteristics?
- Ribosomes are the site of protein synthesis.
- They may be free in the cytosol of attach to ER
- They are NOT organelles
35
What is mitochondria and it’s main characteristics?
- Site of energy-yielding oxidation reactions – cellular respiration.
- It has its own DNA
- Inner membrane is folded into cristae
36
What is the endoplasmic reticulum and it’s main characteristics?
- Continuous membrane throughout cell
- Network of sacs (cisternae)
- Rough ER is where polypeptides are synthesized
- Smooth ER lacks ribosomes, and is where lipids are synthesized
- materials are shuffled from one part of cell to another
- It involves biosynthesis, packaging and secretion.
37
What is the golgi apparatus and it’s main characteristics?
Series of flattened membranes (stacks of cisternae) involved in protein secretion & sugar linkage.
38
What are Lysosomes and their main characteristics?
- Membrane bound organelles containing hydrolytic enzymes
| - They digest unwanted materials in the cytoplasm
39
What are Peroxisomes?
Contain enzymes for H2O2 metabolism
40
What are endosomes?
Contains endocytosed substances
41
How do enzymes work?
Every chemical has a certain amount of Gibbs free energy, and chemical reactions involve a change of free energy (which is the energy available to do work). Exergonic (release E) vs endergonic (use E).
Enzymes enhance rate at which a reaction occurs by lowering Ea. Enzymes stabilize the transition state by binding it with greater affinity than the substrate.
But they speed up reactions in BOTH directions. When S binds to active site, molecules are distorted to have a confirmation that approaches that of the transition state.
Enzymes are highly specific for the reactions they catalyse, and substrate needs to be in a specific orientation.
42
What factors affect enzyme activity?
a) Temperature – rate of reaction will increase, but after a certain temp the protein will be denatured.
b) pH - most have max activity between 6-8. Some AA side chains of enzyme need to be protonated/deprotonated for substrate binding or catalysis (pH above or below average), but extremes of pH disrupt h-bonds and destabilize protein.
c) Cofactors
d) Substrate concentration, but saturation kinetics
43
How is energy released from our foods?
Our main fuels (carbs, fats, proteins) contain lots of reduced bonds, which are electrons not shared with O (i.e. C-H, C-C etc). We oxidize the food we eat by adding O, and we get the energy out of it by breaking the reduced bonds. Therefore, oxidation of sugars and fats releases energy.
This energy can be stored in other molecules that are used to perform work, i.e. ATP, NADH. FADH2, acetyl CoA. Energy can also be stored in ion gradients and other high energy phosphate bonds.
44
What is ATP and how does it work?
ATP: adenosine triphosphate. ATP hydrolyses to ADP (exergonic reaction).
ATP – ADP + P. ADP can have a P added to it to get ATP again but requires energy. ATP hydrolysis yields 29.3 kJ/mol, so energetically unfavorable reactions can be driven by ATP hydrolysis.
45
What is redox potential?
Redox: OIL RIG
E’ = redox potential. More negative E’ more readily donated electron. When electron passes from a compound with negative E’ to positive, energy is released.
NADH is an electron carrier, and is the cellular currency of reductive potential energy produced during respiration. FADH2 is also an electron carrier.
46
Define exon, intron, promoter and codon
Exon – Coding part of a gene
Intron – Non-coding part
Promoter – a site on DNA to which the enzyme RNA polymerase can bind to initiate the transcription of DNA into RNA
Codons – a sequence of three nucleotides which together form a unit of genetic code in a DNA or RNA molecule.
47
What is a Polyadenylation Signal?
Polyadenylation the addition of a poly(A) tail to a messenger RNA. In eukaryotes, polyadenylation is part of the process that produces mature messenger RNA (mRNA) for translation. The signal is required for transcription termination.
48
Define a gene and genome.
Gene – Fundamental physical and functional unit of heredity, carries info from 1 generation to next. It’s a segment of DNA composed of a transcribed region and regulatory sequences.
Genome – entire complement of genetic material in a chromosome set. An organism’s unique and complete set of genetic info (DNA).
49
What are the features of DNA?
- A-T and G-C = Adenine, Thymine, Guanine, Cytosine
- 2 strands
- Double Helix
- Sugar: Deoxyribose
- Polymer of nucleotides
50
What are the features of RNA?
- A-U, G-C - Uracil
- Single strand
- Can form complex secondary structures
- Sugar: ribose
- Polymer of ribonucleotides
51
What are the features of nucleotides?
Nucleotide = Nitrogenous base + pentose monosaccharide + phosphate: (If it doesn’t have a phosphate group then its a nucleoside). It links to others by dehydration reaction causing glycosidic bond.
Nucleotide is negative because of phosphate group, which is why it interacts with positive amino acids.
52
What is the difference between DNA and RNA?
The difference between DNA and RNA is that Ribose has an OH- group where deoxyribose just has an H.
53
What are the nitrogenous bases for DNA and RNA?
1. Purines (2 rings)
- G – Guanine
- A - Adenine
2. Pyrimidines (1 ring)
- C – Cytosine
- T – Thymine (DNA only)
- U – Uracil (RNA only)
A purine always couples with a Pyrimidine – large with small so the radius stays the same. A=T and C=-G. G and C form 3 H-bonds instead of 2.
54
What are the terminals of DNA?
The base joins the 1’ carbon, and phosphate to the 5’. DNA has 5’ and 3’ terminus. The primary structure (sequence of nucleotides) goes from 5’ to 3’. The secondary structure involves two strands of DNA running ANTIPARALLEL.
H-bonds between complementary bases keeps them together and keeps P’s facing outwards.
55
How does replication take place?
To begin, the strands are separated at A=T rich areas (only 2 H-bonds, not 3) with the aid of initiator proteins. The DNA helix then unwinds and separates into templates. Separation and therefore replication occurs at multiple points on DNA strand.
Replication requires replication of ALL DNA – new cells need all info from parents.
The process is semiconservative because the old DNA strands are incorporated into two new ones.
P (at 5’) of incoming nucleotide joins 3’ C of nucleotide on growing strand on DNA, catalyzed by DNA polymerase. Replication is always 5’ to 3’ (of new strand).
56
What is the leading/lagging strand?
Out of the two parent strands, one complementary strand (leading strand – parent is orientated 5’ to 3’, and new nucleotides are laid down 5’ to 3’ in opposite direction, i.e. towards rest of coiled DNA) is made continuously, and one (lagging strand) in fragments. Synthesis is always in 5’-3’ direction of complementary strand. The strand made towards rest of uncoiled DNA is the leading strand.
57
What are the steps in lagging strand synthesis?
Lagging strand synthesis is discontinuous:
1. Short RNA Primers are synthesized by Primase, copied from DNA
2. DNA polymerase III elongates RNA primers with new DNA
3. DNA polymerase I removes RNA and fills in gaps
4. DNA ligase connects adjacent fragments (seals strands)
BUT once last primer is removed, you get one shortened chromosome, so need DNA polymerase to add back nucleotides lost = telomeres.
DNA polymerase has proof reading activity, so if incorrect nt is inserted, it can remove and correct it
58
What is the central dogma?
DNA is transcribed into mRNA, which is translated in a polypeptide (protein).
59
What are the main types of RNA in the process?
Main types of RNA to make a protein:
1. mRNA (messenger) – code
2. tRNA (transfer) – one for each amino acid
3. rRNA (ribosomal) – part of ribosomes
60
How is RNA transcribed?
Transcription is always 5’ to 3’ of RNA, and only one DNA strand is used = template strand (or antisense). The other strand is the coding strand (or sense) as the mRNA mimics this strand, except T becomes U and nucleotides are ribinucleotides. RNA and template strand are antiparallel.
61
How is the promoter used?
Promoter – upstream at 5’ side of CODING strand of DNA. It’s involved in the initiation of transcription. Enzyme that transcribes RNA (RNA Polymerase) binds here with the help of Transcription Factors (other proteins that need to beat promoter first). RNA synthesis starts on promoter side, which is actually 3’ of template strand and therefore RNA goes 5’ to 3’.
62
What are the start and stop codons?
Start codon: Met (AUG)
| Stop Codons: Stop (UAA, UAG and UGA)
63
What are transcription factors?
Transcription Factors are accessory proteins and have a role in all aspects of transcription. They are ‘general’ or ‘cell-specific’. The latter allows for unique genes to be expressed.
64
What is mature mRNA?
The entire gene sequence is transcribed into mRNA (‘pre-RNA’, about same length as DNA), and then non-coding introns are spliced out and the exons are spliced together to make the mature mRNA. Other modification, i.e. adding chemical groups, are also made.
65
How is mRNA translated?
mRNA must be transported through pores in nuclear envelope into cytosol before it can be translated.
tRNA (transfer) binds AA’s to form aminoacyl-tRNA and delivers them to mRNA. Binds to tRNA anticodon, which is complementary to mRNA codon. rRNA (ribosomal) combines with protein to make ribosome.
66
How is the code read?
Triplets of nucleotides = codons, each of which specifies one of the 20 amino acids in our proteins. 64 codons.
Initiation codon = AUG = methionine (met). Met is always the first AA made during translation.
Stop codons – there are 3: UAA, UAG and UGA.
Almost every AA is encoded by more than 1 codon. Sequence of triplets is read from 5’ to 3’ as an uninterrupted reading frame. Translated into a N-terminus to C terminus polypeptide.
67
What are the staged of protein synthesis?
Protein is synthesized in four stages:
1. amino acid activation – need E input, then it binds to tRNA. Need enzymes to catalyze reactions.
2. Initiation – everything comes together, activated AA-tRNA, ribosomes, mRNA.
3. elongation
4. termination
Many ribosomes may translate one mRNA molecule simultaneously – structure known as polysome.
68
What are regulatory sequences?
Regulatory sequences are binding sites for gene regulatory proteins. Can be near or far from promoter, or within introns.
69
What is the difference between centrosomes, centrioles and centromeres?
Centrosomes – main place where microtubules get organized, regulates cell division cycle. It’s a pair of centrioles at right angles to each other. Only have one per cell until cell prepares to divide.
Centrioles – Small set of microtubules arranged in a specific way. Two at right angles are a centrosome.
Centromere – middle bit that links sister chromatids. Kinetochore is a part of the centromere where spindles attach during mitosis.
70
Which protein keeps sister chromatids together?
Cohesin
71
What part of centromere do spindles attached to?
Kinetochore
72
What is a telomere?
the ends of chromosomes containing repeated DNA sequences. Each chromosome has 2, one at each end. Protects from deterioration or fusion.
73
What are histones?
rotein that DNA gets wrapped around Chromatin. Histone H1 holds DNA and 8 Histone proteins together.
74
What is a chromosome?
1 unit of DNA + H1 + 8 Histones = ‘nucleosome’ + H1
75
What is chromatin?
Resulting DNA-protein complex, thread of complex (not yet condensed)
76
What is a chromatid?
when chromosome duplicates itself and has two parts, then each copy is called a chromatid but together are still a chromosome. When cell divides, they will go their separate ways and will each be a chromosome.
77
What is Heterochromatin?
tightly packed DNA which is inaccessible and therefore not transcribed.
78
What is Euchromatin?
more of an open configuration where DNA is more accessible and is hence more actively transcribed.
79
What is the different between diploid and haploid?
Diploid – 2 sets of chromosomes = 46
Hapoloid – 1 set = 23
80
What are homologues?
pairs of homologous chromosomes (i.e. pair of chromosomes), one from mother, one from father
81
What are the phases of a cell cycle?
Interphase:
- (G0)
- G1
- S
- G2
Mitotic Phase
Cytokinesis (cytoplasmic division)
82
What are the details of interphase?
Interphase – period between cell divisions (growth and preparation)
- G0 – cell exits cell cycle and enters non-dividing state where is usually maintains constant size. May stay in G0 for extended period/indefinitely, and can later reenter G1.
a) G1 – first gap phase – cell grows and undertakes normal metabolism.
b) S – synthesis phase, DNA replicated, centrosomes complete replication and nucleus becomes enlarged.
c) G2 – Second gap phase - further growth and protein synthesis, centrosome maturation, prepares to divide.
83
What are the details of mitotic phase?
2. Mitotic Phase – Mitosis – process of nuclear division (karyokinesis). Chromosomes condense, nuclear envelope disintegrates, crhomosomes attach to mitotic spindle and move cell midpoint, sister chromatids pulled to opposite poles of cell.
a) Prophase – Chromosomes condense and each possesses two chromatids. Mitotic spindles form.
b) Prometaphase – nuclear membrane disintegrates. Spindle microtubules attach to chromatids.
c) Metaphase – Chromosomes line up on metaphase plate (line cutting cell in half)
d) Anaphase – Sister chromatids separate and move toward opposite poles
e) Telophase – chromosomes arrive at spindle poles. The nuclear membrane re-forms and the chromosomes relax.
84
How can you tell the difference between a cell in interphase and one in metaphase?
Interphase cells:
- nuclear envelope present
- individual chromosomes cannot be distinguished
- DNA in decondensed state – chromatin
Mitotic Cell:
- nuclear envelope absent
- Individual replicated chromosomes are highly condensed
85
What is the difference between daughter cells of mitosis vs meiosis?
Mitosis daughter cells are diploid (2n) and daughter cells have the same genotype, whereas meiosis daughter cells are haploid (n) and have half the chromosomes of their parent cell.
NOTE: n refers to number of centromeres, so two chromatids joined by 1 centromere counts as 1.
86
In mitosis, In what phase are the number of chromosomes per cell doubled?
Anaphase
This reverts in telophase/cytokenesis
87
In mitosis, In what phase are the number of DNA molecules per cell doubled?
S phase
This reverts in telophase/cytokenesis
88
What is the product of meiosis?
cells with half the number of chromosomes as the parents cells are produced – OUTCOME = GAMETES.
89
Describe Meiosis I
Meiosis I – reduction division – centromere number is reduced by half - 2n – n. Similar to mitosis except instead of separating sister chromotids, homologous pairs couple and cross over, and whole chromosomes are divided but remain with their sister chromatids (which are separated in Meiosis II).
90
Describe Meiosis II
Meiosis II – equational division - centromere number remains equal – n-n. More like mitosis with separation of sister chromatids.
91
What is crossing over?
Results in exchange of genetic material between members of each homologous pair of chromosomes. Allows new combination of genetic material. Occurs at the tetrad state. Leads to genetic variation (Meiosis I only, not Meiosis II).
92
What is synapsis?
Synapsis - Synapsis (also called syndesis) is the pairing of two homologous chromosomes that occurs during meiosis. It allows matching-up of homologous pairs prior to their segregation, and possible chromosomal crossover between them. Synapsis takes place during prophase I of meiosis.
Chiasma is where two homologs connect.
93
What are tetrads?
Tetrads, present only in Meiosis, is a composistion of Four chromatids that are formed after the S1 block during prophase 1. Each tetrads holds two chromosomes, with two chromtids on each chromosome. during Metaphase 1 the tetrads line up the middle of the cell and serve as a place for crossing over to occur.
94
Why does random variation occur in meiosis?
In metaphase I, you have random and independent alignment of chromosomes.
Then in Anaphase I, you have random and independent distribution of chromosomes.
95
What is disjunction?
The pulling apart of either homologous chromosomes or sister chromatids during meiosis I or meiosis II respectfully.
96
What is non-disjunction?
The failure of homologous chromosomes or sister chromatids to separate properly during cell division.
Nondisjunction leads to aneuploidy – an abnormal number of chromosomes in a cell. For example, Trisomy 21 is 3 copies of chromosome 21 (Down’s Syndrome)
97
What is Aberrant Euploidy ?
the gain of one or more entire sets of chromosomes. It usually results in increased size, but the same basic shape and proportions.
In euploids, the ratio of any one gene to another is always 1:1.
98
What is Monoploidy?
the loss of an entire set of chromosomes
99
What is Aneuploidy?
one or more chromosomes of a normal set of chromosomes (i.e. not euploid or monoploid) are either missing or present in more than their usual number of copies. This typically alters an organism’s shape and proportions.
Monosomics (only one chrosome) are typically more abnormal than trisomics. Plants are more tolerant of aneuploidy than animals.
In aneuploids, the ratio differs by 50% from the wild type. It is 50% for monosomicsand 150% for trisomics. This makes the aneuploidy genes out of balance, and the gene-dosage effect will occur.
100
What is the gene-dosage effect?
The amount of transcript a gene makes is proportional to the number of copies of that gene in a cell. So, the more copies of the gene, the more transcripts and the more protein is translated.
101
What is the problem with monosomics?
type of aneuploidy where one chromosome is missing. This results in extreme abnormality due to the expression of any deleterious recessive allelles on the monosomic chromosome.
102
What causes Down’s Syndrome?
- DS is usually caused by an extra chromosome 21, and is sporadic. I.e. trisomy (an extra chromosome).
- Rarer forms result from translocation events (usually exchange of material between nonhomologous chromosomes 21 and 14)
103
What is the sequence of apoptosis?
1. Fragmentation of Chromosomes
2. Organelle Disruption: Organelle structure is disrupted and cell loses its shape
3. Fragmentation of cell – the cell breaks up into small bodies called apoptotic bodies and are phagocytosed.
104
What are caspases and what is their role in Apoptosis?
Caspases drive apoptosis. They are normally present in cell as inactive zymogen (pre-curser protein waiting to be activated).
Zymogen is activated by proteolysis (cleavage). The active caspases target other proteins for destruction.
Caspases cleave target proteins, and these target proteins initiate fragmentation of DNA, organelle disruption etc.
105
What are Initiator and Executioner Caspases?
Initiator caspases are cleaved in response to an activation signal. They in turn cleave on of the executioner caspases, which in turn cleaves another until all are active (cascade).
Executioner caspases also cleave target proteins in the cell, hence driving apoptosis.
106
What protein kinases regulate the cell cycle?
Heterodimeric protein kinases (cdk-cyclins) regulate cell cycle.
107
What are the regulatory and catalytic subunits?
Regulatory subunits = cyclins – levels vary throughout cell cycle and are unstable.
Catalytic subunit = cyclin-dependent protein kinase Cdk.
Cyclin needs to bind to Cdk before it can be active. Cyclin allows the active site on Cdk to be accessible. Together they make a compled – Cdk-cyclin.
Cyclines are a whole family (A, B, D, E) and so are Cdks (Cdk1, Cdk2, Cdk4, Cdk6).
108
What does cdk-cyclin do?
Sequential activation of different Cdk-cyclin complexes control cell cycle progression. Going to the next step in the cell cycle requires activation of genes who’s protein products are necessary for the next phase. If an active complex is present at the wrong time, t will cause inappropriate genes to be transcribed or switched on.
Cdk phosphorylates target protein. A chain of events results in the ‘turning on’ of transcription factors which in turn promote specific gene transcription who’s products are required for the next stage of the cell cycle.
109
How do cdk and cyclin levels vary throughout the cell cycle?
Cyclin is only present in specific phases of the cell cycle and is unstable. Cdks are present throughout the cell cycle, but activity varies. The appearance of a specific cyclin is the result of the proceeding Cdk-cyclin complex which activates the transcription factor for the new cyclin.
110
Give an example in reference to the Rb-E2F pathway.
Rb-E2F pathway, where Rb is the target protein and E2F if the TF that Rb regulates. At a one point, E2F and Rb are stuck in a protein complex in the cytoplasm, which isn’t useful because E2F needs to be in the nucleus. Cdk-cyclin phosphorylates Rb in late G1, changing the shape of Rb, and therefore freeing E2F to move to nucleus where is can promote transcription of particular genes and activate gene expression of next cyclin.
111
What initiated G1 cyclin production?
Extracellular growth factors (mitogens) induce synthesis of G1 cyclins. Once growth factor/mitogen has acted, the cycle proceeds even when mitogens are removed.
112
What is a check point?
Cells stop at a restriction point, i.e. near the end of G1. The cells then check everything is okay, i.e. right number of chromosomes, DNA is correct and intact, proteins aren’t being produced too quickly, there is enough space and O2 etc. If not, growth fact/mitogen won’t be received and cell will go into G0 phase. If GF/M is added, cell with pass through restriction point and is committed to entering and completing the cell cycle.
At the restriction point if things aren’t okay, the cell can stop progression until it sorts it shit out. This relies on Cdk inhibitor proteins.
113
Give an example - P53.
Example of this is G1 checkpoint and P53 – the most commonly mutated tumour suppressor in human cancer (approx.. 50% all human cancers).
If DNA damage is extensive, p53 activates genes that lead to apoptosis. P53 recognises DNA mismatches and proceeds to active protein p21. P21 binds to Cdk-Cyclin complex and inhibits protein kinase activity. Therefore no progression. Once DNA repaired, p53 level drop and cdk-cyclin complex is not longer inhibited.
114
How can cdm-cyclin complex itself be regulateD?
cyclin degradation
Cdk inhibitors can also be regulated by phosphorylation levels. Kinases add phosphate group and phosphatases remove it. Cdk needs one and only one P to be active
115
What is the point of checkpoints?
to ensure that
- chromosomes are present and that critical stages of the CC are completed before the next stage
- entry into S or M is prevented if DNA is damaged and not repaired
- the spindles are properly formed and the chromosomes are properly attached
- cellular environment is favourable
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What are the types of cell signalling?
1. Endocrine = glands secrete hormones - Long distance – circulatory system
2. Paracrine System = Cell in Tissues/Glands extreme signals into EC environment - short distances
3. Autocrine = Cells in tissues - triggers reaction on itself
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What are the 3 staged in cell signalling?
1. Signal Reception – the ligand binds to it’s receptor on a target cell
2. Intracellular signal transduction – step 1 triggers a chain of events inside the cell that passes the message along
3. Cellular response – RESPONSE TO A PARTICULAR HORMONE DETERMINED BY CELL, so same hormone can produce different responses in different cell types
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What effects can signalling ligands have in terms of gene expression?
Ligands can act at the transcription phase by affecting gene expression.
Ligands can act at the translation phase by, for example, targeting proteins involved in translation.
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What is a hormone?
Signals that are produced in one part of the body and travel through the circulation to reach far-away targets = endocrine system
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Which endocrine glands release hormones?
- thyroid
- hypothalamus
- pituitary (growth hormone)
- gonads (testes and ovaries)
- pancreas
Endocrine signaling cascade amplifies signal
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What are 4 common types of hormones and what are their details?
1. Steroids (i.e. Progesterone)
- Synthesized from Cholesterol
- Lipid Soluble
- Can cross cell membrane
- Cytoplasmic or nuclear receptors
2. Thyroid Hormones
- Synthesized from Tyrosine residues on protein thyroglobulin
- Lipid soluble
- Can cross cell membrane
- Nuclear Receptors
3. Catecholamines (i.e. adrenaline)
- Synthesized from phenylalanine/tyrosine in adrenal gland
- Water soluble
- Unable to cross membrane
- Plasma membrane receptors
4. Peptide/Protein Hormones (i.e. glucagon)
- Water soluble
- Unable to cross membrane
- includes cytokines and growth factors
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Which hormones rely on intracellular receptors?
All these hormones are:
- lipid soluble
- have nuclear receptors (steroids also have cytoplasmic)
- Act by regulating expression of various genes
Applies to steroids, thyroid hormones, retinoic acid and 1a, 25 Dihydroxycholecalciferol.
In Cytoplasm or nucleus.
Most of the ligands that use these receptors are small, hydrophobic molecules as they need to be able to cross cell membrane.
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How do the receptors work?
The receptor and hormone form a receptor-hormone complex. The hormone changes the shape of the receptor, exposing regions of the receptor with DNA-binding activity. Then when the receptor binds to these genes, it increase or decreases their transcription. Therefore, the ligand-receptor complex acts as a transcription factor.
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What are response elements?
Response elements are short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes. Under conditions of stress, a transcription activator protein binds to the response element and stimulates transcription.
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What are the types of cell surface receptors?
i) Ligand-gated ion channels:
Ligand binds to protein on cell membrane and allows it to open/close to ions. The ions then set up chain reaction that results in cellular response.
ii) G Protein-coupled receptors – transmits signals inside the cell through G protein.
iii) Receptor Tyrosine Kinases – ligand binding brings two receptors together, forming a two unit complex called a dimer. They then phosphorylate each other, making each other active. Then another protein will come and bind to each and will set off chain reaction of signaling.
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What are the two broad types of hormones?
(i) hydrophobic (not very soluble in water – e.g. steroids, thyroid hormone) – pass through the cell membrane and have intracellular receptors, in the nucleus or cytoplasm and nucleus (steroid receptors)
Applies to steroids, thyroid hormones, retinoic acid and 1a, 25 Dihydroxycholecalciferol. All act by regulating the expression of genes, and all have nuclear receptors (steroids also have cytoplasmic).
(ii) hydrophilic (soluble in water – e.g. catecholamines, peptide or protein hormones/growth factors/cytokines) – cannot pass through the cell membrane and so have receptors in the cell membrane.
All hormone receptors are proteins.
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What are steroid hormones derives from?
Cholesterol
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Where are thyroid hormones derived from?
tyrosine residues that are part of the protein thyroglobulin
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What are the hydrophobic hormones?
Steroids, thyroid hormones, retinoic acid and and 1α, 25 dihydroxycholecalciferol.
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Hydrophobic hormones have similar receptors. What is the family of receptors called and how do they work?
steroid receptor superfamily
All share very similar DNA binding sites and all have a hormone binding site. Steroid receptors also have heat shock protein (hsp) binding sites as it is the hsps that keep the receptors in the cytoplasm until the steroid binds to the receptor when the hsps are displaced and it goes to the nucleus.
The DNA binding sites of these receptors contain two zinc fingers, one positions a helix for binding in the DNA groove, the other provides a dimerisation site. First finger binds to DNA, second finger binds to another receptor which together forms a dimer.
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What is a hormone response element?
A hormone response element (HRE) is a short sequence of DNA within the promoter of a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription.[1]
the receptor binds as a dimer. I.e. estrogen response elements (EREs).
They can either activate or repress gene expression.
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What are the types of positive and negative effects on gene expression?
a) Positive: Synergistic interaction between the hormone- receptor complex dimer when it binds to its responsive element and the transcription factor (TF) to enhance transcription of the gene.
b) Negative: Displacement of the transcription factor resulting in repression of gene expression when the hormone-receptor complex dimer binds to its responsive element.
c) Negative: Direct binding of the hormone-receptor complex dimer to a protein such as Ap 1 which
positive regulator of transcription.
This inhibits its action thus causing repression of gene expression.
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Know how the hormone-receptor complexes can down-regulate receptor gene expression (hydrophobic hormones) or receptor numbers in the cell membrane (hydrophilic hormones) to reduce cellular responses to the hormone.
Down-regulating comes after prolonged exposure to high levels of a hormone.
A. HYDROPHOBIC: cellular levels of mRNA coding for the receptor are lowered, therefore lowering expression. This is done by:
i) Direct repression by binding of the hormone-receptor complex to a responsive element in the promoter region of the gene. Receptor acts on its own gene.
ii) Activation of expression of a gene coding for an enzyme which catalyses the degradation of the receptor mRNA.
B. HYDROPHILIC: Complexes are consumed by cell. Receptor-mediated endocytosis occurs with plasma membrane receptors where the receptor-hormone complexes are taken up into the cell in vesicles made from the membrane lipids
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Know how cortisol produces one response in liver and a completely different response in monocytes and macrophages.
In liver: enhances gluconeogenesis
In Monocytes/Leukocytes: has an anti-inflammatory effect by inhibition of prostaglandin and leukotriene synthesis which mediate the inflammatory response.
In both act by enhancing expression of genes.
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Know how tissues with the mineralocorticoid receptor respond to aldosterone despite the fact that the receptor also binds cortisol with high affinity and understand how this goes wrong in apparent mineralocorticoid excess syndrome.
Although both have an affinity for the receptor, in tissues that express the mineralocorticoid and respond to aldosterone, an enzyme: 11β-hydroxysteroid dehydrogenase is also expressed, and Cortisol to Cortisone which has a low affinity for the receptor.
Mineralocorticoid excess syndrome occurs even though plasma levels of aldosterone are normal. This is either caused by Congenital deficiency of the kidney form of 11β-hydroxysteroid dehydrogenase, or eating too much licorice which inhibits 11… In both cases the activity of 11β-hydroxysteroid dehydrogenase is either absent or greatly reduced, thus in the kidneys the cortisol is not being inactivated by conversion to cortisone and can thus bind to and saturate the mineralocorticoid receptors.
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What can cause variations and adaptations in NORMAL metabolism?
- starvation
- exercise
- pregnancy
- lactation
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What can cause abnormal metabolism?
- nutritional deficiency
- enzyme deficiency
- abnormal secretion of hormones (i.e. diabetes mellitus)
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Where does glycolysis occur?
Cytosol
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What is the molecular formula for glucose?
C6H12O6
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Name the enzymes used in the 3 main points of regulation of glycolysis. Note: these reactions only proceed in the forward direction.
Hexokinase
Reaction: glucose - glucose 6-phosphate (the first ‘priming reaction’).
A phosphate group is added to glucose using ATP.
Phosphofructokinase-1
Reaction: fructose 6-phosphate – fructose 1,6-biphosphate (the second ‘priming reaction’).
A second phosphate group is added to glucose using ATP.
Pyruvate Kinase
Reaction: Phosphoenolpyruvate – pyruvate (2ADP are converted to 2ATP. It is the second ATP-forming reaction)
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Why does the heart muscle survive poorly under conditions of ischemia?
Tissue can survive periods of anoxia because glycolysis can occur in the absence of oxygen. But heart muscle has relatively poor glycolytic ability, so it survives poorly without oxygen.
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Why does fermentation occur in the absence of oxygen?
Glucose will still react to form 2 pyruvate molecules, but NADH accumulates and inhibits pyruvate oxidation. Instead, the pyruvate molecules will be converted to lactate (enzyme=lactate dehydrogenase) and will cause NAD+ regeneration.
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What are the muscle metabolic systems used during exercise?
Anaerobic Exercise:
- Stored ATP and Creatine-P. Lasts about 8-10 seconds during high intensity exercise.
- Anaerobic glycolysis, yielding about 1.3-1.6 minutes of maximal muscle activity.
Oxygen demand in the mitochondria of muscle cells exceeds the capacity of the blood to deliver it.
Aerobic Exercise:
- Aerobic system – metabolic reactions taking place in the mitochondria. Occurs during lower intensity exercise. This can keep going until nutrients are depleted.
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What is the Cori cycle and why do we need it?
The lactic acid cycle. It refers to the metabolic pathway in which lactate produced by anaerobic glycolysis in the muscles moves to the liver and is converted to glucose, which then returns to the muscles and is metabolized back to lactate.
It’s important in preventing lactic acidosis – a low pH in body tissues and blood (acidosis) accompanied by the buildup of lactate.
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How is the oxidation of pyruvate to Acetyl-CoA regulated?
Relative concentrations of Pyruvate, Acetyl CoA, NADH, ATP and ADP regulate the oxidation of pyruvate.
The reaction is an irreversible reaction catalyzed by Pyruvate Dehydrogenase (PDH). PDH is inhibited by NADH, Acetyl CoA and ATP (the first are products of the oxidation of pyruvate to Acetyl CoA and the second is a product of the ETC).
PHD is activated by ADP and pyruvate.
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Which tissues depend predominantly on glycolysis for ATP and why?
Tissues with little or no mitochondria as pyruvate cannot enter the TCA cycle.
Examples: RBCs, cornea, lens, retina, kidney, medulla, testis, leukocytes and white muscle.
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What does one cycle of the TCA cycle produce?
3 NADH, 1 FADH2 and 1GTP. It also releases 2CO2.
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What is anoxia and hypoxia and what does it do to the TCA cycle?
Anoxia – complete lack of oxygen supply to tissue
Hypoxia – decreased supply of oxygen in tissue
They lead to total or partial inhibition of the TCA cycle.
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Why are NADH and FAHD2 important in the Electron Transport Chain (ETC)?
Electrons are transferred from NADH and FADH2 into the ETC and finally to O2 (the terminal electron receptor) to drive the formation of ATP.
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How much ATP does a molecule of NADH and a molecule of FADH2 produce?
NADH – 3ATP
| FADH2 – 2ATP
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What happens to the carbon atoms in glucose after it has been completed metabolized?
They are exhaled as CO2.
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What drives phosphate and pyruvate import into the mitochondrial matrix?
Proton Gradient
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What process drives the oxidative phosphorylation of ATP?
Proton Gradient (also known as the electrochemical or voltage gradient).
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What is the overall equation of glucose oxidation?
(C6H12O6) + 6O2 + 38 ADP3- +38Pi2- +38H+ = 6CO2 + 6H2O + 38 ATP 4-
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What is the generic formula for fatty acids?
Ch3-(Ch2)n-COOH
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Why are Triacyl glycerols an efficient storage of energy?
Triacyl glycerols are an efficient storage of energy, yielding (on a per weight basis) 2.5 times as much ATP as glucose. Also, because glycogen is hydrophilic it binds to 2x its weight of water. So you need 3 times the tissue weight of glycogen for emergency from the same weight in fat. Normal glucose/glycogen stores last about 24h of fasting, but fat supply lasts several weeks.
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What are the processes in triaglycerol metabolism?
1. Lipolysis - Hydrolyze triacyl glycerols by lipases to release fatty acids and glycerol.
2. Beta Oxidation of fatty acids - fatty acids to acetyl coa
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What are the steps in Beta Oxidation of fatty acids?
Stage 1: Activate FAs
- occurs in ER or outer mitochondrial membrane
- Activates FAs for oxidation
- FA + Coenzyme A = Fatty Acyl-CoA. But this is too fatty to get through mitochondria; membrane so need step 2. Long chain fatty acyl-CoA (LC-CoA).
Stage 2: Transport
- overall effect – activated fatty acid is transported into mitochondria via Carnitine Carrier. LC-CoA to LC-Carnatine to LC=CoA
- LC-CoA releases its long chain which is transporter to intermembrane space.
- LC then bins to carnitine = LC-Carnitine.
- LC is then stripped off again and transported to matrix where is it recombined with CoA to form L-CoA.
Note: genetic deficiencies in Carnitine Transport results in mild, recurrent muscle cramping, to severe weakness, to death. It compromises long chain FA oxidation, but can be overcome by dietary carnitine therapy.
Stage 3: Beta Oxidation in Mitochondria
- strips off two carbons each cycle, and produces NADH and FADH2
- Each round = 1 acetly CoA (2 in last round), 1 FADH2 and 1 NADH
- Number of cleavages = n/2 – 1. I.e. C18 has 8 cleavages, producing:
9 ATP
8 FADH2
8 NADH
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What are ketone bodies?
- Lipid based energy source
- Beta-hydroxybutyryl CoA and acetoacetyl CoA
- Primary site of formation is in the liver, and they are produced from fatty acids during periods of fasting, low carb diets, starvation, prolonged intense exercise or untreated type 1 diabetes mellitus.
- It is used by the skeletal and cardiac muscle (in order to conserve glucose)
- BUT the CNS will use it in starvation
- They are acidic, so pH becomes acidic and you can go into a coma.
- They can be converted back into Acetyl CoA
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How does your body get amino acids?
Obtained from die,t synthesized de novo or produced by protein degradation.
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What are the two types of protein?
a) glucogenic: pyruvate or TCA cycle intermediate
b) ketogenic: acetoacetate or Acetyl CoA (CANNOT be converted back into glucose)
All are at least partly glucogenic, EXCEPT:
- leucine – only ketogenic
- lysine - only ketogenic
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How can AAs be used in glycolysis or TCA cycle?
Catabolism leads to net pyruvate or net oxaloacetate (TCA cycle), therefore these can enter gluconeogenesis to make glucose.
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Describe the catabolism of amino acids
1. Phase 1: removal of alpha-amino group. Some free ammonia excreted in urine but most converted to urea.
2. Phase 2: Carbon skeleton converted to intermediated – metabolic pathways – energy.
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/How are AAs synthesized?
- glycolytic
- citric acid cycle
- pentose phosphate pathway intermediates
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What is the urea cycle?
Major route for removal of ammonia produced in metabolism of AA’s in liver and kidney. It’s converted to soluble urea using L-ornithine as a recyclable carrier.
Liver and kidney remove ammonia because it’s toxic and can’t be excreted efficiently as is.
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What are some of the substrates for gluconeogenesis?
- AAs
- Lactate
- Pyruvate
- Glycerol
- Galactose and fructose
- Triaglycerides
- NOT GLYCOGEN (this is glycogenolysis)
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Why can't glucose be synthesised in the brain?
3 of the enzymes in glycolysis only go in forward direction, so we need 3 different enzymes for anabolism. This is why glucose can’t be synthesized in the brain – it doesn’t have the anabolism enzymes.
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How is ATP required for gluconeogenesis supplied?
β-oxidation of Fatty Acids
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What is the overall equation of gluconeogenesis?
2Lactate + 6ATP -> Glucose + 6ADP + 6Pi + 4H+
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How is gluconeogenesis regulated?
Regulation of gluconeogenesis also occurs at the irreversible steps:
- Pyruvate Carboxylase catalyzes pyruvate to oxaloacetate
- Phosphoenolpyruvatecarboxykinase catalyzes oxaloacetate to phosphoenolpyruvate
- Fructose 1,6-bisphophatase catalyzes fructose 1,6-bisphosphate to Fructose 6-phosphat.
Then they can go into TCA cycle, EXCEPT Leu and Lys which go from pyruvate to Acetyl CoA instead of oxaloacetate
NOTE: FATTY ACIDS can’t make glucose for the same reason. They go to Acetyl CoA.
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What are 2 essential FAs?
linoleic (omega 6)
| linolenic (omega 3)
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How are FAs synthesised?
1. Part 1: Commitment step of FA biosynthesis
- carboxyl group is added
- Enzyme = Acetyl CoA carboxylase
- produces Malonyl CoA and uses ATP
2. Part 2: reversal of beta-oxidation
Overall:
Acetyl CoA + Malonyl CoA + 14NADPH + 14H+ = Palmitate + 7CO2 + 14NADP+ + 8CoASH + 6H2O.
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How can we measure Excess storage of fat?
- IBW = ideal body weight
| - BMI = body mass index = wt/ht^2
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What does control of metabolic pathways depend on?
- availability of substrates
- allosteric activation and inhibition of enzymes
- covalent medication of enzymes (i.e. phosphate groups)
- induction and repression of enzyme synthesis (gene induction/repression)
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What happens to diabetics during starvation?
get diabetic ketoacidosis if you’re a diabetic. Not enough glucose in cells (hyperglycaemia), but get ketonemia (ketones in blood) and ketonuria (ketones in urine), and blood becomes acidic.
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What are specific cells and their characteristics in metabolism?
1. RBC
- glycolysis to produce lactate (no mitochondria)
- pentose phosphate pathway (PPP)
- no TCA cycle or beta-oxidation of FAs
2. Brain
- uses glucose or ketone bodies during extended fast
- glycolysis, PPP, TCA
- no beta oxidation (FAs can’t cross blood-brain barrier)
3. Muscle (skeletal and cardiac)
- heart relies entirely on aerobic metabolism
- has many mitochondria
- heart has relatively poor glycolytic ability
4. Adipose
- stores and releases FAs
- widely distributed
5. Liver
- Express pretty much all enzymes
- Key organ in energy maintenance
