Introduction to Biochemistry Flashcards by Catriona Grant

Carbon can form 4 _____ bonds

covalent

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the less oxidised the molecule the ____ energy contained in the bonds.

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alkane (in fats) has ____ energy in its bonds than carbon dioxide (final product of catabolism)

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what is the glycosidic bond in lactose?

galactose beta 1-4- glucose

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what is the glycosidic bond in maltose?

glucose alpha 1,4 - glucose

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what is the glycosidic bond in sucrose?

glucose alpha 1,2 - fructose

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what is the glycosidic bond in cellobiose?

glucose beta 1-4- glucose

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carbs are made of carbon, hydrogen and oxygen in a ___:___:___ ratio

1:2:3

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what is the free energy equation involving enthalpy and entropy

ΔG = ΔH – TΔS

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for a process to occur delta G must be _____

negative

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an endothermic process with a negative ᐃS can never be _______, for example photosynthesis.

spontaneous

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ΔG = (energy of the ______) – (energy of the ______)

ΔG = (energy of the products) – (energy of the reactants)

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exergonic reactions are reactions in which the total free energy of the product(s) is _____ than the total free energy of the reactant(s)

less

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exergonic reactions can occur +_____

spontaneously

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endergonic reactions are reactions in which the total free energy of the product(s) is ____ than the total free energy of the reactant(s)

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endergonic reactions cannot occur _____. They need an Input of _____ to proceed.

spontaneously, energy

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what is the equation for delta G for a given reaction

ΔG = ΔGo’ + RTln([C][D]/[A][B])

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what is R

the universal gas constant

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what is T

the absolute temperature

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what is ΔGo’

the change in free energy under standard conditions

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ΔG is related to the point of equilibrium: The further towards completion the point of equilibrium is, the ____free energy is released

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ΔG values near ___ are characteristic of readily reversible reactions.

zero

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When the system is at equilibrium, forwards and backwards reactions are balanced:
ΔG = 0 and therefore
ΔGo’ = -RTlnKeq

Keq = [C][D]/[A][B]

(substrate and product concentrations at equilibrium)

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reactions with a negative delta Go, i.e. reactions going from high energy reactants to low energy products, are ______

favourable

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What about reactions with a positive delta G - it all depends on the initial concentrations of the _____

reactants

what is the effect of increasing [A][B] relative to [C][D] do the delta G ?

- [C][D]/[A][B] becomes smaller than 1 | - the ln of a number smaller than 1 is negative!

many cellular processes are unfavourable and are driven by ____ to highly favourable processes

coupling

the breakdown of ATP is a very ____ delta G

negative

The negative charges close together in ATP put a ____ (electrostatic repulsion) on the molecule that makes it less ____ than ADP

strain, stable

the phosphate parts of ATP are anhydride bonds. These are ___ energy bonds. So when they break energy is _____

high, released

what are the two ways to make ATP?

1. using creating phosphate | 2. using 2 ADP

what is glycolysis ?

Initial breakdown of glucose for the generation of ATP

Reactions close to equilibrium (ΔG close to 0) are not used as _____ points

control

hydrogen bonds tend to be ____ in form

linear

amphipathic molecules form ____ in water

micelles

Proteins and polypeptides in humans are made up from ___ different __-amino acids

20, L

what is the one exception to the L amino acids?

glycine - it has two of the same group

all amino acids contain an α-carbon bonded to .... 4 things

an amino group (-NH2) a carboxyl group (-COOH) a hydrogen (-H) a side chain (-R)

D and L form AAs are _______

stereoisomers

what are the 4 groups of AAs

- non polar, hydrophobic - polar, uncharged - acidic - basic

what are the characteristic chains on - non polar, hydrophobic ?

mainly hydrocarbons

what are the characteristic chains on - polar uncharges?

mainly carbonyl and hydroxyl groups, NH

what are the characteristic chains on acidic aas?

carboxyl grop

what are the characteristic chains on basic AAs?

ammine | NH3 and

what is a peptide bond the linkage of?

CO and NH groups with the removal of water

peptides have a direction , what is it?

from N terminal residue NH3+ to the C-terminal residue COO-

peptide bonds have a partial ___ bond character

double

____ bonds are planar

peptide

Acids are molecules which can ____ a proton (hydrogen ion, H+)

donate

Bases are proton _____

acceptors

H+ conc of 10 -7 has a pH of 7, what is the pH of a H+ conc of 10 -6

the henderson -hasselbach equation Connects the __ of a weak acid with the __ of a solution containing this acid

Connects the Ka of a weak acid with the pH of a solution containing this acid

what is the quation?

pH = pKa + log[A-/HA]

the H-H equations lets us calculate the properties of _____ solutions

buffer

When the concentration of acid is equal to the concentration of conjugate base: pH = ____

pKa

at their ____value buffers tend to resist a change of pH upon addition of moderate amounts of acid or base

pKa

Amino acids without charged side groups exist as _____ in neutral solution

zwitterions

The pH at which a molecule has no net charge is called the ---_______ pH, pI

isoelectric

The ends of proteins can be ____- and therefore proteins can act as _____

ionised, buffers

give an example of a protein buffer?

haemoglobin in blood

Proteins can act as buffers because each protein molecule is both a weak _____ and a weak _____. The weakly acidic carboxylic acids counteract ____ pHs while the weakly basic amino groups can counteract ____ pHs.

Proteins can act as buffers because each protein molecule is both a weak acid and a weak base. The weakly acidic carboxylic acids counteract rising pHs while the weakly basic amino groups can counteract falling pHs.

polypeptides can rotate around the angles between, which two things in the chain?

the α carbon and the amino group | the α carbon and the carboxyl group

what is the secondary structure of a protein?

Hydrogen-bonded three-dimensional arrangements of a polypeptide chain

secondary structure considers only the ____ of the polypeptide

backbone

what are the three types of secondary structures?

alpha helix beta strands and sheets triple helix

Alpha helix is where the ___ group of one amino acid forms a hydrogen bond with the __group of an amino acid four residues away

-C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away

how do proline residues break alpha helices?

Prolines in alpha helices after the first turn (4th residue) cause a kink in the helix.This kink is caused by proline being unable to complete the H-bonding chain of the helix

beta sheets can run in a _____ or anti_____ direction

parallel

what amino acids occur at turns in the strands? 2

glycine and proline

beta sheets can be in a zig zag shape in which case they are called Beta ____ sheets

pleated

Different ______ structure elements can occur within one protein Example: _______ ______

Different secondary structure elements can occur within one protein Example: phosphoglycerate kinase

collagen triple helix is a component of ___ and _____ tissue

bone and connective

collagen triple helix is made of Three ___-handed helical chains twisted around each other form a ____-handed superhelix

Three left-handed helical chains twisted around each other form a right-handed superhelix

tropocollagen is a repeating sequence of X-Y-Gly in all strands X= Y=

``` X = any amino acid Y = proline or hydroxyproline ```

in collagen triple helix there are inter-chain h bonds involving _____ and______

hydroxylysine and hydroxyproline

______ of collagen occur with age

crosslinking

scurvy results in weakened collagen, how?

- the enzyme which hydroxylates proline requires ascorbic acid (vitamin C) - dietary deficiency of vitamin C results in reduction in hydroxyproline results in weakened collagen

the tertiary structure of a polypeptide is held together by interactions between the ____ chain - the ‘R’ groups.

side

what are fibrous proteins?

Contain polypeptide chains organized approximately parallel along a single axis

fibrous proteins are ____ in water and dilute ___ solutions

insoluble, salt

give some examples

- keratin of hair and wool | - collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels

what are globular proteins

Proteins which are folded to a more or less spherical shape

globular proteins tend to be ___ in water and salt solutions

soluble

in globular proteins most of their polar side chains are on the o____ and interact with the aqueous environment by _____ _____ and___-_____ interactions

most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions

give 2 examples of globular proteins

myoglobin and haemoglobin

give 5 examples of the bonds/forces stabilizing tertiary structures

- Covalent disulphide bonds - Electrostatic interactions = salt bridges - Hydrophobic interactions - Hydrogen bonds - Complex formation with metal ions

______ side groups are normally located on the outside of proteins

Charged (polar) side groups are normally located on the outside of proteins interact with water

Amino acids with hydrophobic side-chains tend to cluster in the ____ of globular proteins

centre

sickle cell anaemia results from a signle nucleotide sequence meaning that there is a change of ___in the proteins

shape

Sometimes folding process is aided by other specialised proteins. what are these called/

chaperones

Detergents, urea, guanidine hydrochloride can disrupt _______ interactions

hydrophobic

myoglobin contains a _____ haem group

prosthetic

haemoglobin is composed of __ alpha and )___ beta subunits

how many haem groups are there in haemoglobin?