Biochemistry from Principles Collated Flashcards

(190 cards)

1
Q

Bond strengths in order. Strongest to weakest?

A
Covalnt 
Ionic 
Hydrogen 
Hydrophobic interactions 
VDW's
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2
Q

Oxidation states of carbon?

A
Alkane (in fats)
Alcohol (in carbs)
Aldehyde 
Carboxylic acid 
Carbon dioxide
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3
Q

What is the function of micelle

A

helps in the absorption of large lipid molecules, once inside an enterocyte, these lipids are processed and packaged via the rough and smooth endoplasmic reticulum and the Golgi body into a chylomicron for absorption into the lymphatic system.

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4
Q

What forms the outer shell of micelles?

A

Bile salts and a single phospholipid layer

Micelles have an important role in aiding the absorption of large lipid compounds in the small intestine. They are formed from an outer shell of bile salts, which act as a surfactant to emulsify fat droplets, and a single phospholipid layer, which provides the amphiphilic property (i.e., both hydrophilic heads and hydrophobic tails). The core of the micelles contain long-chain free fatty acids, monoglycerides, and cholesterol, as well as fat-soluble vitamins

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5
Q

4 major classes of biomolecules and what they consist of?

A

Proteins/peptides= amino acids
Lipids= triglycerides, phospholipids, steroids
Nucleic acids= DNA/RNA
Carbs= Mono, di, poly saccharides

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6
Q

Example of monosaccharide?

A

Glucose

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7
Q

Examples of disaccharides?

A

Lactose

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8
Q

Examples of polysaccharides?

A

Cellulose

Glycogen

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9
Q

1st law of thermodynamics?

A

Energy can neither be created nor destroyed

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10
Q

2nd law of thermodynamics?

A

When energy is converted from one form to another some of that energy becomes unavailable to do work

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11
Q

What type of reaction is it if the change in free energy is negative?

A

Exergonic (can occur spontaneously)

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12
Q

What type of reaction is it if delta G is positive?

A

Endergonic (cannot occur spontaneously)

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13
Q

Entropy?

A

Loss of useable energy

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14
Q

Primary protein structure?

A

Sequence of amino acids

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15
Q

Secondary protein structure?

A

Formation of backbone

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16
Q

Tertiary protein structure?

A

3D structure

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17
Q

Quaternary protein structure?

A

Relative orientation of one polypeptide to another
polypeptide in a multisubunit protein.
Spatial arrangement of multiple subunits.

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18
Q

What holds proteins together?

A

Disulphide bonds (Peptide bonds form the primary structure of protein molecules. Function of this disulphide bond is to stabilize the secondary and tertiary structure of proteins.)

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19
Q

5 elements of a cell?

A
SER
RER
Mitochondria
Golgi apparatus 
Ribosomes
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20
Q

Structure of DNA?

A
Nucleoside = base + sugar 
Nucleotide = nucleoside + phosphate
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21
Q

Examples of purines?

A

Adenine and guanine

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22
Q

What is the collective term for the nitrogenous bases adenine and guanine (A&G) found in DNA and RNA?

A

Purines

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23
Q

Examples of pyramidines?

A

Cytosine
Thymine
Uracil

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24
Q

What is the central dogma?

A

DNA is transcribed to RNA, which is translated into protein

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25
A nucleoside has...
5C sugar + organic base
26
A nucleotide has...
5C sugar + organic base + phosphate group(s)
27
Pol II synthesises only stable RNA. True/False?
False Pol II synthesises all RNA. Pol I and III synthesise only stable RNA
28
DNA polymerase has 3 important characteristics
Can only add to existing nucleic acids Cannot start synthesis on its own Requires an RNA primer to start replication
29
To which "end" of the RNA strand are more nucleotides added during transcription?
3' end
30
What is the catalyst for DNA replication?
DNA polymerase
31
What is required to commence DNA synthesis and replication?
An RNA primer (DNA polymerase can take over after this)
32
In which two ways is DNA formed and why?
Continously or discontinuously Continuously - DNA is built up from the 5' to the 3' end easily - this is the leading strand Discontinuously - the other strand is built from 3' to 5' as it is orientated the other way around - this is the lagging strand
33
The lagging stand in DNA formation must utilise which type of fragments to enable 5' to 3' directional growth?
Okazaki
34
Which enzyme is reponsible for unwinding DNA?
DNA helicase
35
Which enzyme is reponsible for synthesising an RNA primer to initiate replication on the lagging strand?
Primase
36
Describe how Okazaki fragments aid the growth of the lagging strand
Short newly synthesised DNA fragments - Okazaki fragments are added at intervals from the open DNA strands downwards This allows nucleotides to be sythesised in the "correct" direction by essentially filling in the gaps the Okazaki fragments created Each time DNA helicase opens up the strand a little more, a new Okazaki fragment can jump in and allow synthesis back down the chain
37
Which enzyme is key in proofreading?
DNA polymerase
38
What are the three differences between DNA and RNA?
Single vs double stranded DNA - thymine, RNA - uracil RNA - ribose sugar, DNA - deoxyribose sugar
39
Which enzymes are responsible for RNA production?
RNA polymerases
40
Which variation of RNA polymerase will synthesise mRNA?
Pol II
41
Where will RNA polymerase bind on a section of DNA?
Sections of DNA called promotors
42
What is characteristic about promotor regions on DNA?
They all have the TATA box sequence which marks the beginning of the relevant gene
43
What are enhancers?
Short regions of DNA that can be bound by protein activators to increase the liklihood of transcription
44
How can enhancers have an influence if they are far from the promotor sequences?
Looping of the strand allows them to come into contact Which is why mRNA form a stem loops.
45
Q Enzymes can affect the equilibrium position of a reaction. True/False?
False but it reduce the time to reach equilibrium
46
How do enzymes lower the activation energy of a reaction?
Bind to and stablise the transition state and provide alternative reaction pathways
47
How do enzymes lower the activation energy of a reaction?
Bind to and stablise the transition state and provide alternative reaction pathways
48
Enzyme with a cofactor is called a...
Holoenzyme
49
Induced fit model describes enzyme-substrate interaction by...
Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit
50
Trypsin and chymotrypsin work in the ____ and have an optimum pH of _
Small intestine, 7
51
What are isozymes?
Catalyse same reactions as enzymes but have different properties and structure
52
CK is an isozyme. The M form is produced in ____ and the B form is produced in the ___. MB form is produced in the ___
Skeletal muscle, brain, heart
53
Which enzymes carry out phosphorylation?
Kinases
54
What are zymogens?
Inactive precursors of an enzyme
55
Where are trypsinogen and chymotrypsinogen formed? Why is it important they are produced inactive?
Pancreas They would digest the pancreas if active
56
Which enzyme activates trypsinogen? Where does this occur?
Enteropeptidase Small intestine
57
How many nucleotides do anticodons consist of?
3 E P and A
58
What is TFIID?
General transcription factor required for Pol ii transcribed genes
59
What do anticodons from tRNA form with codons of mRNA? How many possible combinations?
Base pairs 64
60
Number of possible amino acid types?
v
61
What is the start codon in translation?
AUG
62
Stages of Translation?
Initiation Elongation Termination
63
What happens in initiation of translation?
-GTP provides energy -Ribosomal sub-unit binds to 5' end of mRNA and moves along until it finds start codon -Initiator tRNA pairs to start codon -Large sub-unit joins assembly and initiator tRNA is locked in P site
64
What happens in elongation stage of translation?
-Elongation factor brings aminoacyl - tRNA to A site -GTP -Second elongation factor regenerates the 1st to pick up next aminoacyl tRNA -Peptidyl transferase catalyses peptide bond formation between the amino acids in P and A sit
65
What happens in termination stage of translation?
-Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA) -Finished protein cleaves off tRNA
66
How many tRNA binding sites and their names?
3 sites E, Aminoacyl (A), Peptidyl (P)
67
What do the terms "degenerate" and "unambiguous" mean in the context of the genetic code?
Degenerate: More than one codon can code for the same amino acid. Unambiguous: Each codon codes for only one amino acid.
68
Induced fit model describes enzyme-substrate interaction by...
Binding of substrate induces a conformational change in the enzyme, resulting in complementary fit
69
Vmax is?
The maximal rate of reaction at unlimited substrate concn
70
Km is?
The concn of substrate which gives 50% maximal rate, i.e. 0.5Vmax
71
A low Km means...
An enzyme only needs a little substrate to work at 0.5Vmax (it has high affinity)
72
Vmax can be obtained from a Lineweaver-Burk plot by looking at the interesection with the X axis. True/False?
False Intersection with X axis is Km; intersection with Y axis is Vmax
73
In non-competitive inhibition, Vmax is ___ and Km is ___
Decreased, stays the same
74
enzymes are stabilised intermediate that are formed as substitutes are converted to products True /false
True
75
enzymes catalyse the transition state to avoid the loss of free energy True/False
True
76
prosthetic group
its tightly bound coenzymes
77
Which amino acid is neither D nor L in configuration.
glycine
78
Which complex does not pump protons as electrons pass through the respiratory chain?
complex II
79
How many ADP molecules (per glucose) are phosphorylated to ATP via substrate phosphorylation reactions during glycolysis?
2
80
How many NAD+ molecules are reduced in the degradation of palmitoyl-CoA to form eight molecules of acetyle-CoA?
7
81
The enzyme glucose-6-phosphatase is only found in cells which have this function or ability:
ability to store glycogen only in the liver
82
what is the carrier molecule for transporting fatty acids through the inner mitochondrial membrane?
The carrier molecule for transporting fatty acids through the inner mitochondrial membrane is "carnitine".
83
which mechanisms is used for ATP synthesis in the glycolytic pathway?
substrate phosphorylation.
84
malignant cancer develops in the glands that line your organs. Common forms of adenocarcinoma include breast, stomach, prostate, lung, pancreatic and colorectal cancers.
An adenocarcinoma
85
What happens when a stop codon is reached by a ribosome (in the A site).
A termination protein binds to the codon, and blocks access to the ribosome's A site. Aminoacyl-tRNA synthesase cleaves the protein from the ribosome
86
allosteric?
Allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Bind to site other than the active site. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
87
proteins which catalyse phosphorylation reactions?
Kinases
88
Enzymes are able to......
increase the velocity of a reaction by decreasing the energy of activation
89
There are hydrogen bonds parallel to the helix axis true / false
True
90
buffering capacity?
The extent to which a buffer solution can counteract the effect of added acid or base
91
which will stay the same in catalyse reaction compare to uncatalyzed reaction
that the activation energy required for the reaction to proceed will be lowered in the catalyzed reaction, resulting in a faster rate of reaction, but the free energy and entropy changes will be the same as in the uncatalyzed reaction.
92
Delta G and what is it depend on ?
is the difference in free energy between the products and the reactants. If this value is negative, the reaction is spontaneous, if it is positive, the reaction is non-spontaneous, and if it is zero, the reaction is at equilibrium. ΔG depends on the concentration of both reactants and products because the concentration of reactants is the determinant of reaction quotient (Q) that forms free energy. Therefore a change in the concentration of products and reactants will cause a corresponding change in Q, which directly affects ΔG . At low temperatures, ΔG will be negative because of the effect of the negative ΔH, but as you increase the temperature, the effect of the positive -TΔS will eventually outweigh that. The value of ΔG will then become positive, and the reaction will no longer be feasible. ENZYME CONCENTRATION ALSO EFFECT ΔG
93
Types of bonds formed in Primary Secondary Tertiary Quaternary structure
-Covalent bond as peptide bonds formed during condensation reaction. - Hydrogen bonds btween alpha helices and Beta-pleated sheets along the backbone of the chain. - Salt bridges , Hydrogen bond , disulfide bonds and hydrophobic/philic interactions. -made of two or more individual polypeptides. similar bonds of tertiary structure
94
glands vs Glandular epithelium,
Gland is an organ Glandular epithelium its a epithelium tissue
95
Which bond is associated with the linear structure of glycogen?
α-1,4-glycosidic bond is associated with the linear structure of glycogen. Glycogenin, a protein primer enzyme, and glycogen synthase are able to add UDP-glucose to the polysaccharide chain via the α-1,4-glycosidic bond. During this process, UDP is cleaved off
96
What is glycogenesis?
Synthesis of glycogen from glucose
97
What is glycogenolysis? A
Breakdown of glycogen to form glucose
98
Glycogenolysis occurs by hydrolysis. True/False? A
False Occurs by phosphorolysis (using phosphate instead of water )
99
Where is glycogen stored in the body? A
Liver Muscle cells
100
What is the role of skeletal muscle glycogen? A
Not used to maintain blood glucose; provides energy via glycolysis and TCA cycle during physical activity
101
Which bonds link glucose molecules to form glycogen? A
Alpha-1,4-glycosidic bonds
102
Which bonds create branches in the glycogen chain? A
Alpha-1,6-glycosidic bonds
103
Glycogen formation can be started by two glucose monomers joining together. True/False? A
False Glucose residues can only be added to an existing glycogen chain known as Glycogenin (primer of at least 4 glucose residues)
104
Glycogen act as long term storage TRUE?FLASE
FLASE Glycogen functions as a form of energy storage for rapid, short-term access compared with triglyceride storage in adipose tissues (i.e., fat), which are for long-term storage.
105
Glycogenesis occurs in six steps
1. **Activation stage** 2. **Formation of UDP-glucose** 3. **Anchoring of UDP-glucose** 4. **Polymerisation stage**
106
Which enzyme effectively adds glucose monomers to Glycogenin to produce glycogen? A
Glycogen synthase (transacetylase)
107
When enough glucose is present, glycogen synthesis begins: glucose-6-phosphate is converted to what? A
Glucose-1-phosphate This is know as isomerisation reaction
108
What is formed from glucose-1-phosphate in glycogen synthesis? A
UDP-glucose
109
What is UDP-glucose? A
Essentially an active form of glucose
110
Transacetylase function during glycogen synthesis
it introduces ⍺ 1-6 glyosidic links (new branches) approx. every 10 glucose residues
111
Glycogen synthase adds only one glucose at a time to UDP-glucose to ultimately form glycogen. True/False? A
True
112
How often are branches introduced into the glycogen chain? A
Every 10 glucose molecules
113
When does glycogenolysis occur? A
Between meals to maintain blood glucose levels
114
Glycogen phosphorylase cleaves off only one glucose at a time from glycogen. True/False? A
True
115
What are the 2 regulatory actions of insulin upon glycogen synthesis? A
Stimulates glycogen synthesis Inhibits glycogen phosphorylase
116
What are the 2 regulatory actions of glucagon upon glycogenolysis? A
Stimulates glycogen breakdown Inhibits glycogen synthase
117
What is gluconeogenesis? When does it occur? A
Gluconeogenesis is a metabolic process in the liver and kidneys that produces glucose from non-carbohydrate sources. It occurs during fasting, exercise, and in certain disease states Occurs when glycogen stores are completely depleted
118
Where does gluconeogenesis mainly occur? A
Liver
119
Name the 3 main precursors for gluconeogenesis A
Lactate (lactic acid) Amino acids Glycerol
120
Which TCA cycle intermediate is needed for gluconeogenesis? Why is it needed? A
Oxaloacetate (4C) Accepts acetyl groups from fat breakdown During gluconeogenesis, oxaloacetate is converted to phosphoenolpyruvate (PEP), which is then used in the production of glucose.
121
Describe the Cori Cycle also called lactic acid cycle, A
Blood transports lactate to liver Liver converts lactate to glucose Glucose is released into blood
122
Which type of amino acids can be used to synthesise new glucose? A
Glucogenic amino acids
123
Which type of amino acids cannot be used to synthesise new glucose? A
Ketogenic amino acids
124
What effect do insulin and glucagon have on gluconeogenesis? A
Insulin inhibits gluconeogenesis Glucagon stimulates gluconeogenesis
125
How does the cellular energy state affect the regulation of gluconeogenesis?
Low levels of ATP and high levels of AMP and ADP activate gluconeogenesis to produce glucose as a source of energy. High levels of ATP inhibit gluconeogenesis to conserve energy.
126
what are the 'non-reversible' enzymes that are key to gluconeogenesis?
Pyruvate carboxylase Pyruvate → oxaloacetate Mitochondria Activator: acetyl-CoA Inhibitor: ADP PEP carboyxlase Oxaloacetate → phosphoenolpyruvate Cytosol Fructose-1,6-biphosphatase Fructose-1,6-biphosphate → fructose-6-phosphate Cytosol Glucose-6-phosphatase Glucose-6-phosphate → glucose Endoplasmic reticulum Deficient in von Gierke's disease Not present in muscle (why muscles cannot generate glucose)
127
What happens when increased fat intake is not coupled with appropriate energy expenditure? A
OBESITY Increase in number and size of adipocytes
128
Fat provides us with 2x more energy than carbohydrates. True/False? A
True
129
Name some fat-soluble vitamins A
Vitamin A, D, E, K
130
What do triglycerides consist of? A
Glycerol attached via ester bond to 3 fatty acids
131
Double bonds in fatty acids are usually in the trans configuration. True/False? A
False Usually in cis configuration
132
What effect do double bonds have on the melting point of fatty acids? A
The greater the no. of double bonds, the lower the melting point
133
What are the main products of lipid digestion? A
Glycerol Fatty acids Monoglycerides
134
What must happen to long-chain fatty acids to make them transportable? A
Resynthesised to triglyceride and coated into a chylomicron, which enters the lymph
135
What happens to chylomicrons at muscle and adipose tissue? A
Cleaved by lipoprotein lipase into free fatty acids
136
What happens to free fatty acids at muscle and adipose tissue? A
Resynthesised into triglyceride or oxidised to provide energy depend on the amount of energy needed
137
Where does further oxidation of fatty acid occur? Why is this a problem for acyl-CoA? A
Oxidation occurs in the mitochondrial matrix acyl-CoA is formed in the cytoplasm!
138
What transports acyl-CoA into the mitochondrial matrix? A
Carnitine shuttle
139
How is acyl-carnitine formed in the cytoplasm? A
Fatty acids are transferred from acyl-CoA to carnitine to form acyl-carnitine
140
How does acyl-carnitine get across the inner membrane into the matrix? What happens to the carnitine? A
Via a transporter Carnitine is cleaved off back into the cytoplasm, leaving acyl group
141
In the matrix, what happens to the free acyl- group? A
Combines with CoA again to form acyl-CoA Net effect: acyl-CoA ends up in the matrix!
142
What happens to acyl-CoA in the matrix? A
Shortened by 2C to form acetyl-CoA and a new acyl-CoA
143
What are the products of one round of B-oxidation of fatty acid? A
1 acetyl-CoA 1 acyl-CoA, shortened by 2C 1 FADH2 1 NADH + H
144
How and where are ketone bodies formed? A
Formed from acetyl-CoA during B-oxidation in liver mitochondria
145
What is lipogenesis? A
Synthesis of fatty acids
146
Lipogenesis is a reductive process (electrons are required). True/False? A
True
147
What transports acetyl-CoA from mitochondrial matrix into cytoplasm? A
Citrate
148
What is the vital first step in lipogenesis from acetyl-CoA? A
Activation of acetyl-CoA by acetyl-CoA carboxylase into malonyl-CoA
149
Which enzyme catalyses synthesis of long chain fatty acid from malonyl-CoA, acetyl-CoA and NADH? A
Fatty acid synthase
150
Which component of fatty acid synthase carries the growing fatty acid chain during synthesis? A
Acyl-carrier protein (ACP)
151
Synthesis of fatty acids is maximal when carbohydrate is scarce. True/False? A
False Synthesis occurs when carbohydrate is in plentiful supply + fatty acids are scarce (otherwise lipolysis would occur)
152
Amino acids which are not used for proteins are stored in the liver. True/False? A
False Amino acids cannot be stored and are degraded if not used as building blocks
153
Where is the major site of amino acid degradation? A
Liver
154
What does amino acid degradation primarily produce? A
Ammonia (NH3) and ammonium ions
155
What are the 3 steps by which urea is formed? A
Transaminiation De-amination Urea cycle
156
Which organ is albumin secreted from? A Name the main liver-derived plasma proteins (4), in order of increasing molecular weight A
Liver -- Albumin alpha-globulins beta-globulins gamma-globulins
157
What characteristic of plasma proteins enables them to maintain osmotic pressure which increases fluid movement out of the tissues into the blood? A
They are insoluble - they do not diffuse into the interstitial fluid and only circulate in the blood
158
What proteoglycans composed of?
are made up of glycosaminoglycans (GAGs) attached to a hyaluronic acid backbone.
159
Why do amino acids exist as zwitterions?
Due to their amino group and their carboxyl group, amino acids exist as zwitterions: there is no overall charge on the molecule, but the separate parts are positively and negatively charged. Which aspect of amino acid structure differentiates different amino acids? All amino acids have the same basic structure, and differ only in their R-groups (the side-chain).
160
How does the structure of fibrinogen help it participate in blood clotting?
Its globular regions allow fibrin to generate a network of fibres, whereas its fibrous regions enable extended insoluble clot formation, blocking the wound.
161
What are 3 examples of mixed fibrous-globular proteins?
Fibrinogen, actin, myosin
162
What is the function of globular proteins?
Their functions are in biological, rather than the purely structural roles of fibrous proteins: they can act as enzymes (e.g. trypsin and lysozyme), transporters (e.g. haemoglobin and transferrin), in protection (e.g. immunoglobulins) and as hormones (e.g. insulin).
163
What forms the secondary structure of the haemoglobin molecule?
is mostly alpha helical.
164
Which amino acid is found at every third residue in collagen?
Glycine `is found at every third residue in collagen; this is necessary for the proper folding of collagen
165
Which protein chains bind to form fibrinogen?
Fibrinogen is a hexamer, made up of two alpha, two beta and two gamma chains. These chains are bonded together by disulfide bonds
166
What are examples of fibrous proteins?
Examples include alpha-keratin, collagen, elastin and proteoglycans.
167
Retention/excretion of CO2 is controlled by ------
the lungs – concentration can be changed rapidly
168
H2CO3 is excreted/reabsorbed by ----------
kidneys – changes in concentration tend to be slower than CO2
169
what is Acidaemia ?and which two ways it can be cause ?
High H+ (low blood pH) Leads to acidosis cause by Decrease in the HCO3 will shift the equilibrium to the right causing increase HCO3 and H+ production decreasing the blood pH - also can be caused by increase Co2 will shift equilibrium to the right.
170
Alkalaemia
- Low H+ (high blood pH) which Leads to alkalosis - cause by Increase in the HCO3 production will shift the equilibrium to the left casing decrease in H+ production increasing the pH of the blood. Decrease CO2 will shift equilibrium to the left causing alkalosis.
171
What is meant by hypoxia? A
Lack of tissue oxygen
172
What is meant by hypoxaemia?
Lack of oxygen in the blood
173
In COPD patients, we aim for SaO2 of between __ and __ %
88 and 92
174
What are the 4 main buffers of pH in the body?
Bicarbonate, Haemoglobin, Ammonium, Phosphate
175
Define acidaemia
pH less than 7.5
176
Define acidosis
A process by which the blood contains excess acid (H+)
177
Define alkalaemia? A
pH greater than 7.45
178
Define alkalosis
A process by which the blood contains excess base
179
Respiratory changes are monitored by looking at CO2 concn. True/False? A
True
180
Metabolic changes are monitored by looking at [H+]. True/False?
False Look at HCO3 concn
181
Metabolic compensation is rapid. True/False? A
False It is slow
182
Respiratory compensation is rapid. True/False? A
True
183
If pH is low, PCO2 is high, HCO3 is normal, this is what? A check the summery table somosis
Respiratory acidosis
184
If pH is high, PCO2 is normal, HCO3 is high, this is what? A
Metabolic alkalosis
185
If pH is low, PCO2 is normal, HCO3 is low, this is what? A
Metabolic acidosis
186
If pH is high, PCO2 is low, HCO3 is normal, this is what?
Respiratory alkalosis
187
If pH is normal, PCO2 is high, HCO3 is high, this is what?
Compensated respiratory acidosis OR Compensated metabolic alkalosis
188
If pH is normal, PCO2 is low, HCO3 is low, this is what? A
Compensated respiratory alkalosis OR Compensated metabolic acidosis
189
If pH is low, PCO2 is high, HCO3 is high, this is what? A
Decompensated respiratory acidosis pH went down as PCO2 went up; compensation occurred by HCO3 increasing to bring pH to normal; PCO2 went up further to cause lower pH again.
190
where is lacteal lymph and what its function
lymphs' which present in the small intestine and absorb chylomicrons (balls of fat ) as fat acid can not be absorbed by capillaries and slowly make their way up to thoracic duct and get dump into the venous blood.